Contacts of the helix formed by residues 63 - 89 (chain T) in PDB entry 3P71
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ALA 63 (chain T).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89C ARG* 3.3 17.3 - - - +
126C VAL 5.1 4.7 - - - +
127C TYR* 5.0 4.0 - - + -
306C ASP* 4.8 2.4 + - - +
61T ARG 4.2 1.0 + - - -
62T LYS* 1.3 74.8 - - - +
64T PRO* 1.4 69.2 - - + +
65T GLU* 3.2 25.1 - - - +
66T ILE* 2.8 28.1 + - + +
67T ASN* 3.3 6.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 64 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126C VAL* 4.0 21.8 - - + +
127C TYR* 3.8 30.5 - - + +
45T TYR* 4.2 0.8 + - - +
62T LYS 3.6 2.9 - - - +
63T ALA* 1.4 85.8 - - + +
65T GLU* 1.3 57.0 + - - +
67T ASN* 3.4 2.1 + - - +
68T ARG* 2.9 36.0 + - - +
300T GLU* 3.5 33.9 - - + +
301T PHE 4.0 6.7 - - - +
302T LEU* 4.0 23.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 65 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89C ARG* 2.8 46.2 + - - -
268C ARG* 3.0 18.4 + - - +
308C PHE* 4.0 3.6 - - - -
63T ALA* 3.0 13.7 + - - +
64T PRO* 1.3 75.5 - - - +
66T ILE* 1.3 67.1 + - + +
68T ARG* 4.4 0.7 - - - -
69T GLY* 2.9 25.5 + - - -
302T LEU* 4.0 19.8 - - + +
307T LEU* 4.8 3.8 - - + -
308T LEU* 3.6 34.7 - - + +
311T LEU* 3.6 24.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 66 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268C ARG* 4.1 9.6 - - - +
306C ASP* 3.7 46.9 - - + +
307C TYR* 4.5 2.5 - - - +
308C PHE* 3.6 11.0 - - + -
36T CYS* 4.2 10.1 - - + -
62T LYS* 4.1 18.2 - - + -
63T ALA* 2.8 17.0 + - + +
65T GLU* 1.3 92.9 - - + +
67T ASN* 1.3 59.0 + - - +
69T GLY 3.3 0.5 + - - -
70T TYR* 2.8 60.7 + - + -
311T LEU* 4.3 8.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 67 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36T CYS 4.5 2.6 - - - +
39T PHE* 3.7 13.1 - - - -
40T ALA* 4.0 15.6 + - + +
43T ILE* 3.8 9.6 - - - +
45T TYR* 3.6 30.0 - - + -
62T LYS* 3.0 40.6 + - - +
63T ALA 3.3 6.1 + - - -
64T PRO 3.8 2.7 - - - +
66T ILE* 1.3 75.6 - - - +
68T ARG* 1.3 59.3 + - - +
70T TYR* 3.4 3.7 + - - +
71T PHE* 3.0 28.4 + - - +
300T GLU* 2.9 23.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 68 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45T TYR* 4.0 13.5 + - + +
64T PRO* 2.9 21.2 + - - +
65T GLU* 4.1 2.9 - - - +
67T ASN* 1.3 74.6 - - - +
69T GLY* 1.3 57.1 + - - +
71T PHE* 3.2 7.0 + - - +
72T ALA* 3.0 29.6 + - - +
285T TYR* 3.4 33.1 + - + -
296T ILE* 4.0 22.7 + - + +
297T GLU* 3.5 29.7 + - - +
300T GLU 3.3 25.3 + - - -
301T PHE* 4.9 0.2 - - - +
302T LEU* 4.1 27.3 + - - +
305T MET* 3.4 29.5 - - - +
308T LEU* 4.0 18.4 - - + -
312T MET* 5.2 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 69 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308C PHE* 3.4 32.3 - - - -
65T GLU 2.9 12.3 + - - -
66T ILE 3.6 0.2 - - - -
68T ARG* 1.3 77.3 - - - +
70T TYR* 1.3 60.1 + - - +
72T ALA* 3.6 2.4 + - - +
73T ARG* 3.2 22.7 + - - +
228T TYR* 4.7 2.3 + - - -
281T MET* 5.0 1.0 - - - +
308T LEU* 4.3 0.8 - - - +
312T MET* 3.8 17.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 70 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307C TYR 3.8 5.8 + - - -
308C PHE* 3.6 19.6 - + - -
309C LEU* 3.0 28.1 + - - +
32T ASP* 4.7 0.9 + - - -
33T ALA* 3.6 17.0 + - + -
36T CYS* 3.4 29.6 - - + +
37T LYS* 3.8 25.6 - - + -
40T ALA* 5.2 2.9 - - + -
46T TRP* 4.0 13.2 - - + -
66T ILE* 2.8 44.0 + - + +
67T ASN* 4.0 5.8 - - - +
68T ARG 3.3 0.2 - - - -
69T GLY* 1.3 69.4 - - - +
71T PHE* 1.3 60.6 + - - +
73T ARG* 3.4 40.1 + - - +
74T VAL* 2.9 32.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 71 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45T TYR* 3.5 29.2 - + + -
46T TRP* 3.6 26.4 - + + -
67T ASN 3.0 15.4 + - - +
68T ARG* 3.4 10.3 - - - +
70T TYR* 1.3 77.6 - - - +
72T ALA* 1.3 59.2 + - + +
74T VAL* 3.0 3.9 + - + +
75T HIS* 2.7 61.8 + + + +
285T TYR* 5.7 2.5 - + - -
288T LEU* 4.2 18.4 - - + -
292T GLU* 3.9 10.3 - - + -
295T ARG* 3.4 22.2 - - - -
296T ILE* 3.0 35.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 72 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68T ARG 3.0 11.3 + - - +
69T GLY 4.1 0.4 - - - +
71T PHE* 1.3 83.8 - - + +
73T ARG* 1.3 53.1 + - - +
75T HIS* 3.8 4.4 - - - +
76T GLY* 2.7 33.3 + - - -
281T MET* 3.6 22.4 - - + +
284T LEU* 4.0 12.7 - - + +
285T TYR* 4.4 12.3 - - + -
288T LEU* 4.9 3.4 - - + -
312T MET* 3.7 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 73 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308C PHE* 3.7 12.0 - - - +
309C LEU 2.7 31.3 + - - +
310C AN6 2.7 31.5 + - - -
33T ALA* 4.4 0.4 - - - +
37T LYS* 4.1 5.8 - - - +
69T GLY 3.2 16.2 + - - +
70T TYR* 3.4 33.7 - - - +
72T ALA* 1.3 78.8 - - - +
74T VAL* 1.3 62.6 + - + +
76T GLY* 3.8 1.1 - - - -
77T VAL* 3.1 29.8 + - - +
198T GLU* 2.6 22.2 + - - +
199T CYS* 3.8 11.8 - - - +
228T TYR* 3.4 53.2 - - + -
281T MET* 3.6 10.0 - - - +
317T LEU* 5.2 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 74 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37T LYS* 4.3 24.5 - - + +
46T TRP* 3.4 53.6 - - + +
70T TYR 2.9 20.5 + - - +
71T PHE* 3.6 2.9 - - + +
73T ARG* 1.3 76.7 - - + +
75T HIS* 1.3 57.3 + - - +
77T VAL* 3.3 3.6 + - - +
78T SER* 2.8 41.6 + - - -
107T ARG* 5.6 7.4 - - - +
198T GLU* 5.0 2.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 75 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71T PHE* 2.7 45.3 + + + +
72T ALA* 3.8 3.8 - - - +
74T VAL* 1.3 73.3 - - - +
76T GLY* 1.3 65.7 + - - +
78T SER* 3.2 6.8 + - - -
79T GLN* 2.9 58.7 + - + +
284T LEU* 5.2 2.0 - - + -
288T LEU* 3.3 29.3 - - + +
289T PRO* 4.5 10.7 - - + +
292T GLU* 4.8 19.1 - - + -
334T TYR* 5.3 2.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 76 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72T ALA 2.7 23.6 + - - -
73T ARG* 3.8 1.8 - - - -
75T HIS* 1.3 76.0 - - - +
77T VAL* 1.3 60.7 + - - +
79T GLN* 3.3 10.5 + - - +
80T LEU* 3.4 16.6 + - - +
284T LEU* 4.2 12.8 - - - -
317T LEU* 3.7 22.0 - - - +
334T TYR* 4.5 3.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 77 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73T ARG 3.1 17.2 + - - +
74T VAL* 4.0 2.7 - - - +
76T GLY* 1.3 72.7 - - - +
78T SER* 1.3 64.3 + - - +
80T LEU* 3.2 8.2 + - - +
81T ILE* 3.0 47.1 + - + +
196T ILE* 4.5 13.5 - - + -
198T GLU* 4.0 30.3 - - + +
226T ILE* 4.2 19.5 - - + -
228T TYR* 4.6 3.1 - - + -
317T LEU* 3.8 22.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 78 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74T VAL* 2.8 29.1 + - - -
75T HIS* 3.5 9.6 - - - -
77T VAL* 1.3 73.5 - - - +
79T GLN* 1.3 56.9 + - - +
81T ILE* 3.4 11.0 + - - +
82T LYS* 3.1 49.5 + - - +
107T ARG* 5.0 9.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 79 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75T HIS* 2.9 48.6 + - + +
76T GLY* 3.9 4.7 - - - +
77T VAL 3.3 0.4 - - - -
78T SER* 1.3 75.5 - - - +
80T LEU* 1.3 58.0 + - - +
82T LYS* 3.6 28.8 + - - +
83T ALA* 3.2 27.0 + - - +
333T THR 4.7 2.3 - - - +
334T TYR* 3.4 33.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 80 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76T GLY 3.4 8.2 + - - +
77T VAL* 3.2 4.3 + - - +
79T GLN* 1.3 74.4 - - - +
81T ILE* 1.3 65.5 + - - +
83T ALA* 3.5 4.3 + - - +
84T PHE* 3.1 23.0 + - - +
224T MET* 4.1 8.7 - - + +
226T ILE* 3.5 37.6 - - + +
317T LEU* 3.7 32.5 - - + -
319T TRP* 3.8 41.1 - - + -
332T ILE* 4.0 14.1 - - + +
333T THR 4.1 0.2 - - - -
334T TYR* 3.8 24.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 81 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77T VAL* 3.0 42.3 + - + +
78T SER* 3.7 8.1 - - - +
79T GLN 3.4 0.2 - - - -
80T LEU* 1.3 76.6 - - - +
82T LYS* 1.3 62.3 + - + +
84T PHE* 3.2 3.6 + - - +
85T LEU* 3.1 39.7 + - + +
94T ILE* 4.3 10.8 - - + -
104T THR* 4.5 19.7 - - + +
108T LEU* 4.6 11.7 - - + -
194T LEU* 4.0 20.4 - - + -
196T ILE* 3.7 24.7 - - + -
226T ILE* 4.2 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 82 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78T SER* 3.1 34.0 + - - +
79T GLN* 3.8 27.8 + - - +
81T ILE* 1.3 77.9 - - + +
83T ALA* 1.3 57.5 + - - +
85T LEU* 3.4 10.7 + - + +
86T ARG* 2.9 32.5 + - - +
108T LEU* 6.1 2.5 - - + -
111T GLU* 3.7 24.0 + - - +
113T LEU* 4.6 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 83 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79T GLN 3.2 16.0 + - - +
80T LEU* 3.8 1.8 - - - +
81T ILE 3.3 0.2 - - - -
82T LYS* 1.3 75.8 - - - +
84T PHE* 1.3 59.6 + - - +
86T ARG* 3.4 9.9 + - - +
87T LYS* 3.0 35.9 + - + +
332T ILE* 3.8 32.5 - - + -
333T THR 4.7 7.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 84 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80T LEU 3.1 13.8 + - - +
81T ILE 3.2 7.6 + - - +
83T ALA* 1.3 76.7 - - - +
85T LEU* 1.3 60.9 + - + +
87T LYS* 3.2 3.0 + - - +
88T THR* 3.0 47.1 + - + +
92T CYS* 3.6 31.6 - - + -
93T GLN 4.2 1.1 - - - -
94T ILE* 5.0 1.1 - - + -
192T PRO* 4.0 3.1 - - + -
193T THR 3.6 16.4 - - - -
194T LEU* 3.5 42.2 - - + -
223T ALA* 4.8 0.9 - - - -
224T MET* 3.8 42.8 - - + -
329T LEU* 4.4 20.4 - - + -
332T ILE* 4.2 8.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 85 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81T ILE* 3.1 31.7 + - + +
82T LYS* 3.6 8.7 - - - +
84T PHE* 1.3 75.4 - - + +
86T ARG* 1.3 60.8 + - - +
88T THR* 3.7 5.2 - - - -
89T GLU* 2.9 26.0 + - - -
90T CYS* 2.9 25.3 + - - -
92T CYS* 3.8 22.9 - - - -
94T ILE* 3.8 17.3 - - + -
108T LEU* 3.8 21.8 - - + -
113T LEU* 3.6 37.2 - - + +
115T SER* 4.0 7.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 86 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82T LYS 2.9 19.4 + - - +
83T ALA* 3.4 10.3 - - - +
85T LEU* 1.3 75.9 - - - +
87T LYS* 1.3 73.1 + - + +
89T GLU* 3.2 19.3 + - - +
113T LEU* 6.3 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 87 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83T ALA* 3.0 20.6 + - - +
84T PHE 3.2 4.5 + - - +
86T ARG* 1.3 87.7 - - + +
88T THR* 1.3 59.9 + - - +
89T GLU* 3.4 2.4 - - - +
327T LEU* 3.6 36.9 + - - +
328T GLY* 3.5 19.5 + - - +
329T LEU* 3.9 16.8 - - + -
331T GLU* 4.3 17.2 - - - +
332T ILE* 4.2 19.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 88 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84T PHE* 3.0 44.4 + - + +
85T LEU* 3.5 5.2 + - - -
87T LYS* 1.3 78.0 - - - +
89T GLU* 1.3 69.6 + - - +
90T CYS 3.7 0.3 + - - -
91T HIS* 3.1 28.3 + - - +
92T CYS* 3.3 22.0 - - - -
192T PRO* 4.0 16.4 - - + -
327T LEU* 4.2 20.0 - - + -
329T LEU* 4.6 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 89 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85T LEU 2.9 7.2 + - - -
86T ARG* 3.2 14.0 + - - +
87T LYS 5.2 2.0 - - - +
88T THR* 1.3 80.1 - - - +
90T CYS* 1.3 65.4 + - - +
91T HIS* 3.0 9.8 + - + +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il