Contacts of the helix formed by residues 90 - 114 (chain F) in PDB entry 2FRV
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 GLU 90 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88F ILE 3.8 1.0 + - - -
89F PRO* 1.3 71.4 - - - +
91F ASN* 1.3 56.8 + - - +
93F THR* 3.0 11.7 + - + -
94F LEU* 2.9 40.6 + - + +
431F LYS* 5.2 14.1 - - - +
435F ASN* 2.9 30.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 91 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89F PRO* 3.2 1.0 - - - +
90F GLU* 1.3 76.3 - - - +
92F ALA* 1.3 63.3 + - - +
94F LEU* 3.9 2.5 - - - +
95F MET* 3.1 25.1 + - - +
234F LEU* 4.7 4.0 - - - +
432F LEU* 3.6 21.0 - - + +
435F ASN* 2.8 34.2 + - - +
436F VAL* 4.1 9.7 - - - +
440F LYS* 2.8 27.5 + - - -
441F ASP* 3.5 15.4 - - - +
442F ASP 3.1 19.9 + - - +
443F LEU* 3.8 10.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 92 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88F ILE* 4.2 6.7 - - + -
89F PRO* 2.6 16.3 + - + +
91F ASN* 1.3 74.6 - - - +
93F THR* 1.3 65.7 + - - +
96F ARG* 3.0 32.9 + - - -
227F GLY* 3.7 17.9 - - - -
228F CYS* 3.8 15.3 - - - -
443F LEU* 3.2 31.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 93 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88F ILE* 3.3 17.0 + - - +
89F PRO 3.0 7.2 + - - -
90F GLU* 3.4 13.0 - - + -
92F ALA* 1.3 79.9 - - - +
94F LEU* 1.3 64.8 + - + +
96F ARG* 3.7 2.1 - - - +
97F ASN* 3.2 28.1 + - - +
287F PRO 3.2 28.5 - - - +
288F THR* 4.4 11.1 + - - +
290F GLU* 2.8 34.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 94 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90F GLU* 2.9 29.6 + - + +
91F ASN* 4.0 6.3 - - - +
93F THR* 1.3 77.1 - - + +
95F MET* 1.3 51.7 + - - +
97F ASN* 3.2 9.9 + - - +
98F LEU* 2.9 39.1 + - - +
428F TRP* 4.0 39.9 - - + +
431F LYS* 3.9 21.8 - - + -
432F LEU* 3.8 31.0 - - + +
435F ASN* 3.9 22.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 95 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91F ASN 3.1 17.0 + - - +
92F ALA 4.3 1.8 - - - +
94F LEU* 1.3 73.3 - - - +
96F ARG* 1.3 60.5 + - - +
98F LEU* 3.5 10.7 + - - +
99F THR* 2.9 29.8 + - - -
213F PHE* 4.1 20.1 - - + +
222F PHE* 3.7 22.7 - - + -
228F CYS* 4.1 15.5 - - - -
230F ASN* 3.9 27.8 - - - +
233F SER* 3.7 16.6 - - - +
234F LEU* 3.5 31.9 - - + -
432F LEU* 4.4 6.1 - - + -
443F LEU* 4.2 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 96 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70F TYR* 2.6 32.1 + - - +
74F LEU* 4.1 12.7 - - + +
77F VAL* 3.5 24.6 - - - +
78F ARG* 4.1 18.9 - - - +
81F ASP* 2.8 25.6 + - - -
88F ILE* 3.7 17.7 - - - +
92F ALA* 3.0 26.7 + - - +
93F THR* 3.7 4.5 - - - +
95F MET* 1.3 75.1 - - - +
97F ASN* 1.3 59.8 + - - +
100F MET* 3.3 18.7 + - - +
222F PHE* 4.6 2.2 - - + -
223F THR* 4.1 12.4 - - + +
224F VAL 3.3 12.9 + - - -
227F GLY* 2.9 33.5 + - - -
228F CYS* 3.6 18.8 - - - -
290F GLU* 4.3 7.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 97 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78F ARG* 4.2 8.1 + - - -
93F THR* 3.2 18.0 + - - +
94F LEU* 3.2 12.0 + - - +
96F ARG* 1.3 77.7 - - - +
98F LEU* 1.3 66.4 + - - +
99F THR 3.2 0.2 - - - -
100F MET* 3.3 1.7 + - - -
101F GLY 2.9 18.2 + - - -
285F GLU* 4.8 0.3 - - - +
286F PHE* 3.6 27.9 + - + +
287F PRO* 3.4 39.7 + - - +
290F GLU* 4.9 0.5 - - - +
428F TRP* 3.3 39.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 98 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94F LEU 2.9 20.1 + - - +
95F MET* 3.8 12.8 - - - +
96F ARG 3.5 0.2 - - - -
97F ASN* 1.3 80.5 - - - +
99F THR* 1.3 55.9 + - - +
101F GLY* 3.3 0.7 + - - -
102F ALA* 3.0 28.4 + - - +
213F PHE* 3.8 32.3 - - + -
242F PHE* 4.2 13.0 - - + -
425F VAL* 3.6 42.0 - - + +
428F TRP* 3.8 26.7 - - + +
429F LEU* 4.0 16.4 - - + +
432F LEU* 4.5 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 99 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70F TYR* 3.8 35.6 - - + -
95F MET 2.9 18.8 + - - -
96F ARG 4.0 0.2 - - - -
97F ASN 3.2 0.6 - - - -
98F LEU* 1.3 78.3 - - - +
100F MET* 1.3 57.7 + - - +
102F ALA* 3.7 6.1 + - - +
103F GLN* 3.2 23.2 + - - +
210F MET* 4.0 31.0 - - + +
213F PHE* 3.3 23.4 - - - +
214F GLY* 4.7 0.4 - - - -
220F THR* 4.3 3.8 - - + -
222F PHE* 3.5 14.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 100 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70F TYR* 3.8 8.9 - - + +
71F VAL* 3.6 30.3 - - + -
74F LEU* 3.6 18.2 - - + -
96F ARG 3.3 17.3 + - - +
97F ASN* 3.3 4.9 + - - +
98F LEU 3.2 0.2 - - - -
99F THR* 1.3 75.3 - - - +
101F GLY* 1.3 65.8 + - - +
103F GLN* 3.1 7.8 + - - +
104F TYR* 3.0 56.6 + - + -
285F GLU* 4.1 10.1 - - + +
286F PHE* 3.7 17.9 - - + -
459F VAL* 3.3 34.5 - - + -
460F ASN 4.5 3.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 101 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97F ASN 2.9 16.9 + - - -
98F LEU 3.8 1.6 - - - -
99F THR 3.3 0.2 - - - -
100F MET* 1.3 77.8 - - - +
102F ALA* 1.3 56.9 + - - +
104F TYR* 3.1 7.0 + - - +
105F MET* 3.0 31.8 + - - +
286F PHE* 3.9 13.9 - - - -
421F ALA* 4.7 4.7 - - - +
425F VAL* 3.8 20.6 - - - -
428F TRP* 4.4 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 102 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98F LEU 3.0 16.9 + - - +
99F THR* 3.9 5.8 - - - +
101F GLY* 1.3 77.6 - - - +
103F GLN* 1.3 57.4 + - - +
105F MET* 3.5 14.8 + - - +
106F HIS* 3.3 23.9 + - - +
206F ALA* 4.3 8.4 - - - +
209F ALA* 5.0 3.1 - - + -
210F MET* 4.0 29.8 - - + +
242F PHE* 4.8 12.3 - - + -
425F VAL* 4.4 2.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 103 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67F VAL 3.2 17.4 + - - +
68F CYS* 3.7 4.8 - - - +
69F THR* 3.7 23.4 - - - +
70F TYR* 4.8 1.3 - - + -
71F VAL* 4.1 11.7 - - + -
99F THR 3.2 14.4 + - - +
100F MET* 3.1 14.8 + - - +
102F ALA* 1.3 72.4 - - - +
104F TYR* 1.3 61.0 + - - +
106F HIS* 4.7 7.9 + - - +
107F ASP* 2.8 69.0 + - - +
210F MET* 3.5 27.9 - - + +
217F ASN* 4.3 2.3 - - - +
462F PRO* 4.0 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 104 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100F MET* 3.0 45.5 + - + -
101F GLY 3.1 6.9 + - - +
103F GLN* 1.3 73.7 - - - +
105F MET* 1.3 69.8 + - - +
106F HIS 3.2 0.3 + - - -
107F ASP* 4.6 0.2 - - - -
108F HIS* 3.2 34.5 + + - +
285F GLU* 3.9 10.7 - - - +
286F PHE* 4.2 16.3 - + - -
298F THR* 5.4 1.1 + - + -
417F GLN* 3.7 40.2 + - + +
418F CYS* 4.7 1.8 - - - -
421F ALA* 3.7 25.8 - - + -
460F ASN* 2.6 41.8 + - - -
461F ALA 4.1 1.6 + - - -
462F PRO* 4.0 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 105 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101F GLY 3.0 13.8 + - - +
102F ALA* 3.5 16.4 - - - +
104F TYR* 1.3 83.2 - - + +
106F HIS* 1.3 58.3 + - - +
109F LEU* 3.4 25.1 + - - +
206F ALA* 5.0 3.4 - - + -
246F TYR* 4.0 29.4 - - + -
249F VAL* 3.4 24.5 - - + -
250F ARG* 3.7 18.6 - - - +
253F ILE* 3.4 26.3 - - + +
418F CYS* 4.0 15.7 - - - +
422F ALA* 4.1 26.9 - - + +
425F VAL* 4.5 6.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 106 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22E GLU* 4.0 6.7 - - - -
26E ARG* 3.4 35.9 + - - -
67F VAL 5.6 3.0 + - - -
102F ALA 3.3 13.2 + - - +
103F GLN* 3.9 12.7 + - - +
105F MET* 1.3 74.3 - - - +
107F ASP* 1.3 72.5 + - - +
109F LEU* 3.4 6.0 + - - +
110F VAL* 2.9 36.3 + - + +
203F GLN* 3.1 49.5 + - + +
206F ALA* 3.6 21.2 - - + +
207F ALA* 3.8 8.5 - - + +
210F MET* 5.8 1.6 - - - -
217F ASN* 5.1 4.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 107 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67F VAL* 3.9 9.5 - - - +
68F CYS* 3.8 4.3 - - - -
103F GLN* 2.8 40.0 + - - +
104F TYR 4.2 0.7 - - - +
106F HIS* 1.3 83.4 - - - +
108F HIS* 1.3 52.0 + - - +
110F VAL* 3.2 4.6 + - - +
111F HIS* 2.8 32.7 + - - +
462F PRO* 3.4 20.5 - - + +
463F ARG* 2.8 44.9 + - - -
528F ASP* 4.5 1.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 108 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104F TYR* 3.2 24.5 + + + +
107F ASP* 1.3 73.0 - - + +
109F LEU* 1.3 61.3 + - - +
111F HIS* 3.4 4.4 + - - +
112F PHE* 3.0 30.3 + - - +
257F TYR* 3.7 9.2 + - + +
371F PRO* 4.1 1.2 - - + +
414F ARG* 3.5 34.1 - - + +
417F GLN* 2.8 47.7 + - + -
418F CYS* 3.1 36.8 - - + +
462F PRO* 3.6 20.1 + - + +
528F ASP* 4.8 4.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 109 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105F MET 3.4 17.8 + - - +
106F HIS* 3.4 7.4 + - - +
108F HIS* 1.3 73.8 - - - +
110F VAL* 1.3 68.0 + - + +
112F PHE* 3.4 1.6 + - - -
113F TYR* 3.3 47.4 + - + +
114F HIS* 4.8 1.4 + - - -
199F ALA* 4.6 5.4 - - + +
202F VAL* 3.8 32.5 - - + -
203F GLN* 4.4 14.8 - - + +
206F ALA* 5.2 0.9 - - + -
249F VAL* 4.8 8.1 - - + -
252F PHE* 3.4 30.7 - - + -
253F ILE* 4.3 11.4 - - + -
257F TYR* 4.2 16.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 110 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22E GLU* 4.6 16.8 - - - +
25E LEU* 5.4 9.0 - - + -
67F VAL* 6.4 0.7 - - + -
106F HIS* 2.9 32.7 + - + +
107F ASP* 3.8 4.5 - - - +
109F LEU* 1.3 77.9 - - - +
111F HIS* 1.3 63.5 + - - +
114F HIS* 3.1 44.1 + - + +
115F LEU* 3.5 17.0 + - + -
203F GLN* 3.5 38.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 111 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16F ARG 5.4 0.7 - - - -
107F ASP* 2.8 20.5 + - - +
108F HIS* 3.7 5.6 - - - +
110F VAL* 1.3 75.8 - - - +
112F PHE* 1.3 66.9 + - - +
115F LEU* 3.2 26.4 + - + +
116F HIS* 2.9 50.1 + + - +
414F ARG* 3.5 34.9 - - - -
463F ARG* 5.5 0.2 - - - +
525F HIS* 2.9 35.1 + - - +
528F ASP* 3.3 37.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 112 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108F HIS 3.0 13.7 + - - +
109F LEU 4.1 2.0 - - - +
110F VAL 3.3 0.4 - - - -
111F HIS* 1.3 79.7 - - - +
113F TYR* 1.3 90.5 + + - +
116F HIS* 3.4 12.8 - - + +
117F ALA* 2.8 44.4 + - + +
120F TRP* 6.1 3.6 - + - -
257F TYR* 3.1 45.3 - + + +
260F ASP* 4.2 11.9 - - + -
261F LEU* 3.9 35.9 - - + -
264F VAL* 5.3 12.1 - - + -
411F THR* 5.0 9.2 - - + -
414F ARG* 6.0 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 113 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109F LEU* 3.3 34.0 + - + +
112F PHE* 1.3 106.1 - + - +
114F HIS* 1.3 79.2 + - + +
117F ALA* 3.5 18.6 + - + +
118F LEU 4.8 0.7 + - - -
192F ALA* 4.7 6.5 - - + -
195F HIS* 3.6 21.1 - - + -
196F TYR* 2.9 39.5 - - + -
199F ALA* 3.5 16.6 - - + -
252F PHE* 3.9 9.4 - + - -
256F VAL* 3.4 10.3 + - + +
257F TYR* 3.4 22.4 - - + -
260F ASP* 2.9 22.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 114 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25E LEU* 6.3 1.2 - - + +
47E THR 4.6 0.9 - - - +
48E LEU* 4.5 22.4 - - + +
16F ARG* 3.6 18.9 - - - +
109F LEU 5.4 0.2 - - - -
110F VAL* 3.1 41.5 + - + +
113F TYR* 1.3 82.5 - - + +
115F LEU* 1.3 64.7 + - + +
118F LEU* 4.9 2.5 - - - +
196F TYR* 3.2 53.9 + + + +
199F ALA* 3.7 33.6 - - + +
200F LEU* 3.5 23.9 - - + +
203F GLN* 4.5 1.1 - - + +
----------------------------------------------------------
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