Contacts of the helix formed by residues 87 - 114 (chain D) in PDB entry 4QYL
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 THR 87 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83D ASN* 3.5 10.5 - - + +
84D ALA* 2.7 40.8 + - + +
86D ASP* 1.3 87.0 - - - +
88D ILE* 1.3 64.6 + - - +
89D PHE* 3.6 12.1 + - + -
90D TYR* 3.2 14.7 + - - +
91D ARG* 3.1 24.1 + - - +
4H GLY* 6.4 1.6 - - - -
5H ALY 6.2 0.2 - - - +
8H GLY* 3.4 15.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 88 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D ILE* 4.8 9.6 - - + +
86D ASP 3.9 0.4 + - - -
87D THR* 1.3 71.9 - - - +
89D PHE* 1.3 78.8 + - + +
91D ARG* 3.3 8.8 + - - +
92D ALA* 2.8 30.7 + - - +
7H GLY 3.2 23.3 - - - +
8H GLY* 2.8 27.3 + - - +
9H LYS 3.9 15.7 - - - +
10H ALA* 4.0 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 89 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D ILE* 3.9 31.9 - - + -
28D PHE* 4.2 0.2 - - - -
79D CYS* 3.2 16.7 - - - -
83D ASN* 3.8 24.7 - - - +
87D THR* 3.1 7.1 - - + +
88D ILE* 1.3 87.1 - - + +
90D TYR* 1.3 65.2 + - - +
92D ALA* 3.3 6.4 + - - +
93D ALA 3.0 17.7 + - - -
5H ALY 3.7 43.1 - - + -
6H GLN 3.6 14.8 - - - -
7H GLY* 3.9 10.8 - - - -
8H GLY* 3.4 26.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 90 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79D CYS* 4.2 5.6 - - - -
80D LEU* 3.5 43.6 - - + +
83D ASN* 3.4 22.1 - - + +
84D ALA 3.1 19.3 - - - +
85D LYS* 3.5 35.7 - - + +
87D THR* 3.2 9.0 + - - +
89D PHE* 1.3 75.2 - - - +
91D ARG* 1.3 65.8 + - + +
93D ALA* 3.1 5.2 + - - +
94D VAL* 3.1 39.7 + - + +
97D ARG* 6.0 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 91 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85D LYS 4.1 12.1 - - - +
86D ASP* 4.3 10.7 + - - +
87D THR 3.1 19.0 + - - +
88D ILE* 3.8 8.5 - - - +
90D TYR* 1.3 80.5 - - + +
92D ALA* 1.3 61.6 + - - +
94D VAL* 3.4 7.6 + - - +
95D ARG* 3.2 32.0 + - - +
201D SO4 2.9 46.3 + - - +
10H ALA* 3.8 24.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 92 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D ASP* 5.8 0.2 - - - +
27D ILE* 3.5 28.3 - - + -
28D PHE* 4.1 13.8 - - + -
88D ILE 2.8 17.7 + - - +
89D PHE 3.5 5.4 - - - +
91D ARG* 1.3 76.9 - - - +
93D ALA* 1.3 56.4 + - - +
95D ARG* 3.3 12.6 + - - +
96D LEU* 2.9 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 93 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28D PHE* 3.8 10.5 - - + -
76D VAL* 3.9 12.7 - - - +
79D CYS* 3.7 24.0 - - + -
80D LEU* 3.7 20.4 - - + -
89D PHE 3.0 13.4 + - - +
90D TYR 3.1 8.0 + - - +
92D ALA* 1.3 74.5 - - - +
94D VAL* 1.3 59.6 + - - +
96D LEU* 3.4 4.1 + - - +
97D ARG* 2.8 30.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 94 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80D LEU* 3.8 8.5 - - + -
90D TYR* 3.1 37.8 + - + +
91D ARG* 3.6 10.3 - - - +
92D ALA 3.4 0.2 - - - -
93D ALA* 1.3 75.5 - - - +
95D ARG* 1.3 62.3 + - + +
97D ARG* 3.3 30.1 + - - +
98D GLU* 3.0 37.3 + - - +
201D SO4 5.9 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 95 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22D LYS 5.9 1.1 - - - +
24D THR* 5.5 4.9 + - - -
91D ARG* 3.2 19.0 + - - +
92D ALA* 3.3 11.9 + - - +
94D VAL* 1.3 74.1 - - + +
96D LEU* 1.3 65.2 + - - +
98D GLU* 3.4 15.4 + - - +
99D GLN* 3.0 48.7 + - - +
201D SO4 2.5 46.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 96 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19D LEU 3.9 11.2 - - - +
22D LYS* 3.8 28.2 + - + +
23D ASP* 4.2 11.0 - - + +
28D PHE* 3.6 32.5 - - + -
50D PHE* 4.2 11.0 - - + -
72D PHE* 3.6 28.7 - - + -
75D ILE* 4.2 6.3 - - + -
76D VAL* 4.1 11.0 - - + -
92D ALA 2.9 17.4 + - - +
93D ALA* 3.6 5.4 - - - +
95D ARG* 1.3 73.3 - - - +
97D ARG* 1.3 62.0 + - - +
99D GLN* 5.0 2.2 - - - +
100D GLY* 2.8 30.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 97 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72D PHE* 4.6 6.8 - - + -
76D VAL* 3.7 25.7 - - + +
80D LEU* 3.4 25.7 - - - +
90D TYR* 6.0 0.4 + - - -
93D ALA 2.8 18.4 + - - +
94D VAL* 3.5 28.5 + - - +
96D LEU* 1.3 76.4 - - - +
98D GLU* 1.3 64.0 + - - +
101D GLY* 3.1 21.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 98 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94D VAL* 3.0 29.0 + - - +
95D ARG* 3.6 24.0 + - - +
97D ARG* 1.3 82.0 - - - +
99D GLN* 1.3 69.3 + - + +
101D GLY* 3.6 6.2 + - - -
102D ALA* 4.0 7.8 + - - +
201D SO4 5.2 2.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 99 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22D LYS* 3.5 55.5 + - + +
24D THR* 5.9 1.2 - - - +
95D ARG* 3.0 43.1 + - - +
98D GLU* 1.3 81.2 + - + +
100D GLY* 1.3 65.6 + - - +
102D ALA* 3.3 15.3 + - - +
103D VAL* 3.6 14.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 100 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19D LEU* 3.7 22.0 - - - -
22D LYS* 4.6 4.1 - - - +
72D PHE* 3.9 6.3 - - - -
96D LEU* 2.8 23.3 + - - -
99D GLN* 1.3 70.6 - - - +
101D GLY* 1.3 65.4 + - - +
103D VAL* 3.1 6.1 + - - +
104D LEU* 2.9 32.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 101 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72D PHE* 4.9 0.8 - - - -
97D ARG 3.1 17.0 + - - -
98D GLU* 3.6 4.0 + - - -
99D GLN 3.2 0.6 - - - -
100D GLY* 1.3 77.9 - - - +
102D ALA* 1.3 59.8 + - - +
104D LEU* 3.4 9.1 + - - +
105D ARG* 3.0 33.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 102 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98D GLU 4.0 5.5 + - - +
99D GLN* 3.3 11.9 + - - +
100D GLY 3.2 0.6 - - - -
101D GLY* 1.3 75.3 - - - +
103D VAL* 1.3 64.1 + - + +
105D ARG* 3.4 9.4 + - - +
106D GLN* 3.2 23.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 103 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15D THR* 4.0 8.5 - - + +
18D GLN* 3.7 44.7 - - + +
19D LEU* 3.7 22.2 - - + -
22D LYS* 3.8 22.0 - - + -
99D GLN 3.7 13.0 - - - +
100D GLY* 3.1 10.2 + - - +
102D ALA* 1.3 78.2 - - + +
104D LEU* 1.3 60.6 - - - +
106D GLN* 3.5 5.8 + - - +
107D ALA* 3.1 22.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 104 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15D THR* 4.5 2.5 - - + -
19D LEU* 4.2 12.3 - - + -
65D PHE* 3.9 25.2 - - + -
68D PHE* 4.2 19.3 - - + -
69D GLU* 4.0 37.7 - - + +
72D PHE* 3.4 34.5 - - + -
73D ASN* 4.7 2.5 - - - +
100D GLY 2.9 20.4 + - - +
101D GLY* 3.8 6.7 - - - +
103D VAL* 1.3 73.3 - - - +
105D ARG* 1.3 59.5 + - + +
107D ALA* 4.5 2.5 - - - -
108D ARG* 2.9 33.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 105 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101D GLY 3.0 25.7 + - - +
102D ALA* 3.7 8.1 - - - +
103D VAL 3.3 0.2 - - - -
104D LEU* 1.3 77.4 - - + +
106D GLN* 1.3 62.2 + - - +
108D ARG* 3.6 4.4 + - - +
109D ARG* 3.3 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 106 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D LEU* 5.6 1.2 - - - +
18D GLN* 4.7 11.4 + - - +
102D ALA 3.2 13.8 + - - +
103D VAL* 3.7 6.1 - - - +
105D ARG* 1.3 79.6 - - - +
107D ALA* 1.3 69.9 + - - +
109D ARG* 3.3 28.1 + - - +
110D GLN* 3.1 50.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 107 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D LEU* 3.8 9.1 - - + +
15D THR* 3.3 37.0 - - + +
18D GLN* 5.1 2.0 - - - +
65D PHE* 3.7 12.3 - - + -
103D VAL 3.1 17.7 + - - +
106D GLN* 1.3 82.4 + - - +
108D ARG* 1.3 68.1 + - - +
110D GLN* 3.1 8.0 + - - +
111D ALA* 2.9 21.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 108 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65D PHE* 3.6 35.1 - - + +
66D ASP* 2.8 36.1 + - - +
69D GLU* 2.8 30.5 + - - +
104D LEU 2.9 19.7 + - - +
105D ARG* 4.0 5.2 - - - +
107D ALA* 1.3 76.9 - - - +
109D ARG* 1.3 58.0 + - + +
111D ALA* 3.0 3.7 + - - +
112D GLU* 2.9 49.8 + - + +
117D ASP* 4.9 12.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 109 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105D ARG* 3.3 15.7 + - - +
106D GLN* 3.3 31.3 + - - +
107D ALA 3.2 0.4 - - - -
108D ARG* 1.3 79.4 - - + +
110D GLN* 1.3 77.8 + - - +
112D GLU* 3.3 17.9 + - - +
113D LYS* 3.0 36.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 110 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D LEU* 4.2 13.5 - - + -
106D GLN* 3.1 47.8 + - - +
107D ALA* 3.1 7.5 + - - +
109D ARG* 1.3 96.1 - - - +
111D ALA* 1.3 65.8 + - - +
113D LYS* 3.3 29.2 + - - +
114D MET* 3.1 48.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 111 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D PHE* 5.1 2.7 - - + -
11D LEU* 3.6 22.4 - - + +
65D PHE* 4.1 15.0 - - + -
107D ALA 2.9 9.9 + - - +
108D ARG* 3.4 8.3 - - - +
110D GLN* 1.3 75.8 - - - +
112D GLU* 1.3 62.4 + - - +
114D MET* 3.4 5.6 + - - +
115D GLY 3.2 12.8 + - - -
116D ILE 3.4 5.2 + - - +
117D ASP* 3.1 37.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 112 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108D ARG* 2.9 36.0 + - + +
109D ARG* 3.6 23.7 + - - +
110D GLN 3.1 0.2 - - - -
111D ALA* 1.3 78.5 - - - +
113D LYS* 1.3 62.1 + - + +
115D GLY* 3.2 12.3 + - - -
117D ASP* 3.5 33.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 113 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109D ARG* 3.0 29.2 + - + +
110D GLN* 3.3 32.5 + - - +
112D GLU* 1.3 76.9 - - + +
114D MET* 1.3 63.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 114 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7D PRO* 5.0 23.8 - - + +
11D LEU* 5.2 11.7 - - + -
110D GLN* 3.1 44.4 + - + +
111D ALA* 3.4 5.4 + - - +
112D GLU 3.2 0.2 - - - -
113D LYS* 1.3 83.0 - - + +
115D GLY* 1.3 58.1 + - - +
116D ILE* 3.5 3.9 + - - +
----------------------------------------------------------
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