Contacts of the helix formed by residues 75 - 93 (chain B) in PDB entry 2QY7
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 ASN 75 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B ASP* 3.0 28.0 + - - +
71B ASP 5.2 1.5 + - - +
72B ASN* 3.7 7.1 + - - +
73B LYS 3.6 0.8 - - - -
74B LYS* 1.3 84.8 + - - +
76B TRP* 1.3 64.4 + - - +
77B ARG* 3.2 4.6 + - - +
78B ARG* 3.3 54.4 + - + +
79B VAL* 3.4 15.8 + - - +
114B TYR* 3.8 3.1 - - - -
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Residues in contact with TRP 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B LYS 3.6 2.2 - - - -
75B ASN* 1.3 74.7 - - - +
77B ARG* 1.3 113.4 + - + +
79B VAL* 3.4 1.3 + - - -
80B TYR* 2.9 45.9 + + + +
114B TYR* 3.4 30.4 + - + +
116B PHE* 3.5 40.1 - + + -
118B ASP* 5.6 0.8 - - - +
124B GLN* 3.6 51.5 - - + +
127B ASN* 4.2 15.5 - - + -
128B ILE* 3.4 9.0 - - + +
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Residues in contact with ARG 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B ASN 4.8 4.0 - - - +
34B ASP* 4.1 20.9 - - - +
35B ASP 4.1 4.4 + - - -
36B PRO* 3.6 50.7 + - - +
37B TRP* 5.5 0.4 - - - +
75B ASN* 3.2 1.5 - - - +
76B TRP* 1.3 127.4 - - + +
78B ARG* 1.3 59.4 + - - +
80B TYR* 3.3 10.2 + - - +
81B LYS* 2.9 46.7 + - + +
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Residues in contact with ARG 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B THR* 3.6 24.7 + - - +
33B ASN 4.9 1.0 + - - -
34B ASP* 5.1 7.3 + - - +
67B ARG* 3.1 68.2 - - + +
70B LYS 4.7 5.3 + - - -
71B ASP* 3.9 19.6 + - - +
72B ASN* 5.9 1.1 - - - -
75B ASN* 3.3 50.3 + - + +
77B ARG* 1.3 78.1 - - - +
79B VAL* 1.3 59.0 + - - +
81B LYS* 3.5 1.4 + - - +
82B SER* 3.0 28.6 + - - -
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Residues in contact with VAL 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B ARG 4.6 1.6 - - - +
68B MET* 3.5 16.4 - - + +
72B ASN* 3.4 39.5 - - + +
75B ASN 3.6 11.9 - - - +
76B TRP* 3.4 8.0 + - - +
77B ARG 3.3 0.4 - - - -
78B ARG* 1.3 75.0 - - + +
80B TYR* 1.3 61.9 + - - +
82B SER* 2.4 25.7 + - - -
83B LEU* 3.0 14.8 + - + +
111B LEU* 4.3 13.9 - - + -
114B TYR* 4.2 6.1 - - + +
128B ILE* 3.6 31.4 - - + -
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Residues in contact with TYR 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B TRP* 2.9 37.7 + + + +
77B ARG* 3.5 11.9 - - - +
79B VAL* 1.3 77.7 - - - +
81B LYS* 1.3 61.6 + - + +
83B LEU* 3.1 8.2 + - + +
84B LEU* 3.0 61.6 + - + +
127B ASN* 3.6 44.0 + - + +
128B ILE* 3.3 14.7 - - + +
131B LYS* 4.3 13.7 - - + +
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Residues in contact with LYS 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B GLU 4.7 0.4 + - - -
31B ALA 3.5 25.0 - - - +
32B THR* 4.0 9.2 - - - -
33B ASN* 2.7 50.7 + - - +
35B ASP* 2.8 21.0 + - - +
37B TRP 3.3 19.3 + - - -
38B GLY 3.6 19.1 - - - +
39B PRO* 4.0 5.8 - - + +
77B ARG* 2.9 33.2 + - + +
78B ARG 4.1 0.4 - - - +
80B TYR* 1.3 74.6 - - + +
82B SER* 1.3 60.0 + - - +
84B LEU* 3.6 12.6 - - + +
85B LEU* 2.9 29.5 + - - +
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Residues in contact with SER 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B THR* 3.8 18.3 - - - +
64B LEU* 4.4 8.9 - - - +
68B MET* 3.1 46.2 - - - +
78B ARG 3.0 14.4 + - - -
79B VAL 2.4 27.2 + - - -
81B LYS* 1.3 78.7 - - - +
83B LEU* 1.3 55.0 + - - +
85B LEU* 3.4 4.1 + - - +
86B LEU* 2.8 29.5 + - - +
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Residues in contact with LEU 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B MET* 3.9 13.9 - - + -
79B VAL* 3.0 18.9 + - + +
80B TYR* 3.1 6.9 + - - +
82B SER* 1.3 80.2 + - - +
84B LEU* 1.3 60.5 + - - +
86B LEU* 3.2 3.6 + - - +
87B ALA* 2.8 32.1 + - - +
108B LEU* 3.8 17.7 - - + -
111B LEU* 4.2 2.0 - - + -
128B ILE* 3.9 44.0 - - + +
131B LYS* 3.8 18.2 - - + -
132B VAL* 3.8 31.2 - - + +
135B LEU* 3.7 12.9 - - + +
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Residues in contact with LEU 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B GLY 4.0 21.1 - - - +
39B PRO* 4.2 11.2 - - + -
44B MET* 3.9 6.9 - - - +
80B TYR* 3.0 56.3 + - + +
81B LYS* 3.6 7.9 - - - +
83B LEU* 1.3 75.6 - - - +
85B LEU* 1.3 62.8 + - - +
87B ALA* 3.4 2.3 + - - +
88B TYR* 3.1 22.7 + - - +
131B LYS* 3.9 27.1 - - + +
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Residues in contact with LEU 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B VAL* 4.0 20.2 - - + -
31B ALA* 4.2 9.6 - - + -
32B THR* 4.7 4.5 - - + -
39B PRO* 4.7 6.0 - - + +
44B MET* 4.0 25.1 - - + -
47B ILE* 3.9 35.0 - - + -
64B LEU* 4.0 17.3 - - + -
81B LYS 2.9 21.2 + - - +
82B SER* 3.7 4.9 - - - +
84B LEU* 1.3 72.8 - - - +
86B LEU* 1.3 58.3 + - - +
88B TYR* 3.2 2.9 + - - +
89B LEU* 2.8 58.1 + - + +
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Residues in contact with LEU 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B MET* 4.3 17.7 - - + -
64B LEU* 4.2 14.3 - - + +
65B TRP* 3.8 24.7 - - + -
68B MET* 4.1 7.4 - - + -
82B SER 2.8 20.3 + - - +
83B LEU 3.2 4.5 + - - +
85B LEU* 1.3 72.5 - - - +
87B ALA* 1.3 56.4 + - - +
89B LEU* 3.2 1.9 + - - -
90B ILE* 2.8 50.1 + - + +
97B VAL* 4.0 15.3 - - + -
101B ALA* 4.6 5.6 - - + -
108B LEU* 3.9 17.3 - - + -
135B LEU* 3.7 22.2 - - + -
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Residues in contact with ALA 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B LEU 2.8 20.0 + - - +
84B LEU 3.6 4.7 - - - +
86B LEU* 1.3 74.4 - - - +
88B TYR* 1.3 63.7 + - - +
90B ILE* 3.5 2.6 + - - +
91B ARG* 3.5 25.6 + - - +
131B LYS* 3.6 28.3 - - - +
135B LEU* 3.9 19.7 - - + +
138B PHE* 5.3 1.7 - - - -
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Residues in contact with TYR 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B GLY* 3.9 10.5 + - - -
44B MET* 3.6 68.9 - - + -
45B GLY* 3.5 21.6 + - - -
48B ALA* 3.9 8.5 - - + -
84B LEU 3.1 7.4 + - - +
85B LEU 3.5 6.7 - - - +
87B ALA* 1.3 74.8 - - - +
89B LEU* 1.3 63.0 + - + +
91B ARG* 3.2 3.9 + - - +
92B ASN* 2.9 67.0 + - + +
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Residues in contact with LEU 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B MET 4.2 2.0 - - - +
47B ILE* 4.1 2.9 - - + -
48B ALA* 3.6 41.1 - - + +
51B THR* 4.2 8.3 - - + -
60B LEU* 4.0 21.8 - - + -
61B MET* 4.6 4.7 - - - -
64B LEU* 3.8 28.0 - - + -
85B LEU* 2.8 37.0 + - + +
86B LEU* 3.2 4.7 + - - +
88B TYR* 1.3 80.7 - - + +
90B ILE* 1.3 57.8 + - - +
93B GLY* 2.8 30.3 + - - +
97B VAL* 3.7 20.7 - - + +
149B ARG* 4.1 0.3 + - - -
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Residues in contact with ILE 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B LEU* 2.8 27.1 + - + +
87B ALA* 3.9 5.8 - - - +
88B TYR 3.3 0.2 - - - -
89B LEU* 1.3 72.7 - - - +
91B ARG* 1.3 57.9 + - - +
97B VAL* 3.8 20.9 - - + +
98B VAL* 4.1 6.0 - - + +
101B ALA* 3.6 26.9 - - + -
135B LEU* 3.7 23.8 - - + -
138B PHE* 3.6 28.7 - - + -
139B ALA* 4.2 13.7 - - + -
145B LEU* 3.7 17.0 - - + -
149B ARG* 2.9 28.8 + - - +
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Residues in contact with ARG 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B ALA* 3.5 14.5 + - - +
88B TYR* 3.2 8.6 + - - +
89B LEU 3.2 0.4 - - - -
90B ILE* 1.3 79.2 - - - +
92B ASN* 1.3 71.2 + - - +
93B GLY 3.8 0.4 - - - -
138B PHE* 3.7 34.3 - - + -
144B ARG* 4.2 19.4 - - - +
148B GLU* 4.0 29.0 + - + +
149B ARG* 3.8 23.3 + - - +
152B ALA* 3.7 20.7 - - + +
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Residues in contact with ASN 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B ALA* 4.2 6.7 - - + +
52B PHE* 3.8 13.3 - - - -
88B TYR* 2.9 65.8 + - + +
91B ARG* 1.3 85.4 - - - +
93B GLY* 1.3 64.7 + - - +
149B ARG* 5.5 0.2 - - - -
152B ALA* 3.6 22.7 - - - +
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Residues in contact with GLY 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B ALA* 4.2 10.0 - - - +
51B THR* 3.4 12.3 - - - -
52B PHE* 3.5 12.3 - - - -
89B LEU* 2.8 19.6 + - - +
92B ASN* 1.3 81.3 - - - +
94B SER* 1.3 62.5 + - - -
97B VAL* 4.4 1.3 - - - -
149B ARG* 2.9 25.6 + - - -
153B LYS* 5.1 0.2 + - - -
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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) + - + + + + + -
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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