Contacts of the helix formed by residues 51 - 68 (chain B) in PDB entry 7V3X
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 GLY 51 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B GLY 3.4 4.0 + - - -
50B THR* 1.3 75.9 - - - +
52B LYS* 1.3 60.3 + - - +
53B THR 3.5 2.0 - - - -
54B LEU* 3.6 11.9 + - - +
55B PHE* 3.0 25.1 + - - +
207B LEU* 3.3 14.6 - - - +
237B PHE* 5.4 0.4 - - - -
239B ILE* 4.1 19.3 - - - +
244B ILE* 3.9 5.4 - - - +
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Residues in contact with LYS 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B VAL* 3.7 17.3 - - - +
45B SER 4.4 1.3 - - - -
46B GLY* 2.9 42.8 - - - +
47B THR 3.4 15.1 + - - -
48B SER* 4.5 5.5 - - - +
49B GLY 4.5 4.4 - - - +
50B THR* 3.8 5.0 + - - +
51B GLY* 1.3 72.8 - - - +
53B THR* 1.3 68.2 + - - +
55B PHE* 3.2 14.2 + - - +
56B SER* 3.2 13.0 + - - -
179B VAL* 5.6 0.2 - - - +
181B THR* 3.5 32.2 + - + +
182B THR 3.1 23.8 - - - +
183B GLU* 4.3 8.5 - - - +
207B LEU* 3.5 11.6 - - + +
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Residues in contact with THR 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B GLY 3.5 0.2 - - - -
52B LYS* 1.3 74.6 + - - +
54B LEU* 1.3 58.2 + - - +
56B SER* 2.6 24.4 + - - -
57B ILE* 2.8 38.4 + - + +
73B PHE* 4.2 7.9 - - + -
78B GLU* 4.2 23.1 + - - +
83B ILE* 6.3 0.7 - - + -
145B ASP* 3.2 29.4 + - - +
181B THR* 5.4 0.2 - - - +
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Residues in contact with LEU 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B GLY* 3.6 13.8 + - - +
53B THR* 1.3 77.7 - - - +
55B PHE* 1.3 56.5 + - - +
57B ILE* 3.4 7.9 + - + +
58B GLN* 2.9 39.0 + - - +
90B PHE* 2.7 44.0 - - + -
92B TRP* 4.2 7.6 - - + -
239B ILE* 3.4 39.5 - - + -
243B GLY* 4.6 4.3 - - - -
244B ILE* 3.9 22.2 - - + -
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Residues in contact with PHE 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B THR* 5.3 0.9 - - + -
25B ILE* 3.7 28.1 - - + +
28B PHE* 3.6 46.2 - + + -
36B LEU* 4.8 6.7 - - + -
42B THR* 5.7 0.2 - - + -
44B VAL* 4.0 30.5 - - + -
51B GLY 3.0 15.2 + - - +
52B LYS 3.3 10.5 - - - +
53B THR 3.2 0.2 - - - -
54B LEU* 1.3 75.0 - - - +
56B SER* 1.3 56.7 + - - +
58B GLN* 3.8 4.1 - - - +
59B PHE* 3.0 26.5 + + + +
179B VAL* 4.2 18.2 - - + -
205B VAL* 5.4 1.3 - - + -
207B LEU* 4.5 10.1 - - + -
220B LEU* 4.1 13.9 - - + -
244B ILE* 3.7 20.6 - - + +
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Residues in contact with SER 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B LYS 3.2 5.7 + - - -
53B THR* 2.6 28.1 + - - -
55B PHE* 1.3 76.9 - - - +
57B ILE* 1.3 64.3 + - - +
59B PHE* 3.3 7.7 - - - +
60B LEU* 3.1 26.5 + - - +
73B PHE* 3.5 13.4 - - - -
143B SER* 3.5 26.3 + - - -
145B ASP* 4.6 3.4 - - - +
179B VAL* 4.0 16.2 - - - -
181B THR* 4.4 7.8 + - - -
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Residues in contact with ILE 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B THR* 2.8 36.2 + - + +
54B LEU* 3.7 8.3 - - + +
56B SER* 1.3 72.2 + - - +
58B GLN* 1.3 51.6 + - - +
60B LEU* 3.1 8.4 + - + +
61B TYR* 2.8 32.9 + - + +
73B PHE* 3.3 34.5 - - + -
83B ILE* 4.6 14.4 - - + +
87B ALA* 4.7 5.2 - - + -
90B PHE* 6.2 0.2 - - + -
92B TRP* 4.5 21.3 - - + -
94B LEU* 4.2 34.0 - - + +
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Residues in contact with GLN 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B MET 4.6 0.8 + - - -
25B ILE* 3.9 26.5 - - + +
54B LEU* 2.9 19.4 + - + +
55B PHE 3.8 4.5 - - - +
57B ILE* 1.3 73.2 - - - +
59B PHE* 1.3 62.0 + - - +
61B TYR* 3.0 7.2 + - + -
62B ASN* 2.7 58.4 + - - +
92B TRP* 3.4 30.0 - - + -
242B HIS 4.5 7.9 + - - -
243B GLY* 3.8 2.0 - - - -
244B ILE* 2.9 46.7 + - - +
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Residues in contact with PHE 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B MET* 4.3 10.1 - - + -
23B THR* 4.4 15.5 - - - -
25B ILE* 4.6 8.0 - - + +
36B LEU* 3.7 27.1 - - + -
55B PHE* 3.0 20.2 + + + +
56B SER* 3.3 11.2 - - - +
58B GLN* 1.3 75.6 - - - +
60B LEU* 1.3 63.2 + - + +
62B ASN* 4.5 0.3 - - - +
63B GLY 3.2 2.3 + - - -
141B ARG* 2.6 70.3 + - + +
142B VAL 3.7 13.9 - - - -
143B SER* 3.6 12.8 - - - -
177B THR* 4.1 21.5 - - + -
179B VAL* 3.3 26.5 - - + -
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Residues in contact with LEU 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B SER 3.1 9.4 + - - +
57B ILE* 3.1 7.2 + - + +
59B PHE* 1.3 73.8 - - + +
61B TYR* 1.3 54.8 + - - +
63B GLY* 2.9 5.4 + - - -
64B ILE* 2.8 35.0 + - - +
69B GLU 4.7 1.7 - - - +
71B GLY* 4.1 13.7 + - - -
72B VAL 3.7 20.9 - - - +
73B PHE* 3.7 43.1 - - + -
103B LEU* 6.5 2.5 - - + -
141B ARG* 3.7 32.0 - - + +
142B VAL 3.9 4.9 - - - +
143B SER* 3.8 14.4 - - - +
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Residues in contact with TYR 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B ILE* 2.8 22.8 + - + +
58B GLN* 3.7 6.1 - - - +
60B LEU* 1.3 70.5 - - - +
62B ASN* 1.3 73.7 + - - +
64B ILE* 2.9 10.0 + - - +
65B ILE* 2.9 45.1 + - + +
91B GLY 4.9 1.2 + - - -
92B TRP* 3.4 63.3 - + + +
93B ASP 4.8 5.1 + - - -
94B LEU* 4.1 17.7 - - + -
97B LEU* 4.0 25.8 - - + -
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Residues in contact with ASN 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B THR 3.3 22.1 + - - +
24B MET* 3.2 34.4 + - + +
25B ILE* 4.0 1.2 - - - +
58B GLN* 2.7 50.2 + - - +
61B TYR* 1.3 91.1 - - - +
63B GLY* 1.3 57.7 + - - +
65B ILE* 4.6 2.9 - - - +
66B GLU* 3.2 29.5 + - - +
67B PHE* 4.7 1.2 - - - -
92B TRP* 5.3 2.9 - - - -
141B ARG* 4.4 0.9 - - - -
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Residues in contact with GLY 63 (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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59B PHE 3.2 6.7 + - - -
60B LEU 2.9 8.2 + - - -
62B ASN* 1.3 75.6 - - - +
64B ILE* 1.3 61.6 - - - +
67B PHE* 3.3 20.4 + - - +
69B GLU* 3.3 18.8 + - - +
141B ARG* 3.2 36.5 - - - +
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Residues in contact with ILE 64 (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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60B LEU 2.8 14.3 + - - +
61B TYR* 2.9 8.0 + - - +
63B GLY* 1.3 70.5 - - - +
65B ILE* 1.3 60.1 + - - +
68B ASP* 3.1 29.2 + - - +
69B GLU 3.4 16.2 + - - +
70B PRO* 5.3 0.2 - - + -
71B GLY 5.8 1.3 - - - +
97B LEU* 4.3 21.1 - - + -
102B LYS* 4.6 22.2 - - + +
103B LEU* 5.7 2.2 - - + +
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Residues in contact with ILE 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B TYR* 2.9 38.9 + - + +
62B ASN* 4.6 2.9 - - - +
64B ILE* 1.3 75.5 - - + +
66B GLU* 1.3 60.9 + - + +
97B LEU* 5.7 2.9 - - + -
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Residues in contact with GLU 66 (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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24B MET* 3.8 30.3 - - + +
62B ASN* 3.2 18.8 + - - +
64B ILE 3.3 0.4 - - - -
65B ILE* 1.3 80.3 - - + +
67B PHE* 1.3 90.4 + - + +
68B ASP 3.5 1.5 + - - -
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Residues in contact with PHE 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B MET* 6.4 0.2 - - + -
22B ARG* 4.0 39.7 - - + -
24B MET* 3.9 17.3 - - + -
62B ASN 4.7 1.8 - - - -
63B GLY 3.3 6.8 + - - +
66B GLU* 1.3 105.8 - - + +
68B ASP* 1.3 70.3 + - - +
69B GLU* 3.0 37.1 + - + +
141B ARG* 4.9 4.0 - - - -
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Residues in contact with ASP 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B ILE* 3.1 19.0 + - - +
65B ILE 4.8 0.2 - - - -
66B GLU 3.5 2.0 - - - -
67B PHE* 1.3 79.5 - - - +
69B GLU* 1.3 59.1 + - - +
70B PRO* 3.4 13.3 - - - +
102B LYS* 5.9 4.0 - - - +
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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