Contacts of the helix formed by residues 67 - 83 (chain B) in PDB entry 1VCB
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 SER 67 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A PHE* 3.7 18.6 - - - -
94A SER* 3.0 18.5 + - - -
23B SER* 3.2 9.1 + - - -
25B ASP* 2.5 39.0 + - - -
27B HIS* 2.9 15.6 + - - -
29B PHE* 4.2 6.6 - - - -
66B PRO* 1.3 70.8 - - - +
68B HIS* 1.3 58.4 + - - +
69B VAL 3.0 0.2 - - - -
70B LEU 4.6 0.2 - - - +
71B SER* 3.0 33.8 + - - -
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Residues in contact with HIS 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A PHE* 4.0 7.4 - - + +
94A SER* 2.6 40.3 + - - +
95A SER 3.9 14.1 - - - -
96A PRO* 3.3 33.5 - - + +
97A PRO* 4.9 0.2 - - + -
66B PRO* 3.3 28.6 - - + +
67B SER* 1.3 77.9 - - - +
69B VAL* 1.3 62.6 + - + +
71B SER* 3.8 11.9 + - - -
72B LYS* 4.3 5.4 - - - +
99B ILE* 3.8 32.6 - - + +
102B GLU* 3.1 28.0 + - - -
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Residues in contact with VAL 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B ILE* 3.3 22.4 - - + -
66B PRO* 3.1 20.5 + - + +
67B SER 3.0 0.8 - - - -
68B HIS* 1.3 91.4 - - + +
70B LEU* 1.3 60.2 + - - +
71B SER 3.1 1.1 - - - -
72B LYS* 2.8 26.2 + - - +
73B VAL* 3.1 9.4 + - + -
99B ILE* 5.0 5.6 - - + +
102B GLU* 3.5 35.7 - - + +
103B LEU* 4.1 12.6 - - + +
106B ALA* 3.4 23.1 - - + -
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Residues in contact with LEU 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B LEU* 4.1 18.4 - - + -
23B SER* 4.0 22.9 - - - +
29B PHE* 3.9 29.6 - - + -
62B PHE* 4.0 25.4 - - + -
65B ILE* 4.0 17.7 - - + +
66B PRO 2.9 19.2 + - - +
67B SER 4.3 0.2 - - - +
69B VAL* 1.3 73.3 - - - +
71B SER* 1.3 61.4 + - - +
73B VAL* 3.8 24.5 - - + -
74B CYS* 3.1 34.0 + - - -
110B LEU* 5.5 1.8 - - + -
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Residues in contact with SER 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A PHE* 3.9 6.8 - - - -
93A PHE* 3.6 37.1 - - - -
29B PHE* 4.1 10.2 - - - -
67B SER 3.0 19.1 + - - -
68B HIS* 3.8 9.9 + - - -
70B LEU* 1.3 76.6 - - - +
72B LYS* 1.3 61.6 + - - +
74B CYS* 3.5 2.8 + - - +
75B MET* 3.1 41.9 + - - +
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Residues in contact with LYS 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A GLN 4.3 11.1 + - - -
68B HIS 4.3 11.0 - - - +
69B VAL 2.8 10.4 + - - +
71B SER* 1.3 79.3 + - - +
73B VAL* 1.3 60.6 + - - +
75B MET* 3.2 18.5 + - + +
76B TYR* 2.9 29.0 + - - +
93B PHE* 3.8 19.1 - - + -
94B PRO* 3.0 41.0 + - - +
95B ILE* 4.8 6.5 - - - +
96B ALA* 5.2 2.0 - - - +
99B ILE* 4.4 23.3 - - + -
103B LEU* 4.2 19.3 - - + -
158C LEU* 5.5 0.2 - - - -
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Residues in contact with VAL 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B ILE* 5.8 0.7 - - + -
65B ILE* 5.3 0.4 - - + -
69B VAL* 3.1 18.1 + - + +
70B LEU* 3.6 23.6 - - + +
72B LYS* 1.3 76.8 - - - +
74B CYS* 1.3 62.7 + - - +
76B TYR* 3.0 11.7 + - - +
77B PHE* 3.0 57.1 + - + -
103B LEU* 3.9 18.2 - - + -
106B ALA* 4.5 3.6 - - + -
110B LEU* 3.6 26.9 - - + -
112B CYS* 5.1 3.1 - - - -
158C LEU* 4.4 7.9 - - + -
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Residues in contact with CYS 74 (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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15A PHE* 3.5 30.7 - - + -
21B LEU* 3.9 19.7 - - - -
29B PHE* 4.0 15.7 - - - -
31B VAL* 3.6 26.9 - - + +
70B LEU* 3.1 21.8 + - - +
71B SER 3.8 0.4 - - - +
73B VAL* 1.3 78.9 - - - +
75B MET* 1.3 62.4 + - - +
77B PHE* 3.0 22.7 + - - +
78B THR* 3.3 15.8 + - - +
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Residues in contact with MET 75 (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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6A MET* 4.1 29.2 - - + -
15A PHE* 4.0 9.9 - - + -
69A PRO 3.5 6.3 - - - +
70A GLN 3.6 24.9 - - - +
71A ALA* 4.7 2.0 - - - -
72A PRO* 4.0 18.2 - - + -
93A PHE* 5.6 1.3 - - + -
71B SER* 3.1 30.9 + - - +
72B LYS* 3.2 25.1 + - + +
74B CYS* 1.3 74.4 - - - +
76B TYR* 1.3 58.0 + - - +
78B THR* 3.2 11.2 + - - -
79B TYR* 3.1 26.7 + - - +
93B PHE* 4.1 6.8 - - + -
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Residues in contact with TYR 76 (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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38B THR* 4.5 8.5 - - + -
72B LYS 2.9 12.7 + - - +
73B VAL* 3.3 11.2 - - - +
75B MET* 1.3 73.2 - - - +
77B PHE* 1.3 75.9 + + - +
79B TYR* 3.4 21.6 - + - +
80B LYS* 2.8 52.4 + - + +
93B PHE* 3.5 24.8 - + + -
112B CYS* 3.6 16.8 + - + -
155C VAL* 4.2 2.5 + - + +
156C TYR 2.8 28.2 + - - -
157C THR* 3.2 10.6 - - - -
158C LEU* 3.5 39.7 - - + -
161C ARG* 5.8 1.8 - - + -
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Residues in contact with PHE 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B LEU* 4.5 8.3 - - + -
31B VAL* 4.7 8.5 - - + -
35B HIS* 3.5 30.3 - - + +
36B ALA* 3.8 22.2 - - + -
38B THR* 3.9 19.1 - - + -
39B SER* 4.0 19.1 - - - -
42B ILE* 4.3 13.5 - - + -
73B VAL* 3.0 44.5 + - + -
74B CYS* 3.0 15.2 + - - +
76B TYR* 1.3 83.6 - + - +
78B THR* 1.3 61.5 + - + +
80B LYS* 3.9 2.8 - - - +
81B VAL* 3.0 30.1 + - - +
110B LEU* 4.9 0.7 - - + -
112B CYS* 4.1 20.4 - - - -
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Residues in contact with THR 78 (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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4A PHE* 4.8 14.5 - - + +
15A PHE* 4.7 25.4 - - + -
69A PRO* 2.9 35.0 + - - +
72A PRO* 5.9 0.7 - - - +
31B VAL* 5.7 2.2 - - + -
35B HIS* 3.7 27.5 + - + +
74B CYS 3.3 12.7 + - - +
75B MET* 3.2 4.5 + - - -
77B PHE* 1.3 75.9 - - + +
79B TYR* 1.3 57.2 + - - +
81B VAL* 3.8 1.4 - - - +
82B ARG* 2.9 32.4 + - - +
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Residues in contact with TYR 79 (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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69A PRO* 3.9 9.9 - - - -
70A GLN* 3.3 32.5 - - + +
75B MET 3.1 18.3 + - - +
76B TYR* 3.4 21.8 - + - +
78B THR* 1.3 77.9 + - - +
80B LYS* 1.3 64.9 + - - +
82B ARG* 3.3 0.6 + - - -
83B TYR* 3.0 52.1 + + - +
90B ILE* 3.5 13.9 - - + +
91B PRO 2.6 29.0 + - - -
92B GLU* 4.3 0.3 - - - -
93B PHE* 3.7 35.6 + + + +
153C LEU* 5.3 1.6 - - - +
154C PRO 4.9 4.0 + - - -
155C VAL* 4.0 19.3 - - + -
156C TYR 5.2 2.0 + - - -
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Residues in contact with LYS 80 (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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38B THR* 4.2 24.5 + - + +
76B TYR* 2.8 50.7 + - + +
77B PHE* 3.9 4.7 - - - +
79B TYR* 1.3 76.9 - - - +
81B VAL* 1.3 72.2 + - - +
84B THR* 3.1 54.5 + - + +
155C VAL* 4.3 7.6 - - + -
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Residues in contact with VAL 81 (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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34B GLU* 5.0 3.4 - - + +
35B HIS* 3.7 41.5 - - + +
38B THR* 3.9 18.4 - - - +
77B PHE 3.0 20.8 + - - +
78B THR 4.0 2.9 - - - +
80B LYS* 1.3 84.8 - - + +
82B ARG* 1.3 60.7 + - - +
84B THR* 4.5 8.2 + - - +
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Residues in contact with ARG 82 (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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1A MET* 6.0 6.5 - - - +
2A ASP* 5.9 2.2 + - - +
4A PHE* 4.2 24.4 - - + -
69A PRO* 3.9 21.9 - - + +
78B THR 2.9 18.5 + - - +
79B TYR 3.8 2.9 - - - +
80B LYS 3.1 0.2 - - - -
81B VAL* 1.3 80.8 - - - +
83B TYR* 1.3 89.9 + - + +
84B THR 4.6 1.8 - - - +
86B SER* 4.2 8.9 + - - -
88B THR* 4.0 18.0 + - - +
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Residues in contact with TYR 83 (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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68A ARG* 5.1 3.3 + - - -
69A PRO* 4.4 7.8 - - + +
70A GLN* 3.8 13.5 + - - -
79B TYR* 3.0 46.8 + + + +
82B ARG* 1.3 117.2 + - + +
84B THR* 1.3 69.3 + - - +
85B ASN 3.3 1.0 + - - -
86B SER* 3.1 18.3 + - - -
88B THR* 4.4 10.8 - - - -
89B GLU 4.4 4.0 - - - -
90B ILE* 3.7 36.4 - - + +
91B PRO* 3.5 38.2 - - + +
155C VAL* 3.8 7.6 - - + -
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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
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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