Contacts of the helix formed by residues 80 - 93 (chain B) in PDB entry 3VZC
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 80 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77B VAL* 4.5 2.4 - - - +
79B SER* 1.3 87.0 + - - +
81B ASP* 1.3 66.3 + - - -
82B GLY 3.1 4.7 + - - -
83B LEU* 3.3 11.6 + - - +
84B MET* 3.5 9.7 + - - +
107B SER* 5.4 4.4 + - - -
111B GLY* 4.5 3.2 - - - +
112B SER 4.2 9.2 - - - -
113B GLY 3.2 13.9 - - - -
114B ASN* 4.0 2.9 - - - -
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Residues in contact with ASP 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B GLY* 1.3 73.0 - - - -
82B GLY* 1.3 56.7 + - - +
84B MET* 3.4 9.3 + - - +
85B HIS* 2.9 28.1 + - - +
112B SER 4.9 0.4 + - - -
113B GLY* 2.8 35.0 + - - +
114B ASN* 3.7 2.3 - - - -
115B ALA* 3.0 19.5 + - - +
116B LEU* 3.1 31.6 + - + +
117B ALA 4.6 0.3 + - - -
166B VAL* 5.0 2.9 - - + +
167B LEU* 3.7 21.2 - - + +
268B LEU 5.0 0.3 - - - +
341B ASP* 3.7 21.1 - - + +
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Residues in contact with GLY 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B GLY* 3.1 2.0 - - - -
81B ASP* 1.3 75.3 - - - +
83B LEU* 1.3 60.2 + - - +
85B HIS* 3.0 11.6 + - - +
86B GLU* 2.9 31.3 + - - +
341B ASP 3.9 8.1 + - - -
342B GLY 6.2 0.2 - - - -
343B GLU* 5.9 6.3 - - - -
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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
----------------------------------------------------------
20B LEU* 3.6 25.1 - - + +
22B ASN* 4.5 6.5 - - + +
54B THR* 4.0 19.7 - - + +
60B ALA* 3.5 30.1 - - + -
77B VAL* 3.4 25.6 - - + -
78B MET 4.5 0.4 - - - +
79B SER* 3.7 32.5 + - - +
80B GLY 3.3 4.7 + - - +
82B GLY* 1.3 74.6 - - - +
84B MET* 1.3 62.3 + - - +
86B GLU* 3.2 10.7 + - + +
87B VAL* 3.0 27.3 + - + +
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Residues in contact with MET 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B VAL* 3.6 23.5 - - + +
80B GLY 3.5 7.4 + - - +
81B ASP* 3.4 10.0 + - - +
82B GLY 3.2 0.6 - - - -
83B LEU* 1.3 74.5 - - - +
85B HIS* 1.3 66.7 + - - +
87B VAL* 3.3 4.2 + - - +
88B VAL* 3.2 32.8 + - + +
105B LEU* 4.2 21.3 - - + -
106B CYS 3.5 38.8 - - - +
107B SER* 3.8 18.2 - - - +
116B LEU* 3.8 22.4 - - + -
166B VAL* 4.1 11.0 - - + -
359B PHE* 5.6 0.9 - - + -
361B MET* 4.5 8.3 - - + -
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Residues in contact with HIS 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B ARG* 4.5 7.6 - - - -
81B ASP 2.9 14.0 + - - +
82B GLY* 3.0 15.9 + - - +
84B MET* 1.3 76.5 - - - +
86B GLU* 1.3 71.3 + - - +
88B VAL* 4.0 2.4 - - - +
89B ASN* 3.0 40.2 + - - +
163B LEU* 4.0 11.6 - - + +
164B PHE 3.1 23.6 + - - -
166B VAL* 4.8 3.7 - - + +
340B VAL* 3.7 16.5 - - + +
341B ASP* 2.9 40.6 - - + +
343B GLU* 4.0 31.7 + - + +
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Residues in contact with GLU 86 (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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58B ASN* 3.7 31.9 + - - +
60B ALA* 4.4 7.6 - - + -
61B ARG* 2.6 61.2 + - - +
82B GLY 2.9 19.1 + - - +
83B LEU* 3.2 15.2 + - + +
85B HIS* 1.3 83.2 + - - +
87B VAL* 1.3 57.5 + - - +
89B ASN* 4.0 0.3 - - - -
90B GLY* 2.9 27.5 + - - -
343B GLU* 4.5 7.2 - - - +
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Residues in contact with VAL 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B LEU* 3.5 29.6 - - + -
60B ALA* 4.7 5.8 - - + -
64B VAL* 3.3 27.0 - - + +
75B LEU* 4.1 19.1 - - + -
77B VAL* 3.9 22.0 - - + -
83B LEU* 3.0 17.9 + - + +
84B MET* 3.3 5.1 + - - +
86B GLU* 1.3 76.3 - - - +
88B VAL* 1.3 58.5 + - - +
91B LEU* 2.9 32.6 + - + +
105B LEU* 4.5 11.9 - - + -
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Residues in contact with VAL 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B MET* 3.2 22.4 + - - +
85B HIS 4.1 1.8 - - - +
87B VAL* 1.3 72.6 - - - +
89B ASN* 1.3 63.3 + - - +
91B LEU* 3.2 9.1 + - - +
92B MET* 2.8 29.5 + - + +
101B ILE* 3.9 16.1 - - + +
105B LEU* 3.6 29.6 - - + -
152B LEU* 4.1 20.4 - - + -
164B PHE* 4.9 3.8 - - + +
166B VAL* 3.8 29.6 - - + -
359B PHE* 5.0 4.3 - - + -
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Residues in contact with ASN 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B ARG* 3.6 29.2 - - - +
85B HIS* 3.0 35.4 + - - +
86B GLU 4.0 0.2 - - - +
88B VAL* 1.3 73.0 - - - +
90B GLY* 1.3 56.1 + - - +
92B MET* 2.9 6.0 + - - +
93B GLU* 2.7 45.4 + - + +
163B LEU* 3.7 10.3 - - - +
164B PHE* 2.8 58.1 - - - +
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Residues in contact with GLY 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B ARG* 3.7 27.6 - - - +
64B VAL* 3.8 7.6 - - - -
65B ARG* 3.6 12.0 - - - +
86B GLU 2.9 18.0 + - - -
87B VAL 3.6 2.7 - - - -
89B ASN* 1.3 77.2 - - - +
91B LEU* 1.3 59.8 + - - +
93B GLU* 3.6 8.7 + - - -
94B ARG* 3.5 16.5 - - - +
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Residues in contact with LEU 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B VAL* 3.5 16.2 - - + -
69B LEU* 3.6 31.0 - - + -
75B LEU* 4.6 4.0 - - + -
87B VAL* 2.9 26.2 + - + +
88B VAL* 3.6 6.3 - - - +
89B ASN 3.2 0.2 - - - -
90B GLY* 1.3 76.0 - - - +
92B MET* 1.3 64.8 + - - +
94B ARG* 3.5 21.9 - - - +
97B TRP* 3.5 13.3 - - - +
100B ALA* 3.4 31.4 - - + +
101B ILE* 4.2 18.8 - - + -
103B LYS* 5.1 2.2 - - + +
105B LEU* 4.1 29.4 - - + -
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Residues in contact with MET 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B VAL* 2.8 21.2 + - + +
89B ASN 2.9 4.0 + - - +
91B LEU* 1.3 74.1 - - - +
93B GLU* 1.3 59.4 + - + +
94B ARG 3.1 7.8 + - - +
97B TRP* 3.5 45.5 - - + +
101B ILE* 3.6 36.1 - - + -
152B LEU* 4.4 7.9 - - + -
164B PHE* 3.5 60.0 - - + -
232B GLY* 5.2 0.4 - - - -
233B PRO* 3.7 14.4 - - + -
358B TYR* 4.0 6.1 - - + -
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Residues in contact with GLU 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B ARG* 3.0 37.6 + - - +
65B ARG* 3.0 45.9 + - - -
89B ASN* 2.7 25.8 + - - +
90B GLY* 3.6 1.7 + - - +
91B LEU 3.3 0.4 - - - -
92B MET* 1.3 72.8 - - + +
94B ARG* 1.3 61.1 + - - +
95B PRO* 4.3 2.3 - - - +
162B ARG 6.1 0.9 - - - +
164B PHE* 6.2 1.6 - - + -
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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
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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