Contacts of the helix formed by residues 74 - 87 (chain B) in PDB entry 3VTW
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 74 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B HIS 3.5 3.2 + - - +
73B VAL* 1.3 78.8 - - - +
75B MET* 1.3 62.3 + - - +
76B SER* 3.2 4.7 + - - -
77B GLU* 2.5 63.3 + - - +
78B LEU* 2.9 25.5 + - - +
106B VAL* 3.7 19.6 - - - +
107B SER* 3.5 26.6 - - - +
108B THR 3.5 19.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 75 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B ASN* 1.3 75.3 - - - +
76B SER* 1.3 58.6 - - - +
78B LEU* 3.0 19.5 + - + +
79B ILE* 2.9 34.5 + - - +
96B LEU* 5.0 5.6 - - - -
98B VAL* 5.1 1.6 - - - -
103B MET* 3.8 47.3 - - + +
105B SER* 3.9 18.2 - - - +
106B VAL 4.9 0.6 - - - +
108B THR 4.2 4.4 + - - +
110B ILE* 3.4 48.7 - - + -
113B VAL* 4.6 15.7 - - + -
126B MET* 4.3 14.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 76 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B ASN* 3.2 4.5 + - - -
75B MET* 1.3 75.4 - - - +
77B GLU* 1.3 65.4 + - - +
79B ILE* 3.7 11.8 - - - +
80B LYS* 3.1 20.8 + - - +
104B VAL* 4.7 13.9 - - - +
105B SER 4.7 0.6 - - - +
106B VAL* 3.2 38.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 77 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B HIS* 4.1 3.0 + - - +
73B VAL* 3.1 20.9 - - + -
74B ASN* 2.5 63.5 + - - +
76B SER* 1.3 73.2 + - - +
78B LEU* 1.3 62.2 + - - +
80B LYS* 3.2 16.6 + - - +
81B ILE* 3.2 22.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 78 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B ILE* 4.6 9.0 - - + -
67B PHE* 6.3 0.2 - - + -
69B VAL* 4.2 24.9 - - + -
73B VAL* 4.5 4.9 - - + -
74B ASN 2.9 13.7 + - - +
75B MET* 3.0 21.9 + - + +
77B GLU* 1.3 75.1 - - - +
79B ILE* 1.3 66.4 + - - +
81B ILE* 3.0 31.0 + - + +
82B ILE* 3.0 24.4 + - + +
96B LEU* 4.1 10.1 - - + -
110B ILE* 4.0 8.5 - - + -
126B MET* 3.8 36.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 79 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B MET* 2.9 20.6 + - + +
76B SER* 3.7 8.5 - - - +
78B LEU* 1.3 74.6 - - - +
80B LYS* 1.3 63.8 + - - +
82B ILE* 3.2 2.1 + - - +
83B ARG* 3.0 34.3 + - - +
94B PHE* 3.7 31.9 - - + +
95B PHE* 5.4 0.7 - - - -
96B LEU* 3.9 34.3 - - + +
102B SER* 6.1 0.2 - - - +
103B MET 3.5 24.0 - - - +
104B VAL* 4.1 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 80 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A ASN* 5.7 7.6 - - - +
117A GLU 6.5 0.2 - - - -
118A LYS 4.7 11.2 - - - +
119A ASP* 3.5 17.4 - - - +
120A GLU* 2.6 60.7 - - + +
76B SER 3.1 14.7 + - - +
77B GLU* 3.5 11.0 - - - +
78B LEU 3.1 1.6 - - - -
79B ILE* 1.3 77.9 - - - +
81B ILE* 1.3 71.7 + - + +
83B ARG* 3.2 9.5 + - + +
84B ARG* 3.0 39.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 81 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A GLU* 6.0 1.6 - - + -
67B PHE* 6.3 1.8 - - + -
73B VAL* 5.1 10.3 - - + -
77B GLU* 3.2 20.5 + - + +
78B LEU* 3.0 19.8 + - + +
80B LYS* 1.3 88.2 - - + +
82B ILE* 1.3 69.8 + - + +
84B ARG* 3.2 6.6 + - - +
85B ARG* 3.0 29.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 82 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B ILE* 3.8 34.8 - - + -
62B LEU* 4.3 22.9 - - + -
67B PHE* 4.5 21.5 - - + -
78B LEU* 3.0 22.8 + - + +
79B ILE 3.2 1.3 + - - +
81B ILE* 1.3 85.2 - - + +
83B ARG* 1.3 61.6 + - - +
85B ARG* 3.7 7.7 - - - +
86B LEU* 2.9 32.8 + - + +
94B PHE* 3.9 30.3 - - + -
96B LEU* 5.0 3.4 - - + -
128B TYR* 4.9 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 83 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A ASN* 3.4 55.5 + - - +
100A GLY* 3.5 1.0 - - - +
79B ILE* 3.0 32.8 + - - +
80B LYS* 3.6 7.2 - - + +
82B ILE* 1.3 77.3 - - - +
84B ARG* 1.3 63.4 + - - +
86B LEU 3.4 0.3 + - - -
87B GLN 2.9 16.3 + - - -
88B LEU* 3.1 40.7 + - + +
89B ASN 3.2 22.6 + - - -
90B ALA* 4.3 0.4 - - - +
92B GLN 2.8 29.7 + - - -
94B PHE* 3.2 36.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 84 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A LYS* 4.7 8.3 - - - +
28A PHE* 3.1 35.3 - - - -
119A ASP* 5.5 1.8 - - - +
120A GLU* 4.2 19.7 + - - +
201A SO4 2.4 54.0 + - - +
80B LYS* 3.0 36.0 + - - +
81B ILE* 3.2 8.9 + - - +
83B ARG* 1.3 75.6 - - - +
85B ARG* 1.3 58.7 + - - +
87B GLN* 2.8 28.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 85 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B LEU* 4.3 12.6 - - + -
63B ASP* 2.7 43.1 + - - +
64B LYS* 4.4 8.7 - - - +
67B PHE* 4.3 27.4 - - - -
81B ILE* 3.0 18.9 + - + +
82B ILE* 3.7 10.1 - - - +
84B ARG* 1.3 79.3 - - - +
86B LEU* 1.3 62.7 + - - +
87B GLN* 3.3 8.5 + - - +
201B SO4 2.9 41.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 86 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B LEU* 5.1 1.1 - - + -
60B PRO* 3.8 41.2 - - + +
61B VAL 4.0 11.2 - - - +
62B LEU* 3.4 29.8 - - + -
82B ILE* 2.9 20.2 + - + +
85B ARG* 1.3 75.1 - - - +
87B GLN* 1.3 70.7 + - - +
88B LEU* 3.3 29.5 + - + +
94B PHE* 4.2 16.8 - - + -
128B TYR* 3.9 19.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 87 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A LYS* 6.3 3.4 - - + +
201A SO4 5.3 8.1 + - - +
83B ARG 2.9 1.3 + - - -
84B ARG* 2.8 24.1 + - - +
85B ARG 3.9 6.4 - - - +
86B LEU* 1.3 82.1 - - - +
88B LEU* 1.3 68.1 + - - +
89B ASN* 3.6 5.2 + - - +
92B GLN* 4.3 2.9 + - - -
----------------------------------------------------------
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