Contacts of the strand formed by residues 61 - 66 (chain A) in PDB entry 2VTX
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 HIS 61 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A LEU* 3.8 23.9 - - + +
56A ALA* 3.9 12.4 - - + +
57A LYS 3.4 26.8 + - - -
59A GLU* 3.0 31.1 + - + -
60A PHE* 1.3 74.4 - - - +
62A ILE* 1.3 62.9 + - - +
79A ALA 4.0 0.3 - - - +
80A THR* 3.3 4.2 - - - +
81A LEU* 2.7 33.2 + - + +
104A LEU* 4.6 5.8 - - + -
106A ALA 3.0 6.5 - - - +
107A GLY* 4.0 2.7 - - - -
108A SER 3.7 7.3 + - - -
109A GLY* 3.0 40.4 + - - -
111A LEU* 4.0 18.0 - - + +
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Residues in contact with ILE 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A PHE* 5.1 0.4 - - + -
61A HIS* 1.3 78.1 - - - +
63A VAL* 1.3 71.6 + - - +
77A PRO* 4.1 14.1 - - + -
79A ALA 3.4 10.5 - - - +
80A THR* 3.4 22.4 - - + +
104A LEU* 3.5 10.8 - - - +
105A LYS* 3.1 52.6 + - + -
106A ALA* 2.8 19.7 + - + +
111A LEU* 5.2 0.2 - - - -
51E CYS* 5.3 0.4 - - - -
52E LEU 4.1 3.1 - - - +
53E GLY* 4.0 7.6 - - - -
54E ASP* 3.4 42.0 - - + +
112E TYR* 5.1 3.1 - - + -
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Residues in contact with VAL 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A LEU* 3.9 20.6 - - + -
50A VAL* 4.4 12.3 - - + -
62A ILE* 1.3 77.3 - - - +
64A GLU* 1.3 70.5 + - - +
77A PRO* 3.5 2.3 - - - +
78A ILE* 2.9 34.6 + - + +
79A ALA* 3.0 30.4 + - + +
102A PHE* 4.4 4.7 - - + -
103A ARG 3.3 9.6 - - - +
104A LEU* 4.8 0.2 - - + -
111A LEU* 4.4 22.9 - - + -
113A ILE* 4.0 16.2 - - + -
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Residues in contact with GLU 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A VAL* 1.3 77.7 - - - +
65A ILE* 1.3 63.8 + - - +
66A VAL* 4.1 11.0 - - + -
75A SER* 3.0 27.7 - - - -
76A VAL 3.2 16.6 - - - +
77A PRO* 3.7 13.3 - - + +
78A ILE* 4.3 1.1 - - - +
102A PHE* 3.4 4.9 - - - -
103A ARG* 2.9 67.3 + - + +
105A LYS* 3.7 39.0 + - + +
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Residues in contact with ILE 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A GLU* 1.3 75.1 - - - +
66A VAL* 1.3 65.3 + - - +
67A ASP* 4.2 2.2 + - + -
74A LYS 3.6 2.1 - - - +
75A SER* 3.4 1.7 - - - -
76A VAL* 2.9 35.0 + - - +
78A ILE* 3.6 39.7 - - + -
94A ILE* 4.8 4.3 - - + -
96A LEU* 4.3 18.6 - - + -
100A VAL* 3.8 24.5 - - + -
101A THR 3.3 3.8 - - - +
102A PHE* 4.0 16.2 - - + -
18E ILE* 3.7 41.7 - - + +
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Residues in contact with VAL 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A GLU* 4.1 3.1 - - + -
65A ILE* 1.3 78.2 - - - +
67A ASP* 1.3 69.8 + - - +
73A GLU* 3.7 37.5 - - + +
74A LYS 3.6 3.4 - - - +
75A SER* 4.0 8.1 - - - +
100A VAL* 5.1 1.4 - - - +
101A THR* 2.9 45.5 + - + +
103A ARG* 3.7 44.4 - - + +
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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