Contacts of the strand formed by residues 61 - 66 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52E LEU* 3.7 29.3 - - + +
56E ALA* 3.8 12.4 - - + +
57E LYS 3.5 20.4 - - - -
59E GLU* 2.7 40.7 + - + -
60E PHE* 1.3 73.4 - - - +
62E ILE* 1.3 61.1 + - - +
79E ALA 3.8 0.3 - - - +
80E THR* 3.2 4.9 - - - +
81E LEU* 2.8 37.9 + - + +
104E LEU* 4.5 2.9 - - + -
106E ALA 3.2 6.7 - - - +
107E GLY* 3.9 8.7 - - - -
108E SER* 3.6 1.2 + - - -
109E GLY* 3.0 39.5 + - - -
111E LEU* 4.0 16.4 - - + -
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Residues in contact with ILE 62 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52D LEU 3.6 23.1 - - - +
53D GLY* 3.7 15.7 - - - -
54D ASP* 3.8 15.5 - - + +
112D TYR* 4.4 7.0 - - + +
60E PHE 5.0 0.2 - - - -
61E HIS* 1.3 79.7 - - - +
63E VAL* 1.3 66.1 + - - +
77E PRO* 4.0 25.8 - - + -
79E ALA 3.2 11.2 - - - +
80E THR* 3.9 9.4 - - + +
104E LEU* 3.4 11.3 - - - +
105E LYS* 3.0 48.8 + - + -
106E ALA* 3.2 17.9 + - + +
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Residues in contact with VAL 63 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23E LEU* 4.9 1.8 - - + -
50E VAL* 4.2 8.3 - - + -
62E ILE* 1.3 77.8 - - - +
64E GLU* 1.3 64.0 + - - +
77E PRO* 3.4 3.1 - - - +
78E ILE* 2.7 50.1 + - + -
79E ALA* 3.0 32.3 + - + +
81E LEU* 6.2 0.2 - - + -
102E PHE* 4.5 7.0 - - + -
103E ARG 3.3 8.5 - - - +
104E LEU* 5.2 0.4 - - + -
111E LEU* 4.0 33.2 - - + -
113E ILE* 4.3 18.8 - - + -
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Residues in contact with GLU 64 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63E VAL* 1.3 75.6 - - - +
65E ILE* 1.3 62.0 + - - +
66E VAL* 3.7 0.8 + - + -
75E SER* 3.3 26.5 + - - -
76E VAL 2.9 24.2 - - - +
77E PRO* 3.5 10.0 - - + +
78E ILE* 4.1 0.7 - - - +
102E PHE* 3.5 5.0 - - - -
103E ARG* 2.9 79.7 + - + +
105E LYS* 3.1 37.9 + - + +
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Residues in contact with ILE 65 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D ILE* 4.1 35.9 - - + -
64E GLU* 1.3 70.0 - - - +
66E VAL* 1.3 66.1 + - - +
67E ASP* 3.6 1.9 + - - +
74E LYS 4.0 0.7 - - - +
75E SER* 3.3 2.6 - - - -
76E VAL* 2.8 38.4 + - - +
78E ILE* 4.1 25.3 - - + +
94E ILE* 5.6 1.6 - - + -
96E LEU* 4.2 14.6 - - + -
100E VAL* 3.9 25.1 - - + -
101E THR 3.5 2.5 - - - +
102E PHE* 3.0 45.3 - - + -
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Residues in contact with VAL 66 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64E GLU* 4.3 2.0 - - + +
65E ILE* 1.3 72.7 - - - +
67E ASP* 1.3 59.4 + - - +
68E GLN* 3.6 22.1 + - + +
74E LYS 4.3 3.4 - - - +
75E SER* 3.9 19.1 - - - +
99E PRO 5.2 0.5 - - - +
100E VAL* 4.1 7.3 - - - +
101E THR* 2.8 47.7 + - + +
103E ARG* 3.8 35.0 - - + -
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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
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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