Contacts of the strand formed by residues 61 - 69 (chain J) 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 J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52J LEU* 3.6 26.8 - - + +
56J ALA* 3.8 13.3 - - + +
57J LYS 3.4 25.1 - - - -
59J GLU* 3.0 22.1 + - + -
60J PHE* 1.3 69.5 - - - +
62J ILE* 1.3 63.6 + - - +
79J ALA 3.6 0.3 - - - +
80J THR* 3.2 5.4 - - - +
81J LEU* 2.8 40.9 + - - +
104J LEU* 4.5 3.4 - - + -
106J ALA 3.4 6.1 - - - +
107J GLY* 4.1 1.8 - - - -
108J SER* 3.7 7.3 + - - -
109J GLY* 3.2 37.9 + - - -
111J LEU* 4.0 20.8 - - + +
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Residues in contact with ILE 62 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52I LEU 3.9 11.0 - - - +
53I GLY* 4.0 5.6 - - - -
54I ASP* 3.7 33.9 - - + +
112I TYR* 4.5 7.2 - - + -
61J HIS* 1.3 79.9 - - - +
63J VAL* 1.3 73.2 + - - +
77J PRO* 4.0 20.9 - - + -
79J ALA 3.3 10.1 - - - +
80J THR* 4.0 13.0 - - + +
104J LEU* 3.5 8.7 - - - +
105J LYS* 2.9 47.5 + - + -
106J ALA* 3.1 22.9 + - + +
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Residues in contact with VAL 63 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23J LEU* 4.7 3.1 - - + -
50J VAL* 4.4 10.1 - - + -
62J ILE* 1.3 76.6 - - - +
64J GLU* 1.3 65.8 + - - +
77J PRO* 3.7 1.6 - - - +
78J ILE* 2.8 45.2 + - + +
79J ALA* 3.1 29.1 + - + +
81J LEU* 6.1 0.2 - - + -
102J PHE* 4.4 5.8 - - + -
103J ARG 3.5 8.3 - - - +
104J LEU* 5.0 0.7 - - + -
111J LEU* 4.0 31.6 - - + -
113J ILE* 4.0 22.9 - - + -
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Residues in contact with GLU 64 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63J VAL* 1.3 79.4 - - - +
65J ILE* 1.3 64.2 + - - +
66J VAL* 4.5 2.5 - - + -
75J VAL* 2.9 35.2 - - - +
76J VAL 3.0 22.9 - - - +
77J PRO* 3.5 7.1 - - + +
78J ILE* 4.1 1.3 - - - +
102J PHE* 3.5 6.6 - - - -
103J ARG* 2.8 71.5 + - + +
105J LYS* 3.4 36.1 + - + +
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Residues in contact with ILE 65 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18I ILE* 3.6 37.9 - - + +
64J GLU* 1.3 73.0 - - - +
66J VAL* 1.3 75.1 + - - +
67J ASP* 5.1 2.0 - - - -
74J LYS 3.6 1.2 - - - +
75J VAL* 3.4 2.9 - - - -
76J VAL* 2.6 36.9 + - + +
78J ILE* 3.6 33.2 - - + +
94J ILE* 4.7 4.3 - - + -
96J LEU* 4.0 29.8 - - + -
100J VAL* 5.1 11.9 - - + -
101J THR 3.5 4.7 - - - +
102J PHE* 3.8 25.6 - - + -
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Residues in contact with VAL 66 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64J GLU* 4.3 4.5 - - + +
65J ILE* 1.3 81.6 - - - +
67J ASP* 1.3 67.6 + - - +
73J GLU* 3.5 38.4 - - + +
74J LYS 3.6 6.7 - - - +
75J VAL* 4.0 7.4 - - + -
100J VAL* 4.6 0.9 - - - -
101J THR* 2.9 45.6 + - - +
103J ARG* 3.3 47.1 - - + +
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Residues in contact with ASP 67 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17I LEU* 3.7 26.5 - - - +
18I ILE* 3.9 20.6 - - - +
65J ILE* 4.3 3.0 - - + +
66J VAL* 1.3 79.0 - - - +
68J GLN* 1.4 72.2 + - - +
69J GLU* 3.8 5.0 + - - +
73J GLU* 3.6 4.0 - - - -
74J LYS* 2.7 40.9 + - - +
99J PRO 4.8 12.6 - - - +
100J VAL* 5.5 6.5 - - + +
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Residues in contact with GLN 68 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17I LEU* 5.2 1.9 - - - +
67J ASP* 1.4 81.5 - - - +
69J GLU* 1.3 58.0 + - - +
70J GLU 4.3 8.1 - - - +
71J GLY* 3.8 16.3 - - - +
72J ALA* 3.4 15.4 - - - +
73J GLU* 3.5 38.6 + - - +
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Residues in contact with GLU 69 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17I LEU* 4.3 17.9 - - + -
18I ILE 5.6 1.6 - - - +
117I HIS* 6.4 1.1 - - + -
67J ASP* 3.8 10.0 + - - +
68J GLN* 1.3 71.9 - - - +
70J GLU* 1.3 84.0 + - - +
71J GLY 3.1 1.4 + - - -
72J ALA* 2.9 18.0 + - - +
74J LYS* 4.5 13.5 - - + -
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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