Contacts of the strand formed by residues 78 - 86 (chain A) in PDB entry 2VWK
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 ARG 78 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74A LYS* 3.5 5.9 - - - +
75A PHE* 2.7 43.7 + - - +
76A LEU* 3.8 18.8 - - + +
77A GLY* 1.3 80.2 - - - +
79A PRO* 1.4 79.6 - - + +
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Residues in contact with PRO 79 (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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72A LYS* 3.8 30.1 - - - +
73A LYS 3.6 7.4 - - - +
74A LYS* 4.5 6.3 - - + -
78A ARG* 1.4 97.9 - - + +
80A ILE* 1.3 59.7 + - - +
81A GLU* 5.9 1.3 - - + -
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Residues in contact with ILE 80 (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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41A LEU* 4.0 31.9 - - + -
71A VAL 4.0 0.2 - - - +
72A LYS* 3.7 4.9 - - - +
73A LYS* 2.8 51.8 + - + +
75A PHE* 3.7 42.8 - - + -
78A ARG 4.6 0.2 - - - +
79A PRO* 1.3 74.1 - - - +
81A GLU* 1.3 66.9 + - - +
82A VAL* 4.0 22.0 - - + -
110A TYR* 4.8 3.6 - - - +
367A LEU* 4.3 9.2 - - + -
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Residues in contact with GLU 81 (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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41A LEU* 3.5 21.4 - - - +
42A LEU 5.2 1.2 + - - +
70A LYS* 3.7 37.3 + - - +
71A VAL 3.8 11.6 - - - +
72A LYS* 4.0 31.5 - - + +
79A PRO* 5.9 1.1 - - + -
80A ILE* 1.3 75.6 - - - +
82A VAL* 1.3 60.4 + - - +
83A TRP* 5.4 1.6 - - - -
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Residues in contact with VAL 82 (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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39A TYR* 3.8 21.1 - - + -
40A ALA 3.6 15.9 - - - +
41A LEU* 4.3 10.1 - - + -
70A LYS* 3.4 6.1 - - - +
71A VAL* 2.8 51.3 + - + +
73A LYS* 3.8 16.8 - - + -
80A ILE* 4.0 27.4 - - + -
81A GLU* 1.3 80.6 - - - +
83A TRP* 1.3 68.3 + - - +
110A TYR* 4.9 4.3 - - + -
367A LEU* 4.6 9.6 - - + -
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Residues in contact with TRP 83 (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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39A TYR* 3.2 7.9 - - - -
40A ALA* 2.8 40.2 + - + +
42A LEU* 3.4 31.1 - - + +
45A ASP* 3.1 36.0 + - + -
48A ILE* 3.8 46.2 - - + -
52A LYS* 6.3 0.9 - - - -
68A ALA* 3.9 7.4 - - + -
69A GLU* 3.4 29.2 - - - -
70A LYS* 3.4 35.2 - - + +
81A GLU 5.4 1.3 - - - -
82A VAL* 1.3 79.8 - - - +
84A LYS* 1.3 61.7 + - - +
85A LEU* 3.6 16.5 + - + +
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Residues in contact with LYS 84 (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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37A TYR* 3.8 36.0 - - + -
38A ILE 3.4 7.2 - - - +
39A TYR* 3.6 32.8 - - + -
67A ARG 3.5 1.6 - - - +
68A ALA* 3.2 6.6 - - - -
69A GLU* 2.8 47.6 + - + +
71A VAL* 4.5 11.2 - - + +
82A VAL 4.2 0.6 - - - -
83A TRP* 1.3 71.7 - - - +
85A LEU* 1.3 60.5 + - - +
86A TYR* 2.7 39.8 + - + +
362A TYR* 5.6 4.4 + - - -
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Residues in contact with LEU 85 (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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37A TYR* 3.1 2.9 - - - -
38A ILE* 2.8 39.6 + - + +
40A ALA* 3.9 20.0 - - + -
48A ILE* 3.9 27.8 - - + -
51A VAL* 4.0 13.7 - - + -
65A VAL* 3.9 13.2 - - + -
67A ARG 3.6 2.9 - - - -
68A ALA* 4.1 6.5 - - + -
83A TRP* 4.0 17.3 - - + +
84A LYS* 1.3 76.8 - - - +
86A TYR* 1.3 61.6 + - - +
87A PHE* 3.0 24.6 - - + -
100A ILE* 4.0 26.0 - - + -
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Residues in contact with TYR 86 (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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35A GLU* 3.9 27.4 - - + +
36A PRO 3.6 13.2 - - - -
37A TYR* 4.2 10.8 - + + -
65A VAL* 3.8 2.8 - - - -
66A VAL* 3.0 26.0 + - + -
67A ARG* 2.7 74.5 + - + +
68A ALA 4.8 0.2 - - - -
69A GLU* 3.3 24.4 + - + -
84A LYS* 2.7 48.0 + - + -
85A LEU* 1.3 73.9 - - - +
87A PHE* 1.3 69.5 + - - +
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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