Contacts of the strand formed by residues 59 - 68 (chain B) in PDB entry 2VCK
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 ALA 59 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47B TRP 3.9 0.2 - - - +
48B ASP* 3.4 0.7 - - - -
49B GLY 2.8 42.8 + - - +
50B GLY* 3.9 2.5 - - - +
57B GLY 4.4 0.2 - - - +
58B ASP* 1.3 80.0 + - - +
60B LYS* 1.3 69.2 + - - +
80B VAL 3.3 3.6 - - - -
81B ASP* 3.7 5.2 - - + -
215B LYS* 3.6 43.1 - - + +
216B PHE* 4.1 7.5 - - + -
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Residues in contact with LYS 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B TRP 3.3 3.6 - - - +
48B ASP* 3.1 39.5 + - - +
57B GLY 3.5 16.4 - - - +
58B ASP 4.9 2.9 - - - +
59B ALA* 1.3 86.4 - - - +
61B LEU* 1.3 60.8 + - - +
62B THR* 5.6 1.3 - - - +
78B HIS 3.6 1.6 - - - +
79B ILE* 3.3 6.1 - - - +
80B VAL* 2.7 42.7 + - + +
216B PHE* 4.3 2.9 - - - -
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Residues in contact with LEU 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B ALA* 4.0 13.5 - - + -
46B LYS* 3.2 7.8 - - - -
47B TRP* 2.9 71.2 + - + +
60B LYS* 1.3 75.6 - - - +
62B THR* 1.3 83.9 + - - +
63B ALA* 4.2 1.6 - - + +
77B ALA* 4.4 0.2 - - + -
78B HIS 3.4 3.4 - - - +
79B ILE* 3.6 31.0 - - + +
212B MSE 4.2 2.5 - - + -
216B PHE* 4.0 17.8 - - + -
224B PHE* 3.8 27.8 - - + -
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Residues in contact with THR 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B VAL* 5.0 1.8 - - + -
45B ALA 3.5 4.9 - - - +
46B LYS* 3.1 34.7 + - - +
60B LYS* 5.6 1.2 - - - +
61B LEU* 1.3 74.1 - - - +
63B ALA* 1.3 62.6 + - - +
64B ASN* 3.7 29.8 - - - +
76B GLU* 3.6 1.7 - - - +
77B ALA* 3.5 1.7 - - - -
78B HIS* 2.8 49.0 + - + +
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Residues in contact with ALA 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B VAL* 3.6 1.4 - - - -
44B TRP* 2.8 51.4 + - + -
45B ALA* 2.8 19.8 + - + +
61B LEU* 4.2 12.1 - - + -
62B THR* 1.3 73.9 - - - +
64B ASN* 1.3 58.3 + - - +
76B GLU 3.3 4.9 - - - -
224B PHE* 4.4 0.4 - - + -
228B PHE* 3.5 29.2 - - + -
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Residues in contact with ASN 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B ILE* 3.7 30.8 - - + +
42B GLU 3.6 4.0 - - - +
43B VAL* 3.7 29.6 - - - +
62B THR* 3.7 21.6 - - - +
63B ALA* 1.3 74.1 - - - +
65B ILE* 1.3 60.6 + - - +
66B ARG* 4.0 2.1 - - + +
74B ALA 3.8 0.7 - - - +
75B ARG* 3.5 0.7 - - - -
76B GLU* 2.8 67.9 + - + +
228B PHE* 3.4 7.8 - - - -
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Residues in contact with ILE 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B ILE* 3.5 2.8 - - - -
41B SER* 2.8 35.4 + - - +
42B GLU* 2.8 52.4 + - + +
44B TRP* 4.1 20.0 - - + -
63B ALA 4.3 0.2 + - - -
64B ASN* 1.3 75.3 - - - +
66B ARG* 1.3 70.5 + - - +
67B THR* 4.3 7.6 - - + -
73B LYS* 4.4 17.3 - - + -
74B ALA 3.8 2.7 - - - +
75B ARG* 4.7 5.4 - - + +
227B ASP 6.1 0.4 - - - +
228B PHE* 3.8 15.9 - - + -
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Residues in contact with ARG 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B ILE* 5.8 1.4 - - - +
32B PHE* 3.3 43.4 - - - +
38B LEU* 3.0 29.9 + - + -
39B GLU* 3.1 9.5 - - - +
40B ILE* 3.7 40.0 - - + +
64B ASN* 4.5 2.8 - - + +
65B ILE* 1.3 77.5 - - - +
67B THR* 1.3 63.8 + - - +
73B LYS* 3.3 7.6 - - - +
74B ALA* 2.8 48.2 + - + +
76B GLU* 2.8 38.2 + - - +
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Residues in contact with THR 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B GLN 3.1 13.4 - - - +
38B LEU* 4.1 7.0 - - - -
39B GLU* 3.0 18.0 + - - +
41B SER* 3.3 30.2 + - - +
65B ILE* 4.3 9.6 - - + -
66B ARG* 1.3 78.6 - - - +
68B GLY* 1.3 59.6 + - - +
71B PHE 5.2 1.1 - - - -
72B LEU 3.9 17.7 - - - +
73B LYS* 4.8 3.1 - - + +
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Residues in contact with GLY 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B GLN* 3.4 17.7 - - - -
38B LEU* 4.1 4.1 - - - +
67B THR* 1.3 78.0 - - - +
69B GLU* 1.3 69.7 + - - -
70B HIS 3.2 0.3 + - - -
71B PHE* 3.0 25.2 + - - +
94B LYS* 4.8 3.3 - - - -
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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