Contacts of the strand formed by residues 89 - 99 (chain B) in PDB entry 2VPF
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 GLN 89 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48B LYS* 6.2 0.4 - - - +
81B MET* 3.3 32.2 - - + +
82B ARG 3.4 12.8 - - - +
83B ILE* 4.0 25.2 - - + +
88B GLY* 1.3 75.0 - - - +
90B HIS* 1.3 67.1 + - - +
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Residues in contact with HIS 90 (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 TYR* 5.1 7.0 - + - -
81B MET* 3.5 7.2 - - - -
82B ARG* 3.0 68.7 + - + +
89B GLN* 1.3 77.7 - - - +
91B ILE* 1.3 71.9 + - - +
92B GLY* 4.7 3.8 - - - -
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Residues in contact with ILE 91 (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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17A PHE* 3.9 32.1 - - + -
79B GLN* 3.8 34.8 - - + +
80B ILE 3.7 6.1 - - - +
81B MET* 3.6 31.1 - - + +
90B HIS* 1.3 81.9 - - - +
92B GLY* 1.3 60.8 + - - +
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Residues in contact with GLY 92 (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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79B GLN* 3.6 3.3 - - - -
80B ILE* 2.9 35.5 + - - +
82B ARG* 5.0 8.7 - - - -
90B HIS* 3.8 6.7 + - - -
91B ILE* 1.3 77.7 - - - +
93B GLU* 1.3 63.6 + - - -
94B MET* 4.5 1.5 - - - +
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Residues in contact with GLU 93 (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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14A VAL* 3.1 42.4 - - + +
77B THR* 3.9 8.5 - - + +
78B MET 3.4 5.2 - - - -
79B GLN* 4.9 8.9 + - + +
82B ARG* 5.2 2.3 + - - -
92B GLY* 1.3 73.1 - - - -
94B MET* 1.3 62.1 + - - +
40H PRO* 3.4 30.1 - - + +
41H ASP* 3.8 26.0 - - + +
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Residues in contact with MET 94 (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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35B ILE* 3.7 26.5 - - + -
39B TYR* 3.9 24.2 - - + -
42B GLU* 4.9 2.5 - - - +
47B PHE* 3.8 32.3 - - + -
77B THR* 3.4 4.3 - - - +
78B MET* 3.0 30.5 + - - +
80B ILE* 3.8 35.9 - - + -
82B ARG* 4.4 19.1 - - - +
92B GLY 4.5 1.8 - - - +
93B GLU* 1.3 78.1 - - - +
95B SER* 1.3 61.3 + - - +
96B PHE* 4.1 13.0 - - + -
40H PRO* 4.1 6.5 - - + -
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Residues in contact with SER 95 (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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39B TYR* 2.6 31.2 + - - -
75B ASN* 3.5 25.1 - - - -
76B ILE 3.3 7.4 - - - -
77B THR* 3.8 2.7 - - - -
94B MET* 1.3 74.8 - - - +
96B PHE* 1.3 69.2 + - - +
40H PRO 2.8 24.1 + - - -
41H ASP* 3.6 7.9 - - - -
43H ILE* 3.2 25.6 + - - +
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Residues in contact with PHE 96 (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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35B ILE* 3.9 28.3 - - + -
38B GLU* 4.1 28.3 - - + +
39B TYR* 3.7 23.6 - + - -
52B VAL* 4.0 29.4 - - + -
54B LEU* 3.6 30.1 - - + -
75B ASN* 3.6 4.3 - - - -
76B ILE* 3.0 35.2 + - + +
78B MET* 4.4 12.3 - - + -
80B ILE* 4.9 2.7 - - + -
94B MET* 4.1 31.4 - - + -
95B SER* 1.3 76.7 - - - +
97B LEU* 1.3 62.7 + - - +
43H ILE* 4.0 9.7 - - + +
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Residues in contact with LEU 97 (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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38B GLU* 5.2 1.0 + - - -
54B LEU* 4.6 1.9 - - - +
56B ARG* 3.0 35.5 + - - +
73B GLU* 3.8 38.6 - - + +
74B SER* 3.5 19.1 - - - +
75B ASN 4.3 2.0 - - - +
96B PHE* 1.3 73.9 - - - +
98B GLN* 1.3 60.8 + - - +
99B HIS* 4.6 0.3 - - - -
44E GLU* 6.4 1.1 - - + -
84E LYS* 6.0 1.6 - - - +
87E GLN* 4.6 16.3 - - - +
43H ILE* 4.0 33.1 - - + +
44H GLU* 4.3 16.6 - - + -
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Residues in contact with GLN 98 (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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53B PRO 4.3 4.4 + - - -
54B LEU* 3.5 12.7 - - + +
55B MET* 2.8 51.1 - - + +
73B GLU* 3.1 29.3 - - - +
74B SER* 2.8 27.4 + - - +
75B ASN 5.0 1.7 - - - +
76B ILE* 3.6 44.3 - - + +
97B LEU* 1.3 74.8 - - - +
99B HIS* 1.3 64.5 + - - +
100B ASN* 3.9 1.1 - - - +
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Residues in contact with HIS 99 (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 PRO* 3.5 17.0 - - - +
55B MET* 2.8 23.2 + - - +
56B ARG* 3.6 31.3 + - + -
57B CYS* 2.9 48.4 + - + +
70B PRO* 3.7 32.5 - - + +
72B GLU 3.7 4.0 - - - +
73B GLU* 3.7 24.8 + - + -
97B LEU 4.6 0.2 - - - -
98B GLN* 1.3 75.2 - - - +
100B ASN* 1.3 61.0 + - - +
101B LYS 3.5 0.4 - - - +
102B CYS* 4.8 0.4 - - - -
44E GLU* 4.2 10.3 + - - -
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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