Contacts of the strand formed by residues 73 - 83 (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 GLU 73 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70B PRO* 4.7 2.0 - - + -
72B GLU* 1.3 85.9 - - - +
74B SER* 1.3 64.5 + - - +
97B LEU* 3.8 36.4 - - + +
98B GLN 3.1 12.8 - - - +
99B HIS* 3.7 24.9 + - + -
100B ASN* 3.4 5.2 - - - -
43E ILE* 4.0 26.1 - - + +
44E GLU* 3.8 30.8 - - - +
87H GLN* 6.0 0.3 + - - -
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Residues in contact with SER 74 (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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73B GLU* 1.3 77.8 - - - +
75B ASN* 1.3 65.7 + - - +
97B LEU* 3.5 8.7 - - - -
98B GLN* 2.8 37.5 + - - +
100B ASN* 2.6 30.6 + - - -
44H GLU* 6.3 0.4 - - - -
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Residues in contact with ASN 75 (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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74B SER* 1.3 80.3 + - - +
76B ILE* 1.3 77.6 + - - +
77B THR* 3.0 17.9 + - - -
95B SER* 3.5 12.9 - - - -
96B PHE 3.6 6.3 - - - -
97B LEU* 4.3 4.7 - - - +
98B GLN* 5.0 2.0 - - - +
41H ASP 2.7 29.7 + - - -
43H ILE* 4.3 2.7 - - + +
44H GLU* 2.9 35.0 + - + +
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Residues in contact with ILE 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A GLU 5.7 1.6 - - - +
15A VAL* 3.9 16.2 - - + -
23A ARG* 5.2 5.6 - - - +
53B PRO 5.4 0.7 - - - +
54B LEU* 3.7 20.4 - - + -
75B ASN* 1.3 78.3 + - - +
77B THR* 1.3 67.6 + - - +
78B MET* 3.8 24.7 - - + -
94B MET 4.0 0.3 - - - +
95B SER* 3.3 3.6 - - - -
96B PHE* 3.0 39.9 + - + +
98B GLN* 3.6 42.4 - - + +
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Residues in contact with THR 77 (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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13A GLU 4.2 4.0 + - - +
14A VAL* 3.5 23.3 - - + -
15A VAL* 2.9 25.5 + - - +
75B ASN* 3.0 20.6 + - - -
76B ILE* 1.3 73.3 - - - +
78B MET* 1.3 68.0 + - - +
93B GLU* 3.9 19.7 - - + +
94B MET 3.4 10.5 - - - +
95B SER* 3.8 1.7 - - - -
41H ASP* 3.7 31.9 - - + +
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Residues in contact with MET 78 (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* 3.9 7.6 - - - -
15A VAL* 3.5 18.6 - - + -
20A VAL* 3.7 25.1 - - + -
23A ARG* 5.3 1.6 - - - +
52B VAL* 3.7 27.4 - - + -
53B PRO* 3.5 27.8 - - + +
54B LEU* 3.9 8.7 - - + -
76B ILE* 3.8 35.2 - - + -
77B THR* 1.3 81.1 - - - +
79B GLN* 1.3 61.7 + - - +
80B ILE* 3.5 10.7 + - + +
93B GLU* 3.4 2.6 - - - -
94B MET* 3.0 32.7 + - - +
96B PHE* 4.4 8.3 - - + -
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Residues in contact with GLN 79 (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* 3.9 14.2 - - + +
15A VAL 2.9 14.9 + - - +
16A LYS* 3.3 33.5 + - - +
17A PHE* 2.9 51.0 + - - +
20A VAL* 4.1 4.3 - - - +
78B MET* 1.3 70.7 - - - +
80B ILE* 1.3 67.4 - - - +
91B ILE* 3.8 24.4 - - + +
92B GLY 3.6 5.4 - - - +
93B GLU* 4.6 9.7 + - + +
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Residues in contact with ILE 80 (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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20A VAL* 4.5 7.0 - - + -
35B ILE* 3.9 20.9 - - + -
47B PHE* 4.0 9.2 - - + -
48B LYS 3.7 9.9 - - - +
49B PRO* 4.2 8.5 - - + +
52B VAL* 3.8 28.9 - - + -
78B MET* 4.0 20.4 - - + +
79B GLN* 1.3 84.6 - - - +
81B MET* 1.3 74.5 + - - +
82B ARG* 3.5 5.9 + - - +
91B ILE* 4.4 2.5 - - - -
92B GLY* 2.9 30.2 + - - +
94B MET* 3.8 36.1 - - + -
96B PHE* 4.9 1.1 - - + -
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Residues in contact with MET 81 (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* 4.0 23.1 - - + -
46B ILE 3.7 0.3 - - - +
47B PHE* 3.3 6.9 - - - -
48B LYS* 2.8 55.4 + - + +
80B ILE* 1.3 73.3 - - - +
82B ARG* 1.3 60.9 + - - +
83B ILE* 3.8 22.1 + - + +
89B GLN* 3.3 29.6 - - + +
90B HIS* 3.5 32.8 - - - -
91B ILE* 3.6 21.8 - - + +
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Residues in contact with ARG 82 (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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42B GLU* 3.2 24.9 + - - -
45B TYR* 3.4 44.7 - - + -
46B ILE 3.8 2.9 - - - -
47B PHE* 3.9 21.2 - - + -
80B ILE 3.5 3.2 + - - +
81B MET* 1.3 72.9 - - - +
83B ILE* 1.3 59.2 + - - +
84B LYS 4.2 0.7 + - - -
89B GLN* 3.4 3.5 - - - +
90B HIS* 3.0 69.0 + - + +
92B GLY* 5.0 12.1 - - - -
93B GLU 5.2 2.0 + - - -
94B MET* 4.4 21.4 - - - +
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Residues in contact with ILE 83 (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* 3.4 7.9 - - - -
46B ILE* 2.8 61.7 + - + +
48B LYS* 4.0 31.2 - - + -
81B MET* 4.0 13.7 - - + +
82B ARG* 1.3 77.0 - - - +
84B LYS* 1.3 63.2 + - - +
85B PRO* 3.3 21.6 - - + +
88B GLY 3.9 10.8 - - - +
89B GLN* 4.0 20.6 - - + +
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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