Contacts of the strand formed by residues 83 - 98 (chain B) in PDB entry 2VDE
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 ASN 83 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303A GLN* 5.8 0.2 - - - +
72B TYR* 3.9 18.2 + - + +
73B SER* 3.2 22.7 - - - +
74B ASN* 3.8 14.0 + - - +
75B GLY 4.8 2.6 + - - -
81B GLY* 3.6 6.2 + - - -
82B ILE* 1.3 84.5 + - - +
84B SER* 1.3 61.6 + - - +
85B ASN* 5.1 1.2 - - - +
282B SER 4.0 0.3 - - - +
283B TYR* 3.9 4.5 - - - -
284B SER* 2.9 47.4 + - - +
285B GLY* 3.9 3.2 - - - -
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Residues in contact with SER 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A GLN* 5.3 2.1 + - - -
72B TYR* 3.5 9.7 - - - -
73B SER* 2.9 44.5 + - - -
82B ILE* 5.0 1.7 - - - +
83B ASN* 1.3 74.0 - - - +
85B ASN* 1.3 68.1 + - - +
86B ALA* 4.9 2.0 - - - -
281B THR* 4.4 11.1 - - - +
282B SER 3.5 9.6 - - - -
283B TYR* 3.2 28.1 + - - -
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Residues in contact with ASN 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B TYR* 3.9 23.1 + - + +
71B THR 3.3 12.8 - - - +
72B TYR* 3.8 21.4 - - + -
83B ASN 5.1 1.2 - - - +
84B SER* 1.3 76.0 + - - +
86B ALA* 1.3 60.5 + - - +
87B THR* 4.3 2.3 + - - +
280B ASP 3.8 4.0 - - - +
282B SER* 3.0 44.4 + - - +
284B SER* 5.3 3.7 + - - -
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Residues in contact with ALA 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B ASP 3.6 3.1 - - - +
70B TYR* 3.5 2.5 - - - -
71B THR* 3.0 42.9 + - + +
84B SER* 4.9 1.9 - - - -
85B ASN* 1.3 74.9 - - - +
87B THR* 1.3 65.2 + - - +
88B SER* 6.4 0.2 - - - -
279B SER* 5.9 1.8 - - - +
280B ASP 3.4 6.3 - - - +
281B THR* 3.9 27.4 - - + +
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Residues in contact with THR 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B ASP 3.7 4.7 - - - -
70B TYR* 3.6 29.2 - - + +
85B ASN 5.2 2.0 - - - +
86B ALA* 1.3 78.7 - - - +
88B SER* 1.3 61.7 + - - +
278B ILE* 4.3 9.7 - - - +
279B SER* 3.5 1.2 + - - -
280B ASP* 2.9 42.3 + - - +
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Residues in contact with SER 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B GLY 4.0 0.9 - - - +
68B ALA* 3.1 4.1 - - - +
69B ASP* 2.7 53.6 + - - +
86B ALA* 6.4 0.4 - - - -
87B THR* 1.3 75.5 - - - +
89B ALA* 1.3 62.0 + - - +
278B ILE* 3.4 20.0 - - - -
279B SER* 4.1 9.2 - - - -
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Residues in contact with ALA 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B LEU* 5.2 5.6 - - + -
67B GLY 3.6 8.1 - - - +
68B ALA* 4.1 10.1 - - + +
88B SER* 1.3 75.4 - - - +
90B SER* 1.3 68.8 + - - +
277B GLY* 3.3 17.1 - - - -
278B ILE* 3.4 28.3 + - + +
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Residues in contact with SER 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B LEU* 3.2 25.1 - - - +
67B GLY* 3.2 23.3 + - - -
89B ALA* 1.3 80.0 - - - +
91B LEU* 1.3 64.6 + - - +
92B GLN* 3.8 17.7 + - - +
275B SER* 5.5 3.1 - - - -
276B THR 3.7 11.0 - - - -
277B GLY* 4.1 7.6 - - - -
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Residues in contact with LEU 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A ILE* 3.8 29.2 - - + -
64B LEU* 5.2 13.9 - - + -
65B GLY 3.8 2.7 - - - +
66B LEU* 4.1 16.8 - - + -
90B SER* 1.3 71.9 - - - +
92B GLN* 1.3 61.3 + - - +
274B ALA 3.8 0.9 - - - +
275B SER* 3.3 24.6 - - - -
276B THR* 3.4 30.0 + - + +
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Residues in contact with GLN 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B GLN 3.6 0.8 - - - +
64B LEU* 3.3 6.4 - - - +
65B GLY* 2.7 51.2 + - - +
66B LEU* 5.3 1.6 - - - +
67B GLY 5.7 0.9 - - - +
90B SER* 4.2 19.7 + - - +
91B LEU* 1.3 76.9 - - - +
93B LEU* 1.3 61.4 + - - +
94B THR* 5.7 3.7 - - + +
273B THR* 5.1 6.9 - - - +
274B ALA 3.7 1.8 - - - +
275B SER* 3.1 26.0 + - - -
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Residues in contact with LEU 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B PRO* 4.5 16.6 - - + -
63B GLN 3.2 6.5 - - - +
64B LEU* 4.0 22.0 - - + -
92B GLN* 1.3 75.8 + - - +
94B THR* 1.3 80.6 + - - +
95B GLN* 4.7 9.6 - - + +
272B LEU* 4.7 11.0 - - + -
273B THR* 3.6 2.1 - - - +
274B ALA* 2.8 56.6 + - + +
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Residues in contact with THR 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B PRO* 3.6 2.1 - - - +
63B GLN* 2.8 55.8 + - - +
92B GLN* 5.7 3.8 - - + +
93B LEU* 1.3 80.4 - - - +
95B GLN* 1.3 63.9 + - - +
271B ASP* 5.9 3.4 - - - -
272B LEU 3.5 6.5 - - - -
273B THR* 3.8 19.7 - - + +
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Residues in contact with GLN 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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60B LEU 3.1 16.3 + - - -
61B LEU 3.3 5.0 - - - -
62B PRO* 3.1 36.6 - - + +
63B GLN* 5.9 0.2 - - - -
93B LEU* 4.7 5.8 - - + -
94B THR* 1.3 75.7 - - - +
96B SER* 1.3 86.5 + - - +
97B ILE* 4.6 4.5 - - + +
271B ASP* 3.6 5.7 - - - +
272B LEU* 2.7 65.1 + - + +
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Residues in contact with SER 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B PRO 4.1 19.7 + - - -
60B LEU* 4.4 12.9 + - - +
61B LEU 5.3 1.0 + - - -
95B GLN* 1.3 100.2 + - - +
97B ILE* 1.3 61.2 + - - +
98B PHE 3.8 1.8 + - - -
99B ASP* 3.0 35.7 + - - +
102B LYS* 4.0 8.7 - - - +
271B ASP* 3.5 13.1 + - - -
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Residues in contact with ILE 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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95B GLN* 3.9 6.5 - - + +
96B SER* 1.3 75.5 - - - +
98B PHE* 1.3 68.2 + - + +
270B LEU* 2.9 48.8 + - + +
272B LEU* 3.3 51.1 - - + +
308B LEU* 4.8 3.6 - - + -
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Residues in contact with PHE 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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96B SER 3.8 2.0 + - - -
97B ILE* 1.3 76.5 - - + +
99B ASP* 1.3 59.7 + - - +
100B MET* 3.9 31.4 - - + -
103B TRP* 5.5 10.1 - + - +
267B LEU* 4.5 15.3 - - + -
268B PRO* 3.5 35.4 - - + -
269B THR* 3.6 1.9 - - - -
270B LEU* 3.0 29.8 + - + -
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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