Contacts of the strand formed by residues 39 - 46 (chain B) in PDB entry 2VN9
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 39 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B ARG* 2.7 40.9 + - + +
31B CYS 3.3 7.0 - - - +
32B MET* 4.1 15.1 - - + +
37B GLY 4.3 4.9 - - - +
38B GLN* 1.3 71.5 - - - +
40B TYR* 1.3 79.6 + - - +
92B LEU* 3.6 29.0 + - + +
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Residues in contact with TYR 40 (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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14B TYR* 4.0 16.2 - + - -
30B ARG* 3.5 8.7 - - - +
31B CYS* 2.9 33.1 + - - -
33B LYS* 4.2 22.6 - - + +
38B GLN* 3.1 49.9 + - + -
39B GLU* 1.3 88.5 - - - +
41B ALA* 1.3 59.2 + - - +
77B HIS* 3.8 35.0 + + + -
89B VAL* 3.6 19.7 - - + -
90B PHE 3.2 16.6 - - - +
91B ASP* 3.9 10.5 - - - -
92B LEU* 4.0 11.2 - - - +
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Residues in contact with ALA 41 (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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20B LEU* 4.0 7.4 - - + -
28B VAL* 3.9 9.2 - - + -
29B ARG 3.7 4.7 - - - -
31B CYS* 4.5 1.3 - - - -
40B TYR* 1.3 72.3 - - - +
42B ALA* 1.3 60.1 + - - +
43B LYS 3.9 0.2 + - - -
88B LEU 3.4 2.8 - - - +
89B VAL* 3.6 0.2 - - - -
90B PHE* 2.7 41.2 + - - +
91B ASP 4.2 0.2 - - - +
92B LEU* 4.1 3.2 - - + +
1310B GVD 3.2 49.4 - - + +
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Residues in contact with ALA 42 (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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0B MET* 4.5 16.6 - - + -
16B LEU* 6.3 1.8 - - + -
27B VAL 3.6 0.9 - - - +
28B VAL* 3.2 4.5 - - - -
29B ARG* 2.8 43.4 + - + +
31B CYS* 3.8 21.7 - - + -
40B TYR 4.1 0.6 - - - -
41B ALA* 1.3 71.5 - - - +
43B LYS* 1.3 62.7 + - - +
44B ILE* 3.6 13.3 + - + +
87B TYR* 5.1 2.5 - - + -
88B LEU 3.5 4.9 - - - +
89B VAL* 4.4 6.3 - - + +
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Residues in contact with LYS 43 (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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26B SER* 3.5 33.0 - - - +
27B VAL 3.4 4.3 - - - -
28B VAL* 4.2 13.0 - - + +
41B ALA 3.9 1.4 + - - -
42B ALA* 1.3 70.7 - - - +
44B ILE* 1.3 60.2 + - - +
45B ILE* 3.9 10.5 - - + +
61B GLU* 2.9 31.2 + - - +
86B HIS 3.6 1.2 - - - +
87B TYR* 3.3 5.0 - - - -
88B LEU* 2.9 50.9 + - + +
90B PHE* 4.1 19.7 - - + -
157B ASP* 3.7 14.5 + - - -
159B GLY* 5.1 0.6 - - - -
1310B GVD 3.4 29.5 + - + +
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Residues in contact with ILE 44 (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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16B LEU* 5.6 4.3 - - + -
26B SER* 3.4 6.8 - - - -
27B VAL* 2.8 38.3 + - + +
29B ARG* 3.4 44.6 - - + +
42B ALA* 3.8 11.4 - - + +
43B LYS* 1.3 75.8 - - - +
45B ILE* 1.3 62.9 + - - +
46B ASN 4.0 1.2 + - - -
85B PHE* 3.7 30.3 - - + -
86B HIS 3.6 2.7 - - - +
87B TYR* 3.7 31.6 - - + +
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Residues in contact with ILE 45 (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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25B PHE* 4.3 12.8 - - + +
26B SER* 4.3 12.3 - - - -
43B LYS* 3.9 19.7 - - + +
44B ILE* 1.3 73.7 - - - +
46B ASN* 1.3 71.0 + - - +
47B THR* 3.2 13.6 + - + +
50B LEU* 4.5 10.1 - - + -
58B LEU* 3.6 38.6 - - + -
85B PHE* 3.5 3.9 - - - -
86B HIS* 2.9 45.7 + - + +
88B LEU* 4.0 18.6 - - + -
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Residues in contact with ASN 46 (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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25B PHE 4.5 7.2 + - - +
44B ILE 4.0 2.8 + - - -
45B ILE* 1.3 74.0 - - - +
47B THR* 1.3 59.8 + - - +
48B LYS* 3.1 28.4 + - - +
49B LYS 4.5 2.4 + - - -
50B LEU* 3.9 13.9 - - - +
84B GLY 3.3 11.9 - - - +
85B PHE* 3.7 29.9 - - + -
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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