Contacts of the strand formed by residues 49 - 58 (chain G) in PDB entry 2OV2
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 LYS 49 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107D HIS* 6.2 4.3 - - + -
45G MET* 3.5 3.3 - - - -
46G VAL* 2.7 40.2 + - - +
47G ASP* 3.3 16.8 - - + +
48G GLY* 1.3 81.7 - - - +
50G PRO* 1.4 71.8 - - + +
51G VAL* 3.7 6.9 + - + +
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Residues in contact with PRO 50 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1G MET* 3.3 41.2 - - + +
2G GLN* 4.3 5.5 + - - +
43G ASN* 6.1 3.8 - - + -
44G VAL 3.6 5.4 - - - +
45G MET* 3.4 24.8 - - + -
48G GLY 4.3 1.1 - - - +
49G LYS* 1.4 88.7 - - + +
51G VAL* 1.3 62.7 + - - +
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Residues in contact with VAL 51 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1G MET* 3.9 3.1 - - - -
2G GLN* 3.4 19.1 - - + +
4G ILE* 3.8 34.5 - - + -
43G ASN* 3.5 4.5 - - - +
44G VAL* 2.9 36.4 + - + +
46G VAL* 3.8 27.8 - - + -
49G LYS* 3.9 8.1 - - + +
50G PRO* 1.3 80.3 - - - +
52G ASN* 1.3 67.9 + - - +
53G LEU* 3.7 4.1 + - + +
173G ILE* 5.3 1.8 - - + -
177G LEU* 3.9 16.2 - - + -
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Residues in contact with ASN 52 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1G MET* 3.8 14.6 - - + +
2G GLN 2.8 14.8 + - - +
3G ALA* 3.2 11.9 - - + +
4G ILE 2.8 27.9 + - - +
41G SER* 3.9 25.6 + - - -
42G ALA 3.8 8.6 + - - -
43G ASN* 3.4 17.1 + - - -
51G VAL* 1.3 74.6 - - - +
53G LEU* 1.3 63.2 + - - +
54G GLY* 4.3 2.6 + - - -
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Residues in contact with LEU 53 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4G ILE* 3.9 27.4 - - + -
6G CYS* 4.2 6.5 - - + -
23G TYR* 4.0 31.6 - - + +
40G TYR 3.8 0.5 - - - +
41G SER* 3.2 6.2 - - - -
42G ALA* 2.7 42.0 + - + +
44G VAL* 4.9 8.3 - - + -
51G VAL* 3.7 4.8 + - + +
52G ASN* 1.3 72.5 - - - +
54G GLY* 1.3 64.6 + - - +
55G LEU* 3.6 31.1 + - + +
77G VAL* 6.0 0.2 - - + -
169G PHE* 4.4 7.2 - - + -
172G ALA* 6.2 2.9 - - + -
173G ILE* 4.4 22.9 - - + -
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Residues in contact with GLY 54 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4G ILE 2.8 17.0 + - - +
6G CYS* 3.0 28.4 + - - +
39G ASN* 5.0 1.1 - - - -
40G TYR 3.6 4.9 - - - -
41G SER* 4.5 6.3 - - - -
52G ASN* 3.7 5.1 + - - -
53G LEU* 1.3 71.7 - - - +
55G LEU* 1.3 66.1 + - - +
56G TRP* 3.7 13.2 - - - -
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Residues in contact with LEU 55 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6G CYS* 3.5 17.7 - - + -
20G LEU* 3.8 26.0 - - + -
23G TYR* 4.8 0.4 - - + -
24G THR* 3.5 32.3 - - + -
38G ASP 3.7 1.6 - - - +
39G ASN* 3.0 7.3 + - - +
40G TYR* 2.6 58.1 + - + +
42G ALA* 5.5 2.2 - - + -
53G LEU* 3.6 33.4 - - + +
54G GLY* 1.3 81.1 - - - +
56G TRP* 1.3 64.3 + - - +
57G ASP 3.8 0.6 + - - -
169G PHE* 4.1 17.0 - - + -
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Residues in contact with TRP 56 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5G LYS* 3.4 49.3 - - + +
6G CYS 2.9 18.5 + - - +
7G VAL* 3.6 16.1 - - + -
8G VAL* 2.9 31.1 + - - +
20G LEU* 4.9 0.2 - - - -
37G PHE* 3.6 25.4 - + + -
38G ASP 3.8 3.6 - - - -
39G ASN* 3.2 22.9 - - - +
54G GLY* 3.7 15.8 - - - -
55G LEU* 1.3 76.9 - - - +
57G ASP* 1.3 60.6 + - - +
58G THR* 3.6 3.7 + - - +
70G LEU 5.0 0.7 - - - -
71G SER* 3.8 13.7 - - - +
36O PRO* 5.7 2.9 - - + -
39O TRP* 4.0 22.2 - + - -
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Residues in contact with ASP 57 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8G VAL* 4.5 1.7 - - - +
16G LYS* 3.9 12.1 - - - +
17G THR* 2.6 32.5 + - - -
20G LEU* 3.5 27.6 - - + +
35G THR* 3.5 12.6 + - - +
37G PHE* 3.4 4.4 - - - -
38G ASP* 2.8 38.6 + - + +
40G TYR* 3.0 28.1 + - + +
55G LEU 3.8 0.2 + - - -
56G TRP* 1.3 70.1 - - - +
58G THR* 1.3 68.4 + - - +
202G MG 3.9 1.2 - - - -
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Residues in contact with THR 58 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7G VAL* 4.0 17.3 - - + -
8G VAL 2.6 27.4 + - - +
9G VAL* 3.5 15.2 - - + +
16G LYS* 3.4 19.6 - - - -
35G THR* 4.0 9.8 - - - -
36G VAL 4.9 0.4 - - - -
37G PHE* 4.6 5.8 - - + -
56G TRP 3.9 7.9 - - - +
57G ASP* 1.3 84.4 + - - +
59G ALA* 1.3 62.7 + - - +
68G ARG* 3.8 28.8 - - + +
71G SER* 4.1 17.7 - - - +
72G TYR* 5.1 0.2 - - + -
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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