Contacts of the strand formed by residues 49 - 58 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45H MET* 3.4 2.6 - - - -
46H VAL* 2.6 48.9 + - - +
47H ASP* 4.9 4.7 - - + +
48H GLY* 1.3 74.8 - - - +
50H PRO* 1.3 74.1 - - + +
51H VAL* 3.8 2.6 + - + +
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Residues in contact with PRO 50 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1H MET* 4.9 18.9 - - + +
2H GLN* 4.3 14.0 + - - +
43H ASN* 5.4 6.5 - - - +
44H VAL 3.6 6.1 - - - +
45H MET* 3.6 20.6 - - + -
48H GLY 4.4 1.1 - - - +
49H LYS* 1.3 91.2 - - + +
51H VAL* 1.3 64.1 + - - +
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Residues in contact with VAL 51 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2H GLN* 3.6 20.0 - - + +
4H ILE* 3.8 29.2 - - + +
43H ASN* 3.4 6.6 - - - +
44H VAL* 2.8 38.4 + - + +
46H VAL* 3.6 31.2 - - + -
49H LYS* 4.2 3.4 - - + +
50H PRO* 1.3 80.1 - - - +
52H ASN* 1.3 74.3 + - - +
53H LEU* 3.7 4.1 + - + +
173H ILE* 5.5 2.5 - - + -
177H LEU* 3.7 14.8 - - + -
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Residues in contact with ASN 52 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2H GLN 3.0 14.2 + - - +
3H ALA* 3.2 12.0 - - + +
4H ILE 2.8 27.9 + - - +
41H SER* 4.2 14.6 - - - -
42H ALA 3.3 18.0 + - - -
43H ASN* 3.7 16.5 + - - +
51H VAL* 1.3 73.2 - - - +
53H LEU* 1.3 67.8 + - - +
54H GLY* 3.9 2.3 + - - -
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Residues in contact with LEU 53 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4H ILE* 3.7 31.0 - - + +
6H CYS* 4.4 4.5 - - + -
23H TYR* 4.0 32.1 - - + +
41H SER* 3.3 6.2 - - - -
42H ALA* 2.8 47.0 + - + +
44H VAL* 4.3 17.9 - - + -
51H VAL* 3.7 4.2 + - + +
52H ASN* 1.3 74.7 - - - +
54H GLY* 1.3 61.4 + - - +
55H LEU* 3.8 30.3 - - + +
169H PHE* 4.6 6.1 - - + -
173H ILE* 4.7 14.4 - - + -
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Residues in contact with GLY 54 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4H ILE 2.8 15.1 + - - +
5H LYS* 3.8 0.6 - - - -
6H CYS* 2.9 29.1 + - - +
39H ASN* 5.4 1.6 - - - -
40H TYR 3.6 5.6 - - - -
41H SER* 4.5 3.8 - - - -
52H ASN* 3.9 4.0 + - - -
53H LEU* 1.3 72.9 - - - +
55H LEU* 1.3 63.9 + - - +
56H TRP* 3.7 14.1 - - - -
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Residues in contact with LEU 55 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6H CYS* 3.5 17.5 - - + +
8H VAL* 5.7 0.4 - - + -
20H LEU* 4.0 24.7 - - + -
23H TYR* 4.7 0.2 - - + -
24H THR* 3.7 30.5 - - + -
38H ASP 3.8 0.2 - - - +
39H ASN* 3.4 5.4 - - - +
40H TYR* 2.7 57.7 + - + +
42H ALA* 5.2 2.7 - - + -
53H LEU* 3.8 31.0 - - + +
54H GLY* 1.3 78.6 - - - +
56H TRP* 1.3 64.7 + - - +
57H ASP* 3.7 1.5 + - - -
169H PHE* 3.9 25.4 - - + -
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Residues in contact with TRP 56 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5H LYS* 3.6 45.5 - - + +
6H CYS 2.9 18.5 + - - +
7H VAL* 3.8 14.8 - - + -
8H VAL* 3.0 28.5 + - - +
20H LEU* 5.0 0.9 - - - -
37H PHE* 3.5 19.3 - + + -
38H ASP 3.9 3.4 - - - -
39H ASN* 3.2 21.2 - - - +
54H GLY* 3.7 15.3 - - - -
55H LEU* 1.3 77.0 - - - +
57H ASP* 1.3 61.0 + - - +
58H THR* 3.7 3.4 + - - +
70H LEU 5.0 0.2 - - - -
71H SER* 3.5 24.5 - - - +
36P PRO* 5.6 3.4 - - + -
39P TRP* 3.7 27.8 - + - -
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Residues in contact with ASP 57 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8H VAL* 4.7 1.6 - - - +
16H LYS* 4.0 13.0 - - - +
17H THR* 2.5 32.8 + - - +
20H LEU* 3.6 27.0 - - + +
35H THR* 3.4 14.8 + - - +
37H PHE* 3.4 5.0 - - - -
38H ASP* 2.7 41.4 + - + +
40H TYR* 3.1 25.8 + - + +
55H LEU 3.7 0.2 + - - -
56H TRP* 1.3 70.2 - - - +
58H THR* 1.3 68.3 + - - +
202H MG 4.2 0.2 - - - -
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Residues in contact with THR 58 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7H VAL* 4.1 12.1 - - + -
8H VAL 2.5 29.0 + - - +
9H VAL* 3.7 13.0 - - + +
16H LYS* 3.2 23.0 - - - -
35H THR* 4.2 8.3 - - - -
36H VAL 4.6 1.1 - - - -
37H PHE* 4.4 7.2 - - + -
56H TRP 4.1 7.0 - - - +
57H ASP* 1.3 81.9 + - - +
59H ALA* 1.3 61.1 + - - +
60H GLY 3.6 0.2 + - - -
68H ARG* 3.8 27.6 - - + +
71H SER* 3.9 22.4 - - - +
200H GCP 4.1 1.9 + - - -
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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