Contacts of the strand formed by residues 3 - 11 (chain H) in PDB entry 2OX4
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 ILE 3 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2H LYS* 1.3 72.0 - - - +
4H THR* 1.3 61.3 + - - +
5H LYS 4.0 3.8 - - - +
6H ILE* 4.0 21.5 - - + -
26H VAL* 3.8 20.2 - - + -
27H SER 3.5 11.9 - - - +
28H THR* 4.3 2.0 - - + +
60H LEU* 3.4 30.5 - - + +
61H ILE* 3.7 6.8 - - - +
62H GLY* 2.8 26.4 + - - +
63H GLU* 2.9 27.7 + - + +
65H PRO* 4.2 15.3 - - + -
71H ILE* 5.0 0.2 - - + -
100H PHE* 3.5 35.4 - - + -
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Residues in contact with THR 4 (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 LYS* 3.7 4.7 - - + +
3H ILE* 1.3 77.4 - - - +
5H LYS* 1.3 63.6 + - - +
27H SER* 2.9 9.2 + - - -
28H THR 3.3 19.2 + - - -
29H ASP* 3.6 30.5 - - + +
61H ILE* 4.0 8.0 - - - +
391H GLU* 3.4 26.0 - - - +
392H ALA* 4.2 3.7 + - - +
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Residues in contact with LYS 5 (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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3H ILE* 4.0 1.1 - - - +
4H THR* 1.3 85.3 + - - +
6H ILE* 1.3 70.5 + - - +
7H GLU* 3.7 40.4 + - + +
25H LYS 4.5 0.4 - - - -
27H SER* 2.8 46.8 + - - +
61H ILE* 4.2 0.4 - - - -
387H TYR* 5.1 0.6 + - - +
389H SER* 3.8 11.7 - - - +
390H ILE 3.4 11.2 - - - +
391H GLU* 4.0 25.6 - - - +
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Residues in contact with ILE 6 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3H ILE* 4.0 11.9 - - + -
5H LYS* 1.3 80.3 - - - +
7H GLU* 1.3 64.6 + - - +
8H ILE* 4.1 9.0 - - + -
24H VAL* 3.8 12.3 - - + -
25H LYS 3.5 2.7 - - - -
26H VAL* 4.5 8.1 - - + -
57H ALA* 3.7 44.4 - - + +
60H LEU* 3.9 16.8 - - + -
61H ILE* 3.8 11.7 - - + -
96H PHE* 3.7 32.3 - - + -
388H VAL 3.9 0.5 - - - +
389H SER* 3.4 2.3 + - - -
390H ILE* 2.8 42.0 + - + +
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Residues in contact with GLU 7 (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* 3.7 33.2 + - + +
6H ILE* 1.3 77.6 - - - +
8H ILE* 1.3 62.5 + - - +
9H PHE* 3.8 15.4 - - + -
24H VAL* 3.3 5.9 - - - +
25H LYS* 2.8 66.5 + - + +
27H SER* 4.3 2.9 + - - -
382H TYR* 3.3 24.4 + - - -
387H TYR* 2.6 33.7 + - + +
388H VAL 3.3 3.8 - - - -
389H SER* 4.1 2.7 - - - +
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Residues in contact with ILE 8 (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 ILE* 4.1 5.4 - - + -
7H GLU* 1.3 78.8 - - - +
9H PHE* 1.3 65.3 + - - +
10H HIS 4.8 0.4 - - - +
22H ILE* 4.4 4.7 - - + -
23H LEU 3.5 5.4 - - - +
24H VAL* 4.0 14.4 - - + -
50H ALA* 4.3 19.1 - - + +
53H LEU* 3.6 33.9 - - + +
54H LYS* 3.5 37.5 - - + +
386H ASP 3.3 6.1 - - - +
387H TYR* 3.4 3.1 - - - -
388H VAL* 2.8 44.4 + - + +
390H ILE* 3.8 17.9 - - + -
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Residues in contact with PHE 9 (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 GLU* 3.8 23.6 - - + -
8H ILE* 1.3 75.1 - - - +
10H HIS* 1.3 61.0 + - - +
11H VAL* 3.4 5.6 + - + +
21H PRO 3.6 0.3 - - - +
22H ILE* 3.4 3.9 - - - -
23H LEU* 2.8 47.9 + - + +
25H LYS* 4.0 11.4 - - + -
35H LEU* 5.5 0.4 - - + -
377H ILE* 3.9 17.5 - - + -
381H LEU* 3.7 30.3 - - + -
382H TYR* 3.7 46.9 - + - -
385H SER* 3.8 13.9 - - - +
386H ASP 3.7 3.6 - - - -
387H TYR* 3.6 30.5 - + - -
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Residues in contact with HIS 10 (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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54F LYS* 5.0 1.2 + - - -
8H ILE* 3.9 1.6 - - - +
9H PHE* 1.3 70.3 - - - +
11H VAL* 1.3 60.4 + - - +
20H ARG* 3.0 44.9 + - - +
21H PRO 3.8 3.6 - - - -
22H ILE* 3.8 20.4 - - + +
46H GLY 3.6 3.6 - - - -
47H SER* 3.4 39.7 + - - -
50H ALA* 4.0 22.9 - - + +
385H SER* 3.9 0.2 - - - -
386H ASP* 2.9 47.8 + - + +
3410H GOL 2.9 25.8 + - - -
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Residues in contact with VAL 11 (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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9H PHE 4.1 7.0 - - - +
10H HIS* 1.3 70.9 - - - +
12H HIS* 1.3 74.0 + - - +
14H ARG* 3.6 22.9 - - - +
20H ARG* 2.8 28.6 + - - +
21H PRO* 2.8 32.8 + - + +
23H LEU* 4.2 14.1 - - + -
353H LEU* 4.1 14.6 - - + -
381H LEU* 4.0 17.5 - - + -
384H ILE* 3.6 15.3 - - + +
385H SER* 3.7 13.2 - - - +
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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