Contacts of the strand formed by residues 14 - 20 (chain A) in PDB entry 2OZS
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 SER 14 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A GLN 3.8 0.2 - - - -
11A ILE* 2.8 40.4 + - - +
13A ASP* 1.3 79.8 - - - +
15A ILE* 1.3 60.4 + - - +
16A PHE* 3.6 23.9 - - - -
30A GLU* 3.1 28.6 + - - +
31A VAL 3.2 8.2 + - - -
32A GLU* 3.9 9.5 + - - +
65A MET* 4.1 1.5 - - - +
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Residues in contact with ILE 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A VAL* 3.9 13.7 - - + -
9A GLU 3.2 9.0 - - - +
10A GLN* 4.6 5.2 - - + -
13A ASP 4.2 0.4 + - - -
14A SER* 1.3 71.8 - - - +
16A PHE* 1.3 64.2 + - - +
17A GLU 3.7 0.7 + - - -
29A ARG 3.6 1.6 - - - +
30A GLU* 3.6 1.9 - - - -
31A VAL* 2.7 44.0 + - + +
33A TYR* 3.6 26.7 - - + -
65A MET* 4.1 17.5 - - + -
88A PHE 4.1 9.0 - - - +
89A LYS* 4.7 4.9 - - - +
92A TYR* 3.5 61.0 - - + +
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Residues in contact with PHE 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A THR 4.6 0.2 - - - -
8A VAL* 3.4 2.6 - - - -
9A GLU* 2.8 37.5 + - + +
11A ILE* 3.3 37.2 - - + -
14A SER* 3.6 28.5 - - - -
15A ILE* 1.3 72.4 - - - +
17A GLU* 1.3 60.1 + - - +
28A THR* 5.5 0.9 - - + -
29A ARG 3.5 11.2 - - - -
30A GLU* 3.4 34.1 - - + -
245A HIS* 3.4 55.0 + + + +
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Residues in contact with GLU 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A TYR* 3.5 7.4 - - + +
7A THR 3.6 10.5 - - - +
8A VAL* 4.2 5.2 - - + +
15A ILE* 3.7 2.0 + - + -
16A PHE* 1.3 73.5 - - - +
18A ARG* 1.3 70.3 + - - +
19A TYR* 4.1 6.8 - - - -
28A THR* 3.3 7.5 - - - -
29A ARG* 2.8 61.3 + - + +
92A TYR* 2.4 47.8 + - + +
93A LEU* 5.3 0.4 - - + -
97A TYR* 2.4 42.1 + - - -
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Residues in contact with ARG 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A LEU* 2.8 32.7 + - + -
7A THR* 3.2 33.4 + - - +
16A PHE 4.3 0.2 + - - -
17A GLU* 1.3 75.8 - - - +
19A TYR* 1.3 63.2 + - - +
26A GLU* 3.4 23.0 + - - +
27A ARG 3.5 6.7 - - - +
28A THR* 4.2 18.6 - - + +
209A THR* 2.8 43.0 + - - +
210A PRO 3.1 18.8 + - - -
211A VAL* 3.8 15.5 - - - +
244A PRO* 3.5 24.2 - - + +
245A HIS* 4.3 7.0 - - + -
267A GLY 2.8 20.3 + - - -
268A ILE* 3.8 0.8 - - - +
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Residues in contact with TYR 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A GLU* 2.9 30.5 + - + -
4A PHE 3.3 14.1 - - - +
5A TYR* 3.9 1.1 - - - -
6A LEU* 3.6 6.4 - - - +
17A GLU* 3.9 8.7 - - - +
18A ARG* 1.3 78.7 - - - +
20A ILE* 1.3 78.7 + - - +
21A ASP* 4.3 7.9 - - + +
26A GLU* 3.1 8.7 - - - +
27A ARG* 2.8 76.1 + - + +
28A THR 5.0 0.3 + - - -
29A ARG* 3.4 59.2 + - + +
97A TYR* 3.7 13.0 - - - +
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Residues in contact with ILE 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A MET* 5.0 4.7 - - - -
2A LYS 5.0 3.6 - - - +
3A GLU* 3.4 8.0 - - - +
4A PHE* 3.0 54.4 + - + +
6A LEU* 3.3 38.3 - - + +
19A TYR* 1.3 80.8 - - - +
21A ASP* 1.3 72.5 + - - +
24A GLY* 3.8 18.8 - - - +
25A ARG 3.2 7.0 - - - +
26A GLU* 3.8 14.1 - - + +
107A LYS* 3.9 32.3 - - + +
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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