Contacts of the strand formed by residues 30 - 36 (chain A) in PDB entry 2OXP
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 GLN 30 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26A MET* 3.4 4.2 - - - -
27A TYR* 2.9 34.6 + - - +
28A LYS* 3.9 8.4 + - - +
29A GLY* 1.3 83.2 - - - +
31A PRO* 1.3 73.1 - - + +
32A MET* 3.5 6.1 + - + +
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Residues in contact with PRO 31 (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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15A ILE* 3.5 21.1 - - + -
24A LYS* 4.6 7.8 + - + -
25A LEU 3.5 7.0 - - - +
26A MET* 3.4 17.2 - - + -
29A GLY 4.1 2.9 - - - +
30A GLN* 1.3 88.1 - - + +
32A MET* 1.3 63.7 + - - +
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Residues in contact with MET 32 (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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24A LYS* 3.6 11.8 - - - +
25A LEU 2.8 39.3 + - - +
27A TYR* 3.9 20.4 - - + +
30A GLN* 4.2 9.0 - - + +
31A PRO* 1.3 76.7 - - - +
33A THR* 1.3 63.1 + - - +
34A PHE* 3.3 34.0 - - + -
76A PHE* 5.3 3.6 - - + -
82A THR* 4.9 9.2 - - + -
86A GLY 4.6 9.0 - - - +
88A GLY* 3.6 36.6 - - - +
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Residues in contact with THR 33 (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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18A ILE* 3.8 10.8 - - + +
22A THR* 3.2 34.1 - - + -
23A VAL 3.6 3.6 - - - -
24A LYS* 2.8 31.1 + - - +
32A MET* 1.3 76.9 - - - +
34A PHE* 1.3 60.5 + - - +
86A GLY 5.4 1.4 + - - -
87A ARG* 3.3 29.0 - - + +
88A GLY* 2.8 22.3 + - - -
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Residues in contact with PHE 34 (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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21A ASP 3.9 0.2 - - - +
22A THR* 3.2 8.7 - - - +
23A VAL* 2.8 39.1 + - + +
25A LEU* 3.7 31.9 - - + -
27A TYR* 3.9 21.5 - + + -
32A MET* 3.3 44.9 - - + -
33A THR* 1.3 73.9 - - - +
35A ARG* 1.3 60.8 + - - +
36A LEU* 3.9 2.5 + - + +
74A VAL* 4.0 18.2 - - + -
76A PHE* 3.8 27.8 - + - -
88A GLY* 3.3 20.6 - - - -
90A ALA* 4.2 13.0 - - + -
92A ILE* 4.4 14.1 - - + -
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Residues in contact with ARG 35 (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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21A ASP* 3.3 33.2 + - - +
22A THR* 3.8 9.0 - - - +
33A THR 4.2 0.4 - - - -
34A PHE* 1.3 72.3 - - - +
36A LEU* 1.3 92.2 + - - +
37A LEU 3.4 2.6 + - - -
39A VAL 2.9 25.1 + - - -
40A ASP* 3.7 2.6 + - - -
87A ARG* 3.7 30.8 - - + +
88A GLY 2.7 19.9 + - - +
89A LEU* 3.6 15.1 - - + +
90A ALA 3.5 9.5 + - - -
92A ILE* 6.1 0.2 - - - -
113A TYR* 3.3 19.6 - - - -
300A THP 2.9 65.4 + - + +
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Residues in contact with LEU 36 (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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20A GLY 4.3 1.6 - - - +
21A ASP* 2.9 32.8 + - - +
22A THR 4.2 1.1 - - - +
23A VAL* 4.3 12.8 - - + -
34A PHE* 4.2 8.1 - - + +
35A ARG* 1.3 98.9 + - - +
37A LEU* 1.3 63.9 + - - +
38A LEU 3.7 0.7 + - - -
39A VAL* 3.7 13.0 - - + +
62A THR* 5.0 1.3 - - + -
90A ALA 3.5 4.7 - - - -
92A ILE* 3.8 21.8 - - + -
99A VAL* 3.8 29.8 - - + -
100A ASN* 3.4 26.0 - - - +
103A LEU* 3.9 18.4 - - + -
300A THP 4.0 2.8 - - - +
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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