Contacts of the strand formed by residues 33 - 37 (chain A) in PDB entry 2ZXI
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 THR 33 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A PHE* 3.8 2.7 - - - -
10A VAL* 3.2 26.4 - - + +
12A VAL* 4.2 2.5 - - + -
23A ALA* 4.1 21.1 - - - +
26A ALA* 3.5 7.7 - - + +
27A ALA* 3.4 13.1 + - - -
31A ALA* 2.8 17.9 + - - +
32A LYS* 1.3 74.2 + - - +
34A ALA* 1.3 65.4 + - - +
118A ASN 2.7 11.4 + - - +
119A LEU* 3.3 21.5 - - + +
120A TYR* 2.7 34.7 + - - -
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Residues in contact with ALA 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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8A PHE* 3.5 38.8 - - + -
10A VAL 3.0 6.7 + - - -
11A VAL* 3.4 5.8 - - + +
12A VAL 2.8 32.6 + - - +
33A THR* 1.3 76.3 - - - +
35A MET* 1.3 55.7 + - - +
36A PHE* 3.9 19.2 + - + -
120A TYR 3.1 7.4 - - - +
122A LYS* 4.5 4.9 - - + -
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Residues in contact with MET 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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12A VAL* 3.3 5.8 - - + +
14A GLY 3.4 17.7 - - - +
15A GLY* 3.9 11.7 - - - -
19A GLY 3.2 31.6 - - - +
20A ILE* 3.3 24.7 - - + +
23A ALA* 3.4 22.7 - - + -
33A THR 4.2 0.2 - - - -
34A ALA* 1.3 72.3 - - - +
36A PHE* 1.3 60.4 + - - +
37A VAL* 3.7 8.2 - - + +
43A ILE* 4.4 18.4 - - - -
113A CYS* 4.4 14.4 - - - -
119A LEU* 4.3 6.3 - - + +
120A TYR 2.8 13.2 + - - +
121A ILE* 3.6 11.0 - - + -
122A LYS 3.0 22.9 + - - +
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Residues in contact with PHE 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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11A VAL* 3.8 35.0 - - + -
12A VAL 2.8 10.5 + - - +
13A ILE* 4.5 1.8 - - - -
14A GLY* 2.7 30.0 + - - -
34A ALA* 3.9 19.1 - - + -
35A MET* 1.3 71.5 - - - +
37A VAL* 1.3 66.7 + - - +
122A LYS* 3.1 29.4 - - + -
124A GLU* 3.8 21.8 - - + +
126A VAL* 3.6 28.0 - - + -
139A VAL* 5.1 3.1 - - + -
141A THR* 3.9 11.7 - - + -
147A TYR* 3.7 42.2 - + + -
618A FAD 3.7 6.5 + - + -
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Residues in contact with VAL 37 (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 GLY* 3.9 17.5 - - - +
35A MET* 3.7 13.5 - - + +
36A PHE* 1.3 82.6 - - - +
38A LEU* 1.3 67.8 + - - +
39A ASN 3.5 25.5 + - - +
40A ALA* 4.5 3.1 - - - +
42A THR* 4.2 3.6 - - - +
43A ILE* 4.0 25.8 - - + +
121A ILE* 4.5 3.8 - - + -
122A LYS 3.0 5.8 + - - +
123A GLN* 3.1 21.9 - - - -
124A GLU 3.1 7.0 + - - -
618A FAD 3.6 31.8 + - - +
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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