Contacts of the strand formed by residues 15 - 21 (chain A) in PDB entry 2ZKW
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 15 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A LEU* 3.2 13.7 - - - +
9A LYS* 4.1 27.3 + - + -
12A GLY 5.3 2.4 + - - +
13A PRO* 3.9 14.2 + - - +
14A VAL* 1.3 77.6 - - - +
16A GLY* 1.3 58.4 + - - +
17A ILE* 5.4 0.7 - - + -
35A ILE* 4.2 5.2 - - - -
36A LYS* 2.9 66.1 + - - +
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Residues in contact with GLY 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 VAL* 3.5 2.8 - - - +
8A LEU* 2.9 36.2 + - - +
15A GLN* 1.3 77.8 - - - +
17A ILE* 1.3 78.6 + - - +
34A SER 3.2 14.6 - - - -
35A ILE* 4.0 7.2 - - - -
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Residues in contact with ILE 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 VAL* 4.0 22.9 - - + -
6A CYS 3.3 4.7 - - - +
7A VAL* 4.4 19.5 - - + -
15A GLN* 6.2 0.4 - - + -
16A GLY* 1.3 98.5 - - - +
18A ILE* 1.3 65.5 + - - +
19A ASN* 4.3 14.4 - - - +
33A GLY* 3.3 4.7 - - - -
34A SER 3.1 29.1 + - - +
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Residues in contact with ILE 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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5A VAL* 3.4 2.9 - - - +
6A CYS 2.8 34.3 + - - +
8A LEU* 3.9 14.4 - - + -
17A ILE* 1.3 84.4 - - - +
19A ASN* 1.3 63.1 + - - +
20A PHE* 3.8 11.7 - - + -
31A VAL* 3.3 34.5 - - + -
32A TRP 3.5 4.3 - - - +
33A GLY* 4.3 13.0 - - - +
34A SER 4.3 0.7 - - - +
35A ILE* 3.9 26.5 - - + -
45A PHE* 4.0 8.3 - - + -
97A VAL* 4.5 7.6 - - + -
117A LEU* 3.5 28.0 - - + -
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Residues in contact with ASN 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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4A ALA 3.5 5.3 - - - +
5A VAL* 3.9 17.5 - - - +
17A ILE* 4.3 13.2 - - - +
18A ILE* 1.3 78.1 - - - +
20A PHE* 1.3 63.8 + - - +
30A LYS 3.6 0.3 - - - +
31A VAL* 3.3 5.4 - - - -
32A TRP* 2.7 81.5 + - + +
33A GLY* 4.4 3.8 - - - -
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Residues in contact with PHE 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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3A LYS* 3.4 5.0 - - - +
4A ALA* 2.7 44.1 + - + +
6A CYS* 4.1 9.4 - - + -
18A ILE* 3.8 24.2 - - + -
19A ASN* 1.3 77.5 - - - +
21A GLU* 1.3 62.8 + - - +
29A VAL* 4.2 6.1 - - + -
30A LYS 3.2 5.2 - - - -
31A VAL* 3.5 29.6 - - + -
32A TRP* 4.3 1.4 - - - -
47A VAL* 5.0 4.3 - - + -
84A LEU* 5.3 2.0 - - + -
104A ILE* 4.3 3.4 - - + -
106A LEU* 3.9 21.8 - - + -
112A ILE* 3.6 26.9 - - + -
117A LEU* 3.9 20.6 - - + -
149A ILE* 3.9 30.5 - - + -
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Residues in contact with GLU 21 (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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2A THR 3.6 8.3 - - - +
3A LYS* 3.1 33.2 + - + +
20A PHE* 1.3 76.1 - - - +
22A GLN* 1.3 65.0 + - - +
29A VAL* 4.1 1.7 - - - +
30A LYS* 2.7 62.0 + - + +
32A TRP* 3.5 30.6 - - + -
106A LEU* 4.6 0.2 - - - -
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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