Contacts of the strand formed by residues 29 - 36 (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 VAL 29 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A PHE* 4.2 10.3 - - + -
21A GLU 3.6 14.6 - - - +
22A GLN* 3.8 25.6 - - + +
28A PRO* 1.3 75.9 - - - +
30A LYS* 1.3 72.5 + - - +
31A VAL* 3.7 7.9 + - + +
99A ILE 3.9 0.2 - - - +
100A GLU* 3.4 1.9 - - - -
101A ASP 2.8 35.8 + - - +
104A ILE* 3.6 46.2 - - + +
105A SER* 3.9 7.6 - - - -
106A LEU* 4.4 6.7 - - + +
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Residues in contact with LYS 30 (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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19A ASN 3.6 0.9 - - - +
20A PHE* 3.2 4.7 - - - -
21A GLU* 2.7 65.5 + - - +
22A GLN* 5.5 3.8 - - - -
28A PRO* 4.8 14.6 - - - +
29A VAL* 1.3 73.4 - - - +
31A VAL* 1.3 60.4 + - - +
32A TRP* 3.7 16.4 - - + -
99A ILE 3.6 5.6 - - - +
100A GLU* 4.3 23.8 - - + +
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Residues in contact with VAL 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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18A ILE* 3.3 30.3 - - + -
19A ASN 3.3 4.0 - - - +
20A PHE* 3.5 31.2 - - + -
29A VAL* 4.0 6.7 - - + +
30A LYS* 1.3 76.8 - - - +
32A TRP* 1.3 62.7 - - - +
45A PHE* 4.7 15.3 - - + -
84A LEU* 5.0 7.9 - - + -
97A VAL* 4.2 3.7 - - + +
98A SER* 3.4 0.7 + - - -
99A ILE* 2.6 56.0 + - + +
101A ASP* 5.4 1.6 - - + +
104A ILE* 4.0 17.0 - - + -
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Residues in contact with TRP 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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18A ILE* 4.4 5.6 - - - -
19A ASN* 2.7 78.6 + - + +
20A PHE 4.9 0.7 - - - -
21A GLU* 3.5 46.2 - - + -
30A LYS* 3.7 21.5 - - + -
31A VAL* 1.3 79.5 - - - +
33A GLY* 1.3 64.5 + - - +
97A VAL* 3.1 15.5 - - - +
98A SER* 4.2 8.5 - - - +
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Residues in contact with GLY 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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17A ILE 3.3 12.6 - - - -
18A ILE* 4.3 4.9 - - - -
19A ASN* 4.4 4.7 - - - -
32A TRP* 1.3 84.9 - - - +
34A SER* 1.3 61.3 + - - -
96A ASP* 3.6 2.8 - - - +
97A VAL* 2.8 31.7 + - - +
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Residues in contact with SER 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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16A GLY* 3.2 2.8 - - - -
17A ILE* 3.1 29.5 + - - +
18A ILE* 4.3 0.2 - - - +
33A GLY* 1.3 74.1 - - - -
35A ILE* 1.3 69.3 + - - +
36A LYS* 4.3 1.6 + - - +
94A VAL* 3.6 14.7 - - - +
95A ALA 3.2 6.5 - - - -
96A ASP* 3.3 23.2 + - - -
97A VAL* 5.3 0.2 - - - -
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Residues in contact with ILE 35 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A LEU* 3.5 31.9 - - + -
14A VAL* 3.7 22.7 - - + -
15A GLN 3.6 11.2 - - - +
16A GLY* 4.3 1.8 - - - +
18A ILE* 3.9 16.8 - - + -
34A SER* 1.3 84.1 + - - +
36A LYS* 1.3 61.0 + - - +
38A LEU* 3.7 21.3 - - + +
45A PHE* 4.1 15.0 - - + -
87A VAL* 4.7 6.1 - - + -
93A GLY 3.7 1.9 - - - +
94A VAL* 3.5 1.2 - - - -
95A ALA* 2.8 39.4 + - + +
97A VAL* 4.5 9.9 - - + -
119A VAL* 4.6 11.9 - - + -
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Residues in contact with LYS 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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13A PRO 4.3 3.1 - - - +
14A VAL* 3.2 8.0 - - - +
15A GLN* 2.9 74.0 + - + +
34A SER* 4.3 1.8 - - - +
35A ILE* 1.3 73.8 - - - +
37A GLY* 1.3 63.4 + - - +
38A LEU 3.3 3.7 + - - -
93A GLY 3.6 5.4 - - - -
94A VAL* 4.0 18.4 - - + -
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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