Contacts of the strand formed by residues 22 - 28 (chain B) in PDB entry 2KZ1
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 ARG 22 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18B LEU* 3.3 4.2 - - - +
19B ARG* 2.8 47.0 + - + +
20B ASN* 2.8 22.0 + - - +
21B PHE* 1.3 105.7 - - + +
23B SER* 1.3 61.6 + - - +
24B ILE* 3.6 10.6 + - + +
67B ASP* 5.4 7.3 + - - +
68B LEU 3.9 15.9 - - - +
69B THR* 4.4 25.0 + - + +
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Residues in contact with SER 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B ILE* 4.1 19.2 - - - +
17B SER 3.9 1.8 - - - -
18B LEU* 3.4 20.6 - - - +
21B PHE 4.1 2.2 + - - -
22B ARG* 1.3 71.0 - - - +
24B ILE* 1.3 61.7 + - - +
25B LEU* 4.3 1.5 + - - +
66B CYS 4.0 0.3 - - - +
67B ASP* 3.6 0.9 - - - -
68B LEU* 3.2 53.5 + - - +
72B TRP* 4.2 12.6 - - - +
101B LEU* 4.8 4.3 - - - +
105B MET* 5.8 0.3 - - - +
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Residues in contact with ILE 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B LYS 4.2 0.3 - - - +
16B ILE* 3.5 3.2 - - - +
17B SER* 2.9 42.3 + - - +
19B ARG* 3.4 57.0 - - + +
22B ARG* 3.9 11.0 - - + +
23B SER* 1.3 77.1 - - - +
25B LEU* 1.3 63.5 + - - +
26B SER* 4.3 3.9 + - - +
65B PHE* 4.5 23.1 - - + -
66B CYS 3.5 12.8 - - - +
67B ASP* 3.8 21.1 - - + -
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Residues in contact with LEU 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B PHE* 6.5 0.9 - - + -
15B LYS 3.5 8.7 - - - +
16B ILE* 4.4 12.8 - - + -
23B SER 5.4 1.3 - - - +
24B ILE* 1.3 73.9 - - - +
26B SER* 1.3 63.7 + - - +
27B TRP* 3.7 23.1 - - + -
41B LEU* 3.9 22.0 - - + -
65B PHE* 3.3 2.4 - - - +
66B CYS* 2.9 49.6 + - + +
68B LEU* 4.5 12.1 - - + -
72B TRP* 3.7 35.9 - - + -
81B THR* 5.2 10.8 - - + +
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Residues in contact with SER 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B THR 4.1 0.3 - - - +
14B PHE* 3.7 3.4 - - - +
15B LYS* 2.9 39.8 + - - +
24B ILE* 4.9 5.2 + - - +
25B LEU* 1.3 76.8 + - - +
27B TRP* 1.3 64.9 + - - +
28B GLU* 4.2 8.5 + - - -
64B SER* 3.5 12.6 - - - -
65B PHE* 3.4 14.9 - - - +
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Residues in contact with TRP 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B THR 3.6 4.0 - - - +
14B PHE* 3.8 23.3 - + + -
25B LEU* 3.7 24.0 - - + -
26B SER* 1.3 79.7 - - - +
28B GLU* 1.3 69.1 + - - +
29B LEU* 3.6 24.4 + - + +
39B TYR* 3.3 42.4 - + + -
41B LEU* 3.6 34.1 - - + -
58B CYS* 5.1 6.3 - - + -
61B THR* 5.6 1.6 - - + -
63B ARG 3.5 19.1 - - - -
64B SER* 3.5 24.3 + - - +
65B PHE 3.9 6.3 - - - -
66B CYS* 3.8 19.3 - - + -
83B LEU* 3.7 19.3 - - + -
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Residues in contact with GLU 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B SER* 3.6 7.7 - - - -
13B THR* 2.8 48.4 + - + +
15B LYS* 5.5 11.4 + - - +
26B SER* 4.2 8.4 + - - -
27B TRP* 1.3 76.3 - - - +
29B LEU* 1.3 67.3 + - - +
30B LYS* 6.0 3.1 - - - -
64B SER* 6.1 0.7 - - - -
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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