Contacts of the strand formed by residues 34 - 39 (chain B) in PDB entry 1KU6
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 34 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A TYR* 2.5 28.9 + - - -
75A THR* 3.7 20.8 + - - +
76A LEU* 3.8 26.5 - - + +
6B HIS* 3.8 2.2 - - + +
8B THR* 5.4 0.3 - - - -
24B ARG* 3.4 36.3 - - + +
25B LYS 3.5 15.7 - - - +
26B SER* 3.7 3.1 - - - -
32B LYS 4.5 0.4 - - - +
33B MET* 1.3 71.6 - - - +
35B LEU* 1.3 61.0 + - - +
36B GLY 3.8 9.2 - - - +
37B ARG* 3.6 30.7 - - + +
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Residues in contact with LEU 35 (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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72A TYR* 4.4 3.1 - - + -
282A VAL 5.8 0.2 - - - +
283A ASP 5.1 5.8 - - - +
286A TRP* 4.3 25.6 - - + -
287A HIS* 3.6 30.7 - - + +
6B HIS* 4.3 2.2 - - - -
7B THR* 3.6 0.7 - - - -
8B THR* 3.3 47.2 + - + +
25B LYS* 2.6 29.3 + - + +
26B SER 4.4 1.3 - - - -
27B ARG* 4.2 11.0 - - + +
33B MET* 3.4 13.4 + - + +
34B VAL* 1.3 77.7 - - - +
36B GLY* 1.3 54.5 + - - -
48B LEU* 3.6 23.1 - - + -
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Residues in contact with GLY 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B HIS* 3.2 21.8 - - - -
7B THR* 4.6 0.4 - - - -
23B TYR* 3.6 8.1 - - - -
25B LYS* 2.9 36.3 + - - +
34B VAL* 3.4 2.8 - - - +
35B LEU* 1.3 81.2 - - - +
37B ARG* 1.3 67.0 + - - +
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Residues in contact with ARG 37 (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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75A THR* 2.7 30.3 + - - -
76A LEU 3.2 12.5 + - - -
78A PRO* 3.2 21.2 - - - +
4B TYR* 3.5 30.7 - - - +
5B SER* 3.1 0.9 - - - -
6B HIS* 2.8 82.0 + - + +
23B TYR* 3.4 23.4 + - - +
24B ARG* 3.8 14.5 - - - +
34B VAL* 3.6 10.8 - - + +
36B GLY* 1.3 76.0 - - - +
38B GLY* 1.3 59.4 + - - +
60B ASN* 3.0 28.0 + - - +
61B TYR* 3.1 20.4 + - - -
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Residues in contact with GLY 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B TYR 3.3 13.4 + - - -
5B SER* 4.2 8.7 - - - -
17B CYS* 4.3 2.5 - - - -
22B CYS* 3.5 4.2 - - - +
23B TYR* 3.0 41.9 + - - -
37B ARG* 1.3 77.0 - - - +
39B CYS* 1.3 63.0 + - - -
60B ASN* 3.8 2.6 + - - -
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Residues in contact with CYS 39 (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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5B SER* 6.3 0.9 - - - -
15B THR* 5.4 6.1 - - - -
16B ASN 4.5 3.4 - - - -
17B CYS* 2.0 59.2 - - + +
20B ASN* 4.3 11.0 - - + +
21B SER 3.7 1.3 - - - -
23B TYR* 3.4 12.7 - - - -
38B GLY* 1.3 72.2 - - - -
40B GLY* 1.3 60.9 + - - +
42B PRO* 5.2 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