Contacts of the strand formed by residues 180 - 186 (chain A) in PDB entry 1KEK
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 ILE 180 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A THR* 3.2 23.8 - - - +
8A THR* 3.1 39.9 - - - +
9A ASP* 4.5 6.7 - - + +
178A HIS 4.3 6.7 - - - +
179A GLU* 1.3 75.9 - - - +
181A GLN* 1.3 72.2 + - - +
435A LYS* 5.1 8.3 - - + -
438A ILE* 4.0 25.8 - - + -
439A LYS* 4.1 14.1 - - - +
450A GLN* 3.2 8.5 - - - +
451A GLY* 2.9 35.5 + - - +
453A PHE* 4.5 16.8 - - + -
1206B PRO* 6.4 2.2 - - + -
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Residues in contact with GLN 181 (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 THR* 3.2 1.3 - - - -
8A THR 3.0 29.4 + - - +
145A SER* 6.5 0.2 - - - -
146A VAL* 3.9 17.3 - - + +
179A GLU* 3.1 25.1 + - - +
180A ILE* 1.3 82.3 - - - +
182A LYS* 1.3 67.8 + - - +
183A ILE* 3.4 21.7 + - + +
448A PHE* 5.1 5.7 - - - +
449A ALA 3.4 22.3 + - - +
450A GLN* 3.6 14.9 + - - +
475A ILE* 3.0 35.9 + - - +
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Residues in contact with LYS 182 (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 MET* 5.0 18.3 - - + +
6A MET 3.6 9.0 - - - +
7A THR* 3.5 21.2 - - + +
181A GLN* 1.3 80.4 + - - +
183A ILE* 1.4 65.8 + - - +
442A GLY* 2.9 36.3 + - - -
443A ASP* 5.8 0.2 - - - -
445A THR 3.1 15.8 + - - -
446A ASP* 3.9 6.9 + - - +
447A LEU 2.9 27.5 + - - +
448A PHE* 4.6 19.5 - - + -
449A ALA* 3.3 23.8 + - + +
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Residues in contact with ILE 183 (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 MET* 3.4 9.9 - - - +
6A MET* 2.7 43.8 + - + +
8A THR* 4.2 11.2 - - - +
13A ALA* 3.9 25.6 - - + -
146A VAL* 3.7 27.1 - - + +
147A GLN* 3.5 30.3 - - + +
150A HIS* 4.4 2.7 - - + -
181A GLN* 3.8 11.9 - - + +
182A LYS* 1.4 80.1 - - - +
184A GLU* 1.3 62.8 + - - +
185A VAL* 3.6 27.1 - - + -
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Residues in contact with GLU 184 (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* 2.7 51.7 + - + +
4A LYS 3.2 4.7 - - - +
5A MET* 3.2 30.5 - - + -
147A GLN* 2.9 27.0 - - - +
150A HIS* 4.1 2.3 + - - -
183A ILE* 1.3 77.3 - - - +
185A VAL* 1.3 74.5 + - - +
186A LEU* 4.2 1.7 + - - +
254A THR* 3.8 10.7 - - - +
256A ARG* 2.9 42.0 + - - +
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Residues in contact with VAL 185 (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 3.8 - - - -
4A LYS* 2.8 55.6 + - + +
6A MET* 3.8 30.3 - - + -
13A ALA* 5.3 1.3 - - - -
16A HIS* 3.6 31.0 - - + +
150A HIS* 3.4 16.4 - - + -
183A ILE* 3.6 25.4 - - + -
184A GLU* 1.3 80.1 - - - +
186A LEU* 1.3 60.9 + - - +
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Residues in contact with LEU 186 (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 GLY 3.5 9.9 - - - +
3A LYS* 4.7 1.6 - - + -
4A LYS* 5.8 0.7 - - - -
16A HIS* 2.8 27.5 + - - -
150A HIS* 3.0 21.1 + - + +
154A LEU* 3.8 28.5 - - + -
184A GLU* 4.3 4.7 - - - +
185A VAL* 1.3 75.7 - - - +
187A ASP* 1.3 68.1 + - - +
190A ASP* 3.6 25.4 - - + +
191A MET* 3.4 9.3 - - + +
194A LEU* 5.5 0.4 - - + -
250A VAL* 4.8 3.1 - - + -
253A LEU* 4.2 26.7 - - + +
254A THR* 3.9 29.4 - - + -
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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