Contacts of the strand formed by residues 336 - 340 (chain A) in PDB entry 2KHO
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 ASP 336 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A LEU* 3.6 28.3 - - + +
188A ARG* 3.8 18.8 - - - -
189A THR 3.5 2.0 + - - -
190A ILE* 3.3 8.4 - - + +
191A ALA 2.7 32.7 + - - +
334A ILE* 3.3 5.7 - - - +
335A ASP* 1.4 85.0 - - + +
337A VAL* 1.4 54.3 + - - +
338A ILE* 4.0 16.8 - - + -
362A ARG* 4.7 18.4 - - - +
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Residues in contact with VAL 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A ALA* 3.3 14.4 - - + +
193A TYR* 4.7 8.1 - - + -
334A ILE* 5.0 0.7 - - + -
335A ASP 4.3 1.0 + - - -
336A ASP* 1.4 72.4 + - - +
338A ILE* 1.4 60.4 + - - +
339A LEU* 5.0 0.2 - - + -
353A VAL* 3.6 24.7 - - + -
357A PHE* 3.8 34.8 - - + -
359A LYS* 3.6 27.8 - - + +
360A GLU 4.6 1.7 + - - +
361A PRO* 3.1 22.2 - - + +
362A ARG* 2.8 31.7 + - - +
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Residues in contact with ILE 338 (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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175A ALA* 3.5 41.3 - - + +
176A ALA* 3.7 8.1 - - - +
179A TYR* 3.8 23.8 - - + -
181A LEU* 5.4 4.5 - - + -
190A ILE* 3.7 19.1 - - + -
191A ALA 2.7 17.6 + - - +
192A VAL* 3.5 12.2 - - + +
193A TYR* 2.9 28.4 + - - +
336A ASP* 4.2 21.5 - - + -
337A VAL* 1.4 78.6 - - - +
339A LEU* 1.4 63.3 + - - +
362A ARG* 3.8 15.7 - - + -
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Residues in contact with LEU 339 (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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179A TYR* 3.3 20.3 - - - -
193A TYR* 3.5 30.5 - - + -
337A VAL* 5.0 0.7 - - + -
338A ILE* 1.4 75.5 - - - +
340A VAL* 1.4 69.9 - - - +
344A THR* 3.8 24.5 - - + +
349A VAL* 6.2 0.7 - - + -
350A GLN* 3.8 29.4 - - + -
353A VAL* 4.8 5.8 - - + -
361A PRO* 3.7 34.5 - - + +
362A ARG 3.2 12.2 + - - +
363A LYS* 4.1 22.4 - - + -
367A PRO* 3.8 7.6 - - - +
370A ALA* 5.1 0.2 - - - +
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Residues in contact with VAL 340 (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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171A GLU 5.4 0.7 - - - +
175A ALA* 3.6 32.1 - - + -
179A TYR* 4.9 2.2 - - + -
192A VAL* 4.2 9.0 - - + -
193A TYR 2.9 6.7 + - - +
194A ASP* 3.4 30.7 - - + +
195A LEU 3.0 21.0 + - - -
338A ILE 5.2 0.2 - - - +
339A LEU* 1.4 80.4 - - - +
341A GLY* 1.4 67.1 + - - +
344A THR* 3.1 11.8 - - - +
367A PRO* 3.9 7.9 - - + +
370A ALA* 5.5 2.0 - - + -
371A VAL* 3.7 36.3 - - + +
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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