Contacts of the strand formed by residues 334 - 339 (chain B) in PDB entry 1KHU
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 334 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294B VAL 3.9 0.5 - - - +
295B LEU* 3.8 2.6 - - - +
296B VAL* 3.1 48.4 + - + +
332B LYS 4.4 2.4 - - - +
333B GLY* 1.3 72.7 - - - -
335B HIS* 1.3 73.3 + - - +
336B LEU* 3.9 12.1 + - + -
345B ALA* 4.4 3.1 - - + -
346B GLU 3.4 16.2 - - - +
348B LEU* 4.6 0.4 - - - -
353B ILE* 3.3 20.6 - - + +
374B ILE* 6.1 0.2 - - + -
414B MET* 3.8 31.6 - - + -
416B PHE* 4.0 12.1 - - + -
436B ILE* 4.5 2.0 - - + -
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Residues in contact with HIS 335 (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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293B SER* 2.4 30.2 + - - -
294B VAL 3.5 11.9 - - - -
295B LEU* 4.0 19.3 - - + -
334B VAL* 1.3 73.5 - - - +
336B LEU* 1.3 69.7 + - - +
337B TYR* 3.8 13.5 + - + +
344B TYR 3.5 4.7 - - - +
345B ALA* 3.5 2.4 - - - -
346B GLU* 2.7 49.2 + - + +
348B LEU* 3.4 23.1 - - + +
462C SER* 3.5 20.5 + - - -
464C VAL* 5.6 0.9 - - + +
465C SER* 3.7 17.7 - - - -
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Residues in contact with LEU 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B TRP* 3.7 17.6 - - + -
274B ILE* 3.3 33.9 - - + -
292B THR 3.4 4.5 - - - +
293B SER* 3.6 0.3 - - - -
294B VAL* 2.8 52.6 + - + +
296B VAL* 4.2 7.9 - - + -
334B VAL* 3.9 18.4 - - + -
335B HIS* 1.3 73.9 - - - +
337B TYR* 1.3 58.3 + - - +
343B VAL* 6.2 0.9 - - + -
344B TYR 3.5 7.6 - - - +
345B ALA* 4.4 3.1 - - + -
382B ILE* 4.5 5.4 - - + -
414B MET* 3.8 28.3 - - + -
436B ILE* 5.0 2.2 - - + -
438B ILE* 3.7 21.5 - - + -
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Residues in contact with TYR 337 (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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271B TRP* 4.6 2.0 - - - -
292B THR* 3.5 17.3 - - - -
293B SER* 4.2 8.5 - - - -
335B HIS* 3.8 15.2 + - + +
336B LEU* 1.3 72.6 - - - +
338B TYR* 1.3 69.8 + - - +
339B VAL* 3.4 45.6 - - + +
342B GLU 3.8 1.0 - - - +
343B VAL* 3.1 4.2 - - - +
344B TYR* 2.6 51.4 + + + +
464C VAL* 3.8 27.4 - - + -
465C SER* 3.5 44.0 + - - -
425D HIS* 4.8 6.0 + - + -
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Residues in contact with TYR 338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B TRP* 3.4 59.0 - + + +
292B THR* 2.9 39.5 + - + +
337B TYR* 1.3 75.3 - - - +
339B VAL* 1.3 63.7 + - - +
340B GLY 6.0 0.2 - - - -
341B GLY* 4.0 14.5 - - - -
342B GLU 3.6 3.1 - - - -
343B VAL* 3.3 28.3 - - + -
383B PHE* 6.1 0.2 - + - -
385B ASN* 3.4 29.7 + - - -
440B LEU* 6.0 0.4 - - + -
442B GLY* 5.6 4.0 - - - -
443B PRO* 5.9 2.7 - - + +
446B TRP* 5.0 7.1 - - - -
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Residues in contact with VAL 339 (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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337B TYR* 3.4 43.7 - - + +
338B TYR* 1.3 78.6 - - - +
340B GLY* 1.3 71.5 + - - +
341B GLY 3.1 2.2 - - - -
342B GLU* 2.9 23.0 + - - +
344B TYR* 3.9 9.6 - - + -
425D HIS* 3.7 40.5 - - + -
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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