Contacts of the strand formed by residues 363 - 366 (chain K) in PDB entry 6X5A
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 TRP 363 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233K ALA 3.3 0.5 - - - +
234K PHE* 3.1 31.0 - - - -
235K TYR* 3.3 16.3 + - + +
237K VAL* 3.1 36.5 - - + +
257K LEU* 4.3 10.5 + - + -
259K ALA* 3.5 30.3 - - + +
262K MET* 5.8 4.7 - - + -
263K LEU* 5.8 1.8 - - + -
312K LEU* 3.4 46.7 - - + -
347K LEU* 3.9 22.2 - - + -
348K VAL 3.5 8.1 - - - -
349K PRO* 3.4 43.7 - - + -
350K LYS* 4.7 0.7 - - - +
361K GLU* 3.4 18.6 + - - +
362K THR* 1.3 80.6 + - - +
364K ARG* 1.3 61.3 + - - +
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Residues in contact with ARG 364 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215K MET* 6.3 0.6 - - - +
233K ALA* 3.6 17.7 - - + +
234K PHE* 4.3 6.7 - - + -
347K LEU* 3.4 8.6 - - - -
348K VAL* 2.9 46.6 + - + +
350K LYS* 3.4 36.8 - - + +
363K TRP* 1.3 73.9 - - - +
365K LEU* 1.3 82.0 + - + +
366K SER* 4.0 15.6 + - - +
421K TYR* 2.9 53.2 + - - -
473K PHE* 6.1 3.4 - - + -
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Residues in contact with LEU 365 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225K LEU* 6.1 1.8 - - + -
232K GLY 4.0 2.9 - - - +
233K ALA* 3.8 14.6 - - - +
235K TYR* 3.6 35.7 - - + +
319K PRO* 4.9 17.5 - - + -
321K SER* 5.6 1.6 - - - +
322K THR* 5.7 4.0 - - - -
345K PHE* 5.8 4.9 - - + -
346K TYR 3.4 7.2 - - - +
347K LEU* 4.9 5.8 - - + +
364K ARG* 1.3 97.8 + - + +
366K SER* 1.3 63.0 + - - +
367K PHE* 3.5 35.3 - - + -
467K HIS* 5.9 0.7 + - - -
470K ILE* 3.6 29.4 - - + -
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Residues in contact with SER 366 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215K MET* 6.1 5.2 - - - -
311K ALA* 5.6 0.4 - - - -
346K TYR* 2.7 56.3 + - - +
348K VAL* 3.0 35.2 - - - +
364K ARG* 3.9 8.0 + - - +
365K LEU* 1.3 77.9 + - - +
367K PHE* 1.3 68.8 + - - +
368K SER* 3.7 8.1 - - - -
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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