Contacts of the strand formed by residues 381 - 385 (chain A) in PDB entry 5KJH
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 381 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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370A LEU* 4.1 15.0 - - + -
373A ALA* 3.5 39.0 - - + +
374A GLN* 3.6 22.4 - - + +
377A TYR* 4.7 0.4 - - + -
379A GLY 2.9 12.1 + - - +
380A ARG* 1.3 75.6 - - - +
382A VAL* 1.3 65.8 + - - +
383A VAL* 4.1 3.8 + - + +
404A GLY* 3.4 7.6 - - - +
406A VAL* 3.7 31.0 - - + -
487A PRO 4.3 0.3 - - - +
488A PHE* 3.4 28.8 - - + +
489A GLY 3.5 7.4 + - - +
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Residues in contact with VAL 382 (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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381A VAL* 1.3 72.4 - - - +
383A VAL* 1.3 69.2 + - - +
384A VAL* 5.2 3.8 - - + +
399A HIS* 3.6 39.9 - - + +
403A VAL* 3.5 22.2 - - + -
404A GLY 2.8 9.5 + - - +
405A VAL* 3.3 10.5 - - + +
406A VAL 3.0 23.4 + - - +
487A PRO* 4.5 13.0 - - + +
488A PHE* 3.7 19.7 - - + -
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Residues in contact with VAL 383 (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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366A PHE* 3.7 9.6 - - + -
370A LEU* 4.1 21.3 - - + -
381A VAL* 4.1 4.9 + - + +
382A VAL* 1.3 82.7 - - - +
384A VAL* 1.3 62.2 + - - +
385A ASP* 5.3 1.4 - - - +
406A VAL* 3.3 13.0 - - + +
408A LYS* 3.3 37.7 - - + -
487A PRO 5.7 0.4 + - - -
489A GLY* 5.6 3.8 - - - +
490A PHE* 3.6 38.8 - - + -
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Residues in contact with VAL 384 (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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382A VAL* 5.3 4.5 - - + +
383A VAL* 1.3 74.2 - - - +
385A ASP* 1.3 68.8 + - - +
390A ILE* 4.5 29.2 - - + -
395A ALA* 4.0 12.3 - - + -
399A HIS* 6.3 1.6 - - + -
405A VAL* 3.8 18.6 - - + -
406A VAL 2.9 6.9 + - - -
407A MET* 3.3 37.9 - - + +
408A LYS* 2.8 27.2 + - - -
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Residues in contact with ASP 385 (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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383A VAL 5.3 0.7 - - - +
384A VAL* 1.3 87.7 - - + +
386A GLN* 1.3 67.4 - - - +
387A GLY 3.8 7.4 + - - +
390A ILE* 4.7 4.3 - - - +
407A MET* 4.1 6.3 - - - +
408A LYS* 2.8 42.2 + - - -
410A ALA* 3.6 22.9 - - + +
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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