Contacts of the strand formed by residues 389 - 392 (chain A) in PDB entry 6C90
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 389 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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378A VAL* 5.3 2.7 - - + -
381A ILE* 4.0 36.3 - - + -
382A MET* 4.3 6.7 - - + -
388A PRO* 1.3 75.5 - - - +
390A ILE* 1.3 78.8 + - - +
391A ILE* 3.8 15.7 - - + -
471A PHE* 4.3 2.0 - - - -
477A LYS 2.9 18.8 + - - +
478A ALA* 3.4 13.8 + - + -
479A LEU* 3.0 25.1 + - - +
493A ALA* 4.3 0.4 - - - -
495A THR* 3.2 27.4 - - + +
497A LEU* 4.1 3.6 - - + -
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Residues in contact with ILE 390 (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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389A VAL* 1.3 72.3 - - - +
391A ILE* 1.3 58.7 + - - +
392A PHE* 3.7 36.0 + - + -
471A PHE* 3.5 31.4 - - + -
479A LEU* 3.4 9.6 - - + +
481A ALA* 4.5 4.3 - - + -
485A PHE* 3.6 31.2 - - + -
491A MET 3.9 9.4 - - - +
493A ALA* 3.8 14.8 - - + +
495A THR 3.0 8.6 + - - +
496A VAL* 3.4 5.8 - - + +
497A LEU 2.8 32.7 + - - +
523A ARG* 4.4 17.0 - - + +
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Residues in contact with ILE 391 (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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374A VAL* 5.1 1.3 - - + -
378A VAL* 4.3 5.4 - - + -
389A VAL* 3.8 28.3 - - + -
390A ILE* 1.3 72.3 - - - +
392A PHE* 1.3 60.7 + - - +
393A SER* 3.6 3.3 + - - +
478A ALA* 4.0 2.7 - - + -
479A LEU 2.7 27.4 + - - +
480A PHE* 3.4 47.9 - - + +
481A ALA 2.9 26.4 + - - +
497A LEU* 3.4 29.2 - - + +
499A THR* 3.3 32.1 - - + -
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Residues in contact with PHE 392 (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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390A ILE* 3.7 28.0 + - + -
391A ILE* 1.3 70.3 - - - +
393A SER* 1.3 59.8 + - - +
394A PHE* 5.5 6.2 - - + -
481A ALA* 3.3 4.5 - - + -
482A THR 3.6 29.6 - - - -
483A GLU* 4.4 0.7 - - - +
485A PHE* 4.3 7.2 - + + -
486A ALA* 4.0 25.4 - - + -
496A VAL* 3.6 25.4 - - + -
497A LEU 2.7 12.1 + - - +
498A PHE* 3.9 10.3 - + + +
499A THR* 3.1 26.9 + - - -
500A ASN 4.7 0.5 + - - -
520A MET* 3.7 60.6 - - + -
523A ARG* 4.7 5.6 - - + -
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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