Contacts of the strand formed by residues 375 - 381 (chain A) in PDB entry 4I2C
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 LEU 375 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366A THR* 3.5 29.6 - - + +
369A TRP* 3.5 5.8 + - + -
370A LYS* 3.8 41.3 - - + +
373A GLY 3.7 2.2 - - - -
374A LEU* 1.3 74.6 - - - +
376A LEU* 1.3 62.5 + - - +
377A TYR 3.2 26.2 - - - +
378A CYS* 3.5 26.2 - - + -
406A LEU* 4.2 8.1 - - + -
407A ILE 4.1 0.7 - - - -
408A LEU* 4.2 16.4 - - + -
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Residues in contact with LEU 376 (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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291A ALA* 5.0 1.6 - - - +
295A TYR* 3.6 44.6 + - + +
373A GLY 4.9 3.4 - - - +
374A LEU 4.5 1.6 - - - +
375A LEU* 1.3 78.1 - - - +
377A TYR* 1.3 62.0 + - - +
407A ILE* 2.9 16.4 + - + +
408A LEU 4.0 4.3 - - - -
409A LYS* 3.9 41.5 - - + +
428A TRP* 3.8 29.6 - - + -
430A ALA* 4.0 11.0 - - + -
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Residues in contact with TYR 377 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A PHE* 3.6 27.6 - + - -
287A GLN* 4.1 11.7 - - + -
288A MET* 3.4 53.8 + - + +
291A ALA* 3.9 17.7 - - + -
375A LEU* 3.2 14.6 - - - +
376A LEU* 1.3 77.5 - - - +
378A CYS* 1.3 66.6 + - - +
379A ASP* 3.6 23.1 + - + +
405A PHE* 3.7 21.5 - - + -
406A LEU* 3.4 3.8 - - - -
407A ILE* 3.0 42.9 + - + -
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Residues in contact with CYS 378 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366A THR* 3.7 22.7 - - - -
375A LEU* 3.5 22.0 - - + -
377A TYR* 1.3 87.3 - - - +
379A ASP* 1.3 60.8 + - - +
380A ILE* 3.7 22.0 - - - -
405A PHE 3.7 5.6 - - - -
406A LEU* 3.4 19.7 - - - -
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Residues in contact with ASP 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A MET* 4.3 11.8 - - - +
377A TYR* 3.6 27.5 + - + +
378A CYS* 1.3 74.7 - - - +
380A ILE* 1.4 69.5 + - - +
381A LEU* 4.0 14.9 + - - +
404A CYS* 3.1 3.5 - - - -
405A PHE* 2.9 52.7 + - + +
4C A 5.9 0.2 + - - -
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Residues in contact with ILE 380 (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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362A LEU* 4.3 8.3 - - + +
363A HIS* 3.6 35.0 - - + +
366A THR* 3.6 23.6 - - - +
378A CYS* 3.7 19.7 - - - -
379A ASP* 1.4 78.6 + - - +
381A LEU* 1.3 66.2 + - - +
382A GLU* 3.7 24.7 + - - +
402A GLN* 4.3 13.5 - - + +
403A LYS 3.5 8.5 - - - +
404A CYS* 3.8 12.6 - - + -
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Residues in contact with LEU 381 (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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379A ASP* 4.0 15.7 + - - +
380A ILE* 1.3 77.0 - - - +
382A GLU* 1.3 67.7 - - - +
401A PHE 4.4 0.8 - - - +
402A GLN* 3.4 4.3 - - - +
403A LYS* 2.7 48.8 + - + +
405A PHE* 3.5 35.9 - - + -
4C A 5.3 3.6 - - + -
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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