Contacts of the strand formed by residues 369 - 373 (chain A) in PDB entry 1P22
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 ILE 369 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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361A VAL* 3.7 25.1 - - + -
362A THR 3.1 15.3 - - - +
363A CYS* 3.7 13.0 - - + -
367A ARG 5.6 0.2 - - - +
368A SER* 1.3 82.2 - - - +
370A ALA* 1.3 63.4 + - - +
371A VAL* 4.6 0.7 - - + -
385A VAL* 3.2 7.2 - - - +
386A LEU* 2.8 53.2 + - + +
389A HIS* 4.0 14.6 - - + -
393A VAL* 4.0 3.6 - - + -
396A VAL* 4.0 4.5 - - + -
403A ILE* 4.9 1.1 - - + -
405A SER* 3.4 33.7 - - - +
415A TRP* 3.7 21.5 - - + +
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Residues in contact with ALA 370 (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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345A HIS* 3.4 29.6 - - + +
346A HIS* 3.9 1.5 + - - +
361A VAL* 3.6 1.6 - - - -
362A THR* 2.7 54.0 + - + +
369A ILE* 1.3 74.1 - - - +
371A VAL* 1.3 63.8 + - - +
372A TRP* 3.4 12.2 - - + +
382A LEU* 3.7 10.8 - - + -
384A ARG 3.4 4.3 - - - -
385A VAL* 4.4 0.4 - - + -
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Residues in contact with VAL 371 (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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359A MET* 4.3 9.0 - - - -
360A MET 3.6 6.7 - - - +
361A VAL* 4.3 10.8 - - + -
369A ILE* 4.6 0.2 - - + -
370A ALA* 1.3 76.0 - - - +
372A TRP* 1.3 58.1 + - - +
382A LEU* 3.7 1.3 - - - -
383A ARG* 2.6 76.1 + - + +
384A ARG 2.7 19.4 + - - +
386A LEU* 4.5 14.1 - - + -
403A ILE* 3.6 26.5 - - + -
420A CYS* 4.3 13.9 - - - -
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Residues in contact with TRP 372 (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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329A VAL* 5.3 5.8 - - + +
343A LEU* 4.0 29.4 - - + -
345A HIS* 3.3 49.6 - + + -
346A HIS* 5.0 2.0 - + - -
359A MET* 3.1 5.2 - - - +
360A MET* 2.7 60.1 + - + +
362A THR* 2.9 28.6 - - + +
370A ALA* 3.4 15.9 - - + +
371A VAL* 1.3 74.5 - - - +
373A ASP* 1.3 58.2 + - - +
374A MET* 4.8 0.4 - - + -
380A ILE* 3.8 30.5 - - + -
381A THR* 3.1 10.1 - - - +
382A LEU* 3.6 35.9 - - + -
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Residues in contact with ASP 373 (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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358A GLY 3.6 7.6 - - - +
359A MET* 3.9 2.5 - - + -
371A VAL 4.2 0.2 - - - -
372A TRP* 1.3 71.9 - - - +
374A MET* 1.3 62.0 + - - +
375A ALA* 3.9 1.4 + - - +
381A THR* 3.2 31.1 + - - +
383A ARG* 2.5 58.2 + - - +
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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