Contacts of the strand formed by residues 368 - 371 (chain A) in PDB entry 1W21
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 368 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A VAL* 3.0 37.3 + - + +
101A ASN 3.6 27.4 - - - -
102A SER* 4.6 0.9 - - - -
103A TRP* 3.2 50.5 - + + -
360A ALA* 3.3 5.4 - - - +
361A PHE* 2.8 45.3 + - + +
366A ASN* 4.2 8.0 + - - -
367A SER* 1.3 79.8 - - - +
369A LEU* 1.3 63.9 + - - +
370A GLY 4.2 0.2 + - - -
383A MET* 3.8 28.0 - - + +
384A LEU 3.4 6.3 - - - -
385A LYS* 3.5 45.1 - - + +
399A SER* 3.4 18.2 - - - -
401A GLN* 4.8 5.2 - - + -
2E NAG 4.9 6.1 - - + -
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Residues in contact with LEU 369 (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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324A LEU* 3.8 17.3 - - + -
326A SER* 4.3 5.4 - - - -
328A VAL* 3.9 19.5 - - + +
330A THR* 3.7 28.7 - - + -
359A PHE 5.2 0.2 - - - +
360A ALA* 3.5 25.4 - - + -
362A LEU* 4.2 5.6 - - + -
368A TRP* 1.3 76.8 - - - +
370A GLY* 1.3 59.5 + - - +
382A GLU 3.9 0.7 - - - +
383A MET* 3.5 4.5 - - - -
384A LEU* 2.8 48.0 + - + +
386A VAL* 3.8 29.8 - - + -
389A ALA* 3.9 21.1 - - + -
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Residues in contact with GLY 370 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A ARG* 5.0 1.9 + - - -
330A THR* 3.4 17.5 - - - +
358A GLY* 5.8 0.5 - - - -
359A PHE* 3.6 19.3 + - - +
368A TRP 4.2 0.2 + - - -
369A LEU* 1.3 75.8 - - - +
371A ARG* 1.3 65.7 + - - +
381A TYR* 3.2 19.2 + - - -
382A GLU 3.4 7.4 - - - -
383A MET* 3.7 15.4 - - - +
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Residues in contact with ARG 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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307A ARG* 6.2 0.2 - - - +
328A VAL* 3.6 6.4 - - - +
329A LEU 2.9 26.6 + - - -
330A THR* 3.8 25.1 - - + +
334A ARG* 3.5 22.7 - - - +
337A ASP* 2.9 25.6 + - - -
369A LEU* 6.3 0.2 - - + -
370A GLY* 1.3 78.2 - - - +
372A THR* 1.3 67.1 - - - +
375A LYS* 6.2 1.6 - - - +
381A TYR* 3.4 14.4 - - - -
382A GLU* 2.8 60.1 + - + +
384A LEU* 3.7 23.7 - - + +
1485A MAN 5.3 1.6 + - - -
1486A MAN 2.7 29.7 + - - -
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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