Contacts of the strand formed by residues 382 - 390 (chain B) in PDB entry 2WJX
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 GLY 382 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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251B GLN* 3.1 16.3 + - - -
378B LEU* 5.2 2.7 - - - -
379B LYS* 3.1 37.9 + - - +
381B ASN* 1.3 80.2 - - - +
383B PRO* 1.3 74.0 - - - +
384B ARG* 4.4 2.9 - - - +
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Residues in contact with PRO 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242B PHE* 3.8 20.9 - - + -
243B THR* 3.2 37.0 - - + -
248B LEU* 4.0 7.6 - - + -
251B GLN* 3.3 14.6 - - - +
376B MET* 4.1 5.9 - - + +
377B GLU 3.6 7.4 - - - +
378B LEU* 5.2 1.3 - - + -
382B GLY* 1.3 82.7 - - - +
384B ARG* 1.3 71.5 + - - +
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Residues in contact with ARG 384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376B MET* 3.4 11.1 - - - +
377B GLU* 3.1 31.0 + - + +
379B LYS* 3.8 41.4 - - + +
381B ASN* 6.5 0.2 - - - -
382B GLY 4.4 4.9 - - - +
383B PRO* 1.3 86.2 - - - +
385B LYS* 1.2 61.0 + - - +
386B ILE* 3.6 4.9 + - + +
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Residues in contact with LYS 385 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264B ASP* 4.0 9.3 + - - +
374B ASN* 3.0 42.3 + - + +
375B ILE 3.3 8.5 - - - +
376B MET* 3.9 11.8 - - + +
384B ARG* 1.2 71.0 - - - +
386B ILE* 1.3 61.8 + - - +
387B GLY 3.6 25.8 - - - +
388B TYR* 4.4 13.0 - - - +
398B THR* 4.3 20.0 - - + +
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Residues in contact with ILE 386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142B TYR* 4.1 23.8 - - + +
143B TYR* 4.0 5.6 - - - +
375B ILE* 2.8 35.3 + - + +
377B GLU* 3.2 59.2 - - + +
384B ARG* 4.1 3.6 - - + +
385B LYS* 1.3 77.8 - - - +
387B GLY* 1.3 59.4 - - - +
395B MET* 4.2 4.7 - - + -
397B VAL* 3.6 12.3 - - + +
398B THR* 2.8 25.6 + - - +
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Residues in contact with GLY 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375B ILE* 2.9 29.6 + - - -
385B LYS* 3.5 12.9 - - - +
386B ILE* 1.3 83.9 - - - +
388B TYR* 1.3 66.0 + - - +
395B MET* 5.3 0.2 - - - -
396B VAL 3.1 14.4 - - - -
397B VAL* 4.2 0.4 - - - -
398B THR* 3.6 13.5 + - - -
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Residues in contact with TYR 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372B THR* 3.6 26.2 - - + -
373B ILE 3.3 13.0 - - - +
374B ASN* 4.2 8.5 - - - +
375B ILE* 3.5 7.9 - - - +
385B LYS* 4.4 13.0 - - - -
387B GLY* 1.3 78.8 - - - +
389B TRP* 1.3 64.7 + - - +
390B SER* 4.9 7.6 - - - -
393B ASP* 5.3 5.0 + - - -
394B LYS 3.6 0.2 - - - +
395B MET* 3.4 2.4 - - - -
396B VAL* 2.7 75.1 + - + +
397B VAL 6.0 0.2 - - - -
398B THR* 4.7 6.3 - - - -
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Residues in contact with TRP 389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131B ASP 5.0 0.7 - - - -
134B GLY* 3.4 26.0 + - - -
135B ALA* 3.5 31.6 - - + +
138B SER* 2.9 35.9 + - - -
371B TYR* 3.5 35.0 - + - -
372B THR* 3.4 6.1 - - - -
373B ILE* 2.8 37.8 + - + +
375B ILE* 4.7 7.2 - - + -
388B TYR* 1.3 78.9 - - - +
390B SER* 1.3 69.8 + - - +
391B GLU* 3.5 28.5 - - + -
394B LYS* 3.2 45.6 - - + +
395B MET* 3.6 3.6 - - + -
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Residues in contact with SER 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370B ASN* 5.9 2.9 - - - -
371B TYR 3.7 15.9 - - - -
372B THR* 4.7 6.1 - - - -
388B TYR* 4.9 7.1 - - - -
389B TRP* 1.3 86.1 - - - +
391B GLU* 1.3 65.8 + - - +
392B VAL* 3.3 14.2 - - - +
393B ASP* 3.2 28.2 + - - +
394B LYS* 2.8 25.2 + - - -
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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