Contacts of the helix formed by residues 343 - 352 (chain B) in PDB entry 2WSC
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 343 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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339B ALA* 4.1 1.4 - - - +
340B SER 3.4 5.8 + - - +
342B GLY* 1.3 75.3 - - - +
344B ILE* 1.4 59.5 + - + +
346B SER* 3.7 5.1 + - - -
347B LEU* 3.5 16.7 + - + +
383B MET* 4.1 21.7 - - + -
1755B CLA 4.2 34.4 - - + +
1756B CLA 3.3 53.6 - - + +
1777B BCR 4.4 25.8 - - + -
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Residues in contact with ILE 344 (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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340B SER 2.6 41.9 + - - +
341B LEU* 3.5 10.1 - - + +
343B VAL* 1.4 69.3 - - + +
345B THR* 1.3 57.1 + - - +
346B SER 3.1 2.7 - - - -
347B LEU* 3.7 10.3 - - + -
348B VAL* 2.7 35.0 + - + +
1743B CLA 3.8 16.6 - - + -
1748B CLA 3.6 39.7 - - + +
1754B CLA 4.3 12.6 - - + -
1756B CLA 4.3 22.4 - - + +
1758B CLA 3.5 32.1 - - + -
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Residues in contact with THR 345 (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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341B LEU* 2.2 40.1 + - - +
342B GLY* 3.7 4.3 + - - -
343B VAL 3.5 0.4 - - - -
344B ILE* 1.3 71.8 - - - +
346B SER* 1.3 58.1 + - - +
348B VAL* 3.6 4.2 - - - +
349B ALA* 3.3 14.6 + - - +
375B HIS* 3.1 25.1 - - - +
378B ILE* 4.2 3.8 - - + -
379B ALA* 3.6 30.7 + - + +
382B ILE* 5.2 2.4 - - - +
1758B CLA 3.5 50.2 - - + +
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Residues in contact with SER 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342B GLY 3.8 5.5 + - - -
343B VAL* 3.7 8.2 + - - -
345B THR* 1.3 78.5 - - - +
347B LEU* 1.3 56.1 + - - +
348B VAL 3.2 1.6 - - - -
349B ALA* 3.3 1.1 - - - +
350B GLN* 2.4 65.9 + - - +
375B HIS 3.9 5.8 - - - -
376B GLN* 3.2 20.2 + - - -
379B ALA* 4.7 3.4 - - - -
1755B CLA 3.1 20.7 + - - -
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Residues in contact with LEU 347 (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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343B VAL 3.5 7.9 + - - +
344B ILE* 3.6 21.3 - - + +
346B SER* 1.3 74.1 - - - +
348B VAL* 1.3 58.3 + - - +
350B GLN* 4.9 2.2 - - + -
351B HIS* 2.6 81.3 + - + +
1747B CLA 4.8 9.2 - - + +
1748B CLA 3.4 33.5 - - + +
1755B CLA 5.1 1.8 + - - -
1756B CLA 3.4 54.7 - - + +
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Residues in contact with VAL 348 (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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344B ILE* 2.7 23.4 + - + +
345B THR 3.6 10.8 - - - +
347B LEU* 1.3 73.0 - - - +
349B ALA* 1.3 63.0 + - + +
351B HIS* 3.6 1.2 - - - +
352B MET* 2.7 41.9 + - + +
375B HIS* 4.4 5.6 - - + -
1743B CLA 4.8 1.6 - - + -
1748B CLA 3.5 33.4 - - + +
1758B CLA 3.4 63.0 - - + -
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Residues in contact with ALA 349 (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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345B THR 3.3 9.9 - - - +
346B SER* 2.9 5.9 + - - +
348B VAL* 1.3 81.5 - - + +
350B GLN* 1.3 56.9 + - - +
352B MET* 4.0 13.0 - - - +
353B TYR 4.6 2.1 + - - -
372B TYR* 3.0 35.5 - - - +
375B HIS* 3.2 44.0 - - + +
376B GLN* 5.3 1.1 - - + -
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Residues in contact with GLN 350 (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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346B SER* 2.4 51.2 + - - +
347B LEU* 4.8 2.7 - - - +
349B ALA* 1.3 67.7 - - - +
351B HIS* 1.3 61.3 + - + +
352B MET 3.5 0.2 - - - -
353B TYR* 2.7 42.1 - - + +
372B TYR* 3.5 21.5 - - + +
376B GLN* 3.8 2.8 + - - -
1755B CLA 3.4 18.4 - - - +
1756B CLA 3.4 26.1 - - + +
1767B CLA 2.9 53.0 + - + +
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Residues in contact with HIS 351 (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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347B LEU* 2.6 70.2 + - + +
348B VAL 3.7 1.6 - - - +
350B GLN* 1.3 75.6 - - + +
352B MET* 1.3 55.6 + - - +
353B TYR 2.7 22.9 + - - +
354B SER* 4.7 0.2 - - - -
355B LEU* 3.1 20.5 + - + +
1747B CLA 3.3 30.2 + + - +
1748B CLA 4.0 5.1 - - + +
1756B CLA 2.6 73.7 + + + -
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Residues in contact with MET 352 (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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348B VAL* 2.7 34.7 + - + +
349B ALA* 4.1 10.1 - - - +
350B GLN 3.5 0.6 - - - -
351B HIS* 1.3 71.0 - - - +
353B TYR* 1.3 55.9 + - - +
355B LEU 3.9 8.3 - - - -
356B PRO* 3.3 28.8 - - + +
357B ALA 5.9 0.7 - - - +
358B TYR* 5.4 7.0 - - + -
361B ILE* 6.1 1.3 - - + -
368B GLN* 3.4 14.4 + - - +
371B LEU* 3.8 24.9 - - + +
372B TYR* 6.3 0.7 - - - -
375B HIS* 5.1 6.3 - - - -
1748B CLA 4.7 18.6 - - + -
1758B CLA 2.6 53.2 - - + +
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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