Contacts of the helix formed by residues 411 - 420 (chain A) 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 ALA 411 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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407A ILE 3.1 0.6 + - - -
408A VAL 2.6 13.5 + - - +
409A GLY 2.5 4.9 + - - -
410A ALA* 1.3 76.0 - - - +
412A ALA* 1.3 68.3 + - - +
413A HIS 3.1 0.9 - - - -
414A ALA* 2.8 16.3 + - - +
415A ALA 3.0 8.3 + - - -
556A LEU* 3.3 21.5 - - + -
560A VAL* 3.4 14.9 - - + +
598A VAL* 5.1 0.9 - - + -
1806A BCR 3.1 30.3 - - + -
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Residues in contact with ALA 412 (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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408A VAL 2.9 6.7 + - - +
409A GLY* 2.7 11.6 + - - +
411A ALA* 1.3 69.2 - - - +
413A HIS* 1.3 55.6 + - + +
415A ALA* 2.7 28.9 + - - +
416A ILE* 2.8 15.2 + - + +
577A PHE* 4.2 5.1 - - + -
598A VAL* 3.3 42.8 - - + +
1785A CLA 4.0 26.5 - - + -
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Residues in contact with HIS 413 (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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355A HIS* 3.1 34.4 + + - +
358A LEU* 2.9 52.5 - - + +
359A SER* 3.6 7.2 - - - -
409A GLY 2.9 10.7 + - - +
412A ALA* 1.3 76.5 - - - +
414A ALA* 1.3 56.5 + - - +
416A ILE* 3.0 31.8 - - + +
417A PHE 2.9 20.3 + - - -
1785A CLA 2.7 70.9 + + + -
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Residues in contact with ALA 414 (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 SER* 3.1 25.5 + - - +
410A ALA 4.2 2.9 - - - +
411A ALA* 2.8 16.1 + - - +
413A HIS* 1.3 67.9 - - - +
415A ALA* 1.3 52.4 + - - +
417A PHE* 2.8 10.7 + - - +
418A MET* 2.5 43.8 + - + +
560A VAL* 4.7 11.7 - - + -
1776A CLA 6.2 1.3 - - + -
1805A BCR 4.1 18.8 - - + -
1806A BCR 5.2 5.2 - - + -
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Residues in contact with ALA 415 (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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411A ALA 3.0 4.0 + - - -
412A ALA* 2.7 20.6 + - - +
414A ALA* 1.3 71.1 - - - +
416A ILE* 1.3 54.0 + - - +
418A MET* 4.2 5.4 - - - -
419A VAL* 2.8 38.5 + - - +
560A VAL* 3.8 27.4 - - + +
563A ALA* 4.9 2.5 - - + -
577A PHE* 3.6 21.5 - - + -
594A ALA* 4.2 14.6 - - + +
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Residues in contact with ILE 416 (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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355A HIS* 2.4 42.6 - - + +
412A ALA* 2.8 16.7 + - + +
413A HIS* 3.0 50.7 - - + +
415A ALA* 1.3 72.1 - - - +
417A PHE* 1.3 54.1 + - - +
419A VAL* 5.0 0.2 - - - -
420A ARG* 2.4 54.7 + - - +
577A PHE* 4.1 30.1 - - + -
1785A CLA 3.9 23.6 - - + +
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Residues in contact with PHE 417 (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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347A TYR* 3.1 45.5 - + - -
349A ILE* 4.0 6.7 - - + -
353A SER* 4.4 0.9 - - - -
355A HIS* 4.5 2.2 - - - +
356A ALA* 3.1 39.3 - - + +
413A HIS 2.9 12.0 + - - +
414A ALA* 2.8 19.4 + - + +
416A ILE* 1.3 68.4 - - - +
418A MET* 1.3 82.3 + - + +
419A VAL 2.7 3.1 + - - -
420A ARG 2.9 11.5 + - - -
421A ASP* 2.7 37.9 - - - +
422A TYR* 3.2 32.5 + + - -
432A LEU* 4.9 7.6 - - + -
1805A BCR 5.0 12.6 - - + -
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Residues in contact with MET 418 (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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414A ALA* 2.5 25.0 + - + +
415A ALA* 3.8 1.6 - - - +
417A PHE* 1.3 83.6 - - + +
419A VAL* 1.3 58.4 + - - +
422A TYR* 3.0 12.1 + - - -
432A LEU* 4.6 22.7 - - + -
436A LEU* 4.5 23.8 - - + -
560A VAL* 3.3 25.8 - - + +
561A LEU* 4.2 8.1 - - + +
563A ALA* 3.4 17.7 - - + -
564A ARG* 2.8 34.5 - - + -
1776A CLA 4.4 23.1 - - + -
1805A BCR 5.8 7.4 - - + -
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Residues in contact with VAL 419 (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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415A ALA* 2.8 21.1 + - + +
416A ILE 4.4 1.3 - - - +
417A PHE 2.7 3.6 + - - -
418A MET* 1.3 71.6 - - - +
420A ARG* 1.3 70.6 + - + +
422A TYR* 3.8 6.8 - - - -
563A ALA* 3.5 29.8 - - + +
564A ARG* 3.0 26.2 + - - +
573A ALA* 5.0 15.3 - - + -
575A LEU 5.7 1.1 - - - +
576A GLY* 4.2 11.2 - - - +
577A PHE* 3.5 38.6 - - + +
594A ALA* 6.0 1.1 - - + -
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Residues in contact with ARG 420 (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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63A ASP* 4.7 9.3 + - - -
64A PHE 3.9 20.3 + - - -
65A ASP* 3.0 33.7 + - - +
355A HIS* 5.2 2.5 - - - +
416A ILE* 2.4 56.2 + - - +
417A PHE 2.9 4.8 + - - -
419A VAL* 1.3 87.3 - - + +
421A ASP* 1.3 82.3 + - - +
422A TYR* 3.6 10.1 - - - +
575A LEU 5.2 1.8 + - - -
576A GLY* 5.2 11.1 - - - -
577A PHE* 5.7 7.3 - - - +
1785A CLA 5.1 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