Contacts of the strand formed by residues 417 - 422 (chain A) in PDB entry 2WNW
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 ARG 417 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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389A TYR* 2.9 34.2 + - - -
390A ASP* 2.9 32.3 + - - +
392A LEU* 4.3 8.9 - - - +
393A LEU* 4.1 17.8 - - + +
411A ASN* 3.4 28.7 - - - +
413A ASP* 3.0 28.6 + - - +
415A GLN* 3.4 11.0 + - - +
416A GLU* 1.3 85.4 - - - +
418A ARG* 1.3 64.1 + - - +
431A THR* 3.4 2.8 - - - +
432A LEU* 2.8 36.9 + - - +
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Residues in contact with ARG 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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32A GLU* 2.8 45.6 + - - +
389A TYR* 2.6 31.4 + - - -
393A LEU* 3.6 2.5 - - - +
416A GLU* 5.7 2.5 - - - +
417A ARG* 1.3 79.8 - - - +
419A CYS* 1.3 64.4 + - - +
430A LEU 3.3 6.1 - - - +
431A THR* 3.6 25.4 - - + +
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Residues in contact with CYS 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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32A GLU* 3.2 13.7 - - - +
34A ILE* 3.7 30.1 - - + -
389A TYR* 4.1 1.1 - - + -
393A LEU* 3.9 15.0 - - + -
409A VAL* 4.7 4.0 - - - -
418A ARG* 1.3 79.1 - - - +
420A ARG* 1.3 63.2 + - - +
421A VAL* 4.8 4.5 - - - -
429A ALA* 3.5 2.6 - - - +
430A LEU* 2.8 58.2 + - - +
432A LEU* 4.3 13.2 - - - -
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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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26A ARG* 4.7 1.0 - - - +
27A GLN* 3.6 25.1 + - - +
29A ASP* 2.6 54.6 + - - -
31A SER* 2.9 21.2 + - - +
32A GLU* 2.8 17.4 + - + +
33A LEU* 3.5 24.2 - - + +
34A ILE* 3.0 21.9 + - - -
419A CYS* 1.3 78.7 - - - +
421A VAL* 1.3 64.2 + - - +
422A LEU 3.2 2.1 + - - -
427A GLU* 2.8 58.8 + - + +
428A ILE 3.6 4.9 - - - +
429A ALA* 4.2 15.0 - - + -
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Residues in contact with VAL 421 (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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23A PHE* 4.2 7.9 - - + -
34A ILE* 3.4 11.7 - - + +
36A VAL* 4.2 15.7 - - + -
407A LEU* 3.7 34.3 - - + -
409A VAL* 5.2 0.9 - - + -
419A CYS* 4.8 7.4 - - - -
420A ARG* 1.3 70.3 - - - +
422A LEU* 1.3 58.7 + - - +
423A ASP 4.0 0.5 + - - -
426A LYS 4.0 0.2 - - - +
427A GLU* 3.1 6.8 - - - -
428A ILE* 3.0 38.8 + - + +
430A LEU* 3.8 28.7 - - + -
440A LEU* 4.0 16.2 - - + -
442A TRP* 4.6 2.9 - - + -
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Residues in contact with LEU 422 (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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26A ARG* 3.6 49.4 - - + +
33A LEU* 4.0 26.9 - - + -
34A ILE 2.9 11.7 + - - +
35A SER* 3.6 13.9 - - - +
36A VAL* 2.9 31.2 + - - +
420A ARG 3.2 1.0 + - - +
421A VAL* 1.3 72.7 - - - +
423A ASP* 1.3 58.6 + - - +
424A GLY* 3.4 23.6 - - - +
426A LYS 3.3 15.9 - - - +
427A GLU* 3.8 9.2 - - + +
247B ASP* 6.0 2.2 - - - +
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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