Contacts of the strand formed by residues 492 - 498 (chain A) in PDB entry 2WIN
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 LEU 492 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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437A SER* 5.5 0.4 - - - +
452A ASN* 3.6 39.3 - - + +
453A PHE 3.2 12.3 - - - +
454A LEU* 4.4 14.8 - - + +
490A GLN* 3.5 3.7 - - - +
491A ASP* 1.3 82.4 - - + +
493A VAL* 1.3 71.3 + - - +
494A VAL* 5.2 7.2 - - + +
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Residues in contact with VAL 493 (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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452A ASN* 3.8 0.2 - - - -
453A PHE* 3.0 53.1 + - + +
468A TYR* 4.0 17.7 - - + +
484A GLN* 4.0 22.9 - - + +
485A VAL 4.3 9.0 - - - +
486A ARG* 4.5 4.9 - - + -
490A GLN* 3.3 36.8 - - + +
491A ASP 6.0 0.2 - - - -
492A LEU* 1.3 81.4 - - - +
494A VAL* 1.3 63.2 + - - +
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Residues in contact with VAL 494 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450A ASN* 3.8 38.8 - - + +
451A VAL 3.3 4.3 - - - +
452A ASN* 3.9 14.4 - - - +
484A GLN* 3.1 16.5 + - - -
492A LEU* 5.2 8.3 - - + +
493A VAL* 1.3 77.4 - - - +
495A LEU* 1.3 66.1 + - - +
496A PRO* 3.4 12.2 - - + +
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Residues in contact with LEU 495 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449A LEU 3.0 10.9 - - - +
451A VAL* 2.8 30.7 + - + +
453A PHE* 3.5 30.3 - - + -
470A TYR* 3.7 51.8 - - + +
483A ARG 5.4 0.9 - - - +
484A GLN* 3.2 21.8 - - - +
494A VAL* 1.3 74.9 - - - +
496A PRO* 1.3 65.8 - - + +
497A LEU* 2.8 28.8 + - + +
509A LEU* 5.6 1.8 - - + -
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Residues in contact with PRO 496 (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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448A THR* 4.2 9.9 - - - +
449A LEU 4.0 4.3 - - - +
450A ASN* 5.1 5.4 - - - +
484A GLN* 4.9 2.2 - - - +
494A VAL* 3.4 13.9 - - + +
495A LEU* 1.3 91.2 - - + +
497A LEU* 1.3 62.0 + - - +
498A SER* 3.6 6.5 + - - -
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Residues in contact with LEU 497 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448A THR* 4.0 1.3 + - - -
449A LEU* 2.9 38.2 + - + +
451A VAL* 4.1 19.3 - - + -
470A TYR* 5.2 10.5 - - + +
472A ILE* 3.9 30.3 - - + -
480A LYS* 5.0 17.3 - - + +
495A LEU* 2.8 22.3 + - + +
496A PRO* 1.3 69.0 - - - +
498A SER* 1.3 73.4 + - - +
499A ILE* 3.5 7.8 + - + +
503A PHE* 4.4 11.2 - - + -
507A PHE* 4.1 19.3 - - + -
509A LEU* 5.1 5.2 - - + -
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Residues in contact with SER 498 (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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447A GLU 4.0 7.2 - - - -
448A THR* 4.4 9.7 + - - +
496A PRO 3.6 6.2 + - - -
497A LEU* 1.3 75.6 - - - +
499A ILE* 1.3 61.5 + - - +
500A THR* 3.8 7.5 + - - +
503A PHE* 3.4 20.6 - - - -
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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