Contacts of the strand formed by residues 477 - 485 (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 ARG 477 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A PRO* 5.1 1.1 - - - -
13A ARG* 4.9 5.4 - - - +
17A GLU 5.2 8.7 - - - +
18A GLU* 4.2 15.7 - - - +
19A THR* 5.6 2.5 - - - +
133A LYS* 3.4 47.8 - - - +
472A ILE 3.6 1.2 - - - +
473A MET* 3.7 7.3 - - - +
474A ASN* 2.9 68.6 + - - +
475A LYS* 3.8 17.4 - - - +
476A GLY* 1.3 80.7 - - - +
478A LEU* 1.3 66.3 + - - +
479A LEU* 3.2 27.0 + - - +
502A ASP* 4.4 9.5 + - - +
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Residues in contact with LEU 478 (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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7A ILE 4.2 10.5 - - - +
9A PRO* 4.2 15.2 - - + +
18A GLU* 5.1 0.6 + - - -
19A THR* 3.3 52.6 + - + +
21A VAL* 4.0 25.6 - - + -
471A LEU* 4.0 22.0 - - + -
472A ILE 3.4 7.9 - - - +
473A MET* 3.5 24.9 - - - -
477A ARG* 1.3 76.5 + - - +
479A LEU* 1.3 65.1 + - - +
480A LYS* 3.5 4.5 - - - +
622A LEU* 3.8 15.0 - - + -
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Residues in contact with LEU 479 (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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472A ILE* 2.9 32.6 + - + +
474A ASN* 4.1 18.6 - - + +
477A ARG* 3.2 31.0 + - - +
478A LEU* 1.3 74.6 - - - +
480A LYS* 1.3 65.2 + - + +
500A THR* 5.2 0.2 - - - +
502A ASP* 3.9 31.4 - - + +
503A PHE* 4.1 28.3 - - + +
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Residues in contact with LYS 480 (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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470A TYR* 4.2 24.7 + - + +
471A LEU* 3.6 0.3 - - - +
472A ILE* 2.7 46.2 + - + +
478A LEU* 3.5 4.1 - - - +
479A LEU* 1.3 85.9 - - + +
481A ALA* 1.3 78.3 + - - +
482A GLY* 5.0 1.1 - - - +
497A LEU* 5.0 16.2 - - + +
503A PHE* 6.3 2.7 - - + -
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Residues in contact with ALA 481 (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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21A VAL* 4.0 26.5 - - + -
61A MET* 4.0 12.4 - - + +
469A THR* 6.0 1.1 - - + -
470A TYR* 3.3 15.5 - - - +
471A LEU* 4.0 16.4 - - + -
478A LEU* 6.1 1.1 - - + -
480A LYS* 1.3 88.0 - - - +
482A GLY* 1.3 57.5 + - - +
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Residues in contact with GLY 482 (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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61A MET* 3.8 13.5 - - - +
469A THR* 3.8 2.3 - - - +
470A TYR* 3.2 48.6 + - - +
480A LYS* 5.6 1.3 - - - -
481A ALA* 1.3 74.5 - - - +
483A ARG* 1.3 70.3 + - - +
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Residues in contact with ARG 483 (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 GLU* 3.4 20.0 + - - +
24A ALA 5.1 2.6 + - - -
25A HIS* 4.2 7.3 + - - -
59A ASN* 3.4 53.9 + - + +
60A HIS 4.5 1.6 + - - -
61A MET* 3.3 33.5 - - + +
467A TYR* 3.2 46.9 + - + -
468A TYR 3.3 8.5 - - - -
469A THR* 3.0 22.7 + - - -
470A TYR* 3.4 10.2 + - - -
482A GLY* 1.3 77.4 - - - -
484A GLN* 1.3 62.9 + - - +
485A VAL* 4.0 5.6 + - + +
495A LEU* 5.4 0.9 - - - +
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Residues in contact with GLN 484 (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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453A PHE* 4.2 19.7 - - + -
467A TYR* 3.3 4.7 - - - -
468A TYR* 3.0 48.5 + - + +
470A TYR* 4.2 6.0 - - + -
483A ARG* 1.3 73.7 - - - +
485A VAL* 1.3 82.1 + - - +
493A VAL* 4.0 23.3 - - + +
494A VAL 3.1 26.9 + - - -
495A LEU* 3.2 26.3 - - + +
496A PRO* 4.9 2.2 - - - +
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Residues in contact with VAL 485 (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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59A ASN* 5.6 8.1 - - - +
466A ARG 3.7 7.6 - - - +
467A TYR* 4.5 2.9 - - + +
483A ARG* 4.0 6.1 + - + +
484A GLN* 1.3 96.0 + - - +
486A ARG* 1.3 60.8 + - - +
487A GLU* 4.5 12.1 - - - +
490A GLN* 4.9 0.5 + - - -
493A VAL* 4.3 7.3 - - - +
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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