Contacts of the strand formed by residues 465 - 470 (chain A) in PDB entry 2W93
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 TYR 465 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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377A PHE* 3.9 11.7 - + - -
437A ARG* 3.9 23.3 - - + -
438A VAL 2.8 19.3 + - - +
439A ILE* 4.0 15.5 - - + -
440A LEU* 2.9 28.8 + - - +
463A LYS 4.2 4.0 - - - -
464A PRO* 1.3 74.6 - - - +
466A LEU* 1.3 61.1 + - - +
467A PHE* 3.8 16.5 - + + -
527A PHE* 2.6 59.9 + + - -
528A ASN 3.3 12.8 + - - -
529A ASP 3.1 10.0 + - - -
530A ASN* 3.6 13.2 + - + -
534A ARG* 3.1 31.6 + - + -
536A ILE* 4.5 2.7 - - + -
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Residues in contact with LEU 466 (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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419A THR* 6.3 0.2 - - + -
422A THR* 4.1 7.9 - - + -
440A LEU* 3.8 28.3 - - + -
442A ILE* 5.9 0.2 - - + -
454A ILE* 4.2 26.7 - - + -
457A MET* 4.1 7.6 - - + -
464A PRO* 3.9 28.5 - - + +
465A TYR* 1.3 72.3 - - - +
467A PHE* 1.3 62.4 + - - +
468A VAL* 4.6 3.1 - - + -
499A LEU* 4.9 2.0 - - + -
533A ILE* 4.3 19.5 - - + -
534A ARG 2.8 19.8 + - - +
535A MET* 3.3 29.7 - - + +
536A ILE* 2.9 25.6 + - - +
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Residues in contact with PHE 467 (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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377A PHE* 4.1 25.6 - + - -
439A ILE* 4.2 5.4 - - + -
440A LEU 2.8 21.2 + - - +
441A PHE* 3.5 38.1 - + + -
442A ILE* 2.9 30.1 + - - +
465A TYR* 3.8 20.2 - - + -
466A LEU* 1.3 69.9 - - - +
468A VAL* 1.3 61.0 + - - +
469A LEU* 4.0 0.6 + - - -
518A TRP* 4.0 18.6 - + - -
522A THR* 4.5 10.3 - - + -
527A PHE* 4.2 10.1 - + - -
536A ILE* 3.4 49.6 - - + +
538A VAL* 4.0 11.7 - - + -
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Residues in contact with VAL 468 (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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442A ILE* 3.3 16.4 - - + +
443A GLY 4.6 0.7 - - - +
444A ASP* 4.2 10.3 - - - -
447A LEU* 4.0 31.9 - - + -
466A LEU* 4.1 12.1 - - + +
467A PHE* 1.3 76.9 - - - +
469A LEU* 1.3 62.6 + - - +
470A ASN 3.3 3.4 + - - +
495A HIS* 4.2 26.9 - - + +
535A MET* 4.2 21.3 - - + -
536A ILE 2.8 11.8 + - - +
537A GLU* 3.7 7.2 - - + +
538A VAL* 2.8 28.7 + - - +
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Residues in contact with LEU 469 (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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367A GLN* 4.2 1.8 - - - +
370A MET* 4.1 9.6 - - + -
371A TRP* 3.9 19.5 - - + -
390A THR* 4.0 14.8 - - - +
391A SER* 3.2 27.4 - - - +
441A PHE* 4.1 14.1 - - + -
442A ILE 2.9 15.8 + - - +
443A GLY* 4.0 5.9 - - - -
444A ASP* 3.1 22.9 + - - +
467A PHE 5.0 1.1 - - - +
468A VAL* 1.3 68.9 - - - +
470A ASN* 1.3 61.1 + - - +
471A ASN* 3.2 11.1 + - - +
538A VAL* 3.7 30.5 - - + -
540A LEU* 3.9 22.7 - - + -
600A TPP 4.8 4.7 - - - +
601A MG 4.1 0.3 - - - -
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Residues in contact with ASN 470 (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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444A ASP* 3.5 10.2 - - - +
468A VAL 3.3 1.8 + - - +
469A LEU* 1.3 69.3 - - - +
471A ASN* 1.3 59.0 + - - +
472A ASP* 3.1 20.4 + - - +
493A TRP 5.2 2.8 + - - -
495A HIS* 3.9 14.9 - - + -
537A GLU* 2.9 32.1 + - + +
538A VAL 2.7 16.1 + - - +
539A MET* 3.7 24.8 - - - +
540A LEU* 3.0 26.2 + - - +
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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