Contacts of the strand formed by residues 464 - 468 (chain B) in PDB entry 1GPU
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 ILE 464 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376B LEU* 5.8 0.2 - - + -
425B MET* 3.8 2.6 - - - +
436B LYS* 5.8 3.4 - - + +
437B PRO 3.3 9.8 + - - +
438B TYR* 3.0 23.8 - - + +
439B GLY 2.8 26.2 + - - -
462B PRO 3.9 8.3 - - - +
463B VAL* 1.3 81.2 - - - +
465B TRP* 1.3 69.2 + - - +
466B VAL* 4.5 4.9 - - + -
511B TYR* 4.7 8.3 - - + -
514B SER* 3.8 29.6 - - - +
515B LEU* 3.5 33.2 - - + -
522B SER* 3.4 8.3 - - - +
524B ILE* 3.9 26.9 - - + -
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Residues in contact with TRP 465 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418B GLU* 3.5 15.5 - - + -
421B MET* 3.5 25.1 - - + -
422B GLY* 3.4 25.7 - - - -
425B MET* 3.6 15.3 - - + +
439B GLY 3.4 5.8 - - - -
441B THR* 3.9 17.0 - - + -
446B VAL* 3.9 28.7 - - + -
449B ALA* 3.5 22.9 - - + -
453B VAL* 3.8 30.3 - - + +
456B SER* 5.1 1.8 + - - -
463B VAL* 4.1 15.3 - - + +
464B ILE* 1.3 77.9 - - - +
466B VAL* 1.3 61.2 + - - +
467B ALA 3.3 2.9 + - - +
496B ILE* 6.1 0.7 - - + -
521B PRO* 6.0 0.9 - - + -
522B SER 2.8 20.5 + - - +
523B ILE* 3.7 23.3 - - + -
524B ILE* 2.8 31.4 + - - +
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Residues in contact with VAL 466 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362B SER* 3.8 4.9 - - - +
387B ASN 4.6 1.6 - - - +
389B THR* 3.8 22.9 - - + -
438B TYR* 3.7 35.9 - - + -
439B GLY 2.8 11.9 + - - +
440B GLY* 3.2 18.5 - - - -
441B THR* 3.2 7.5 + - - +
464B ILE* 4.5 6.5 - - + -
465B TRP* 1.3 71.4 - - - +
467B ALA* 1.3 57.6 + - - +
468B THR* 3.6 11.1 + - + +
511B TYR* 3.5 22.4 - - + +
524B ILE* 4.1 4.3 - - + -
526B LEU* 3.5 26.2 - - + -
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Residues in contact with ALA 467 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441B THR 3.2 6.7 - - - -
443B LEU* 3.6 39.5 - - + +
446B VAL* 3.9 13.0 - - + -
465B TRP 3.3 2.2 + - - +
466B VAL* 1.3 70.0 - - - +
468B THR* 1.3 59.6 + - - +
523B ILE* 4.2 9.6 - - + -
524B ILE 3.0 15.3 + - - +
525B ALA* 3.3 2.6 - - - -
526B LEU* 2.8 28.4 + - - +
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Residues in contact with THR 468 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359B ARG* 4.0 15.0 - - + -
387B ASN* 2.8 55.6 + - + +
441B THR 3.2 4.4 + - - -
442B PHE* 3.3 4.2 - - - -
443B LEU 2.9 19.2 + - - -
466B VAL* 4.3 4.7 - - + +
467B ALA* 1.3 73.3 - - - +
469B HIS* 1.3 94.9 + - - +
526B LEU* 3.4 25.1 - - + -
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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