Contacts of the strand formed by residues 436 - 442 (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 LYS 436 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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338B LEU* 4.4 8.3 - - + -
373B LEU* 6.1 1.1 - - + -
375B GLU* 2.8 24.2 + - + +
376B LEU* 3.5 16.3 - - + +
377B ILE* 3.0 18.8 + - - -
434B ASN* 3.4 33.5 + - - +
435B TYR* 1.3 77.1 - - - +
437B PRO* 1.3 65.8 - - - +
462B PRO* 4.0 22.6 - - + +
464B ILE* 5.8 2.0 - - + +
514B SER 4.8 0.6 + - - -
515B LEU* 3.0 53.5 + - + +
516B GLU 4.8 0.6 + - - -
517B SER 3.0 21.4 + - - -
518B LYS* 5.0 2.4 - - - +
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Residues in contact with PRO 437 (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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377B ILE* 3.1 13.2 - - + +
414B TYR* 5.2 0.9 - - - +
425B MET* 3.5 43.9 - - + +
428B ILE* 3.9 29.4 - - + -
429B SER* 4.1 8.3 - - - +
435B TYR 3.3 10.3 - - - +
436B LYS* 1.3 89.0 - - + +
438B TYR* 1.3 61.2 + - - +
462B PRO 4.9 1.5 - - - +
463B VAL* 3.9 9.9 - - + -
464B ILE* 3.3 22.7 + - - +
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Residues in contact with TYR 438 (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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366B LEU* 3.5 28.5 - - + +
376B LEU* 3.6 35.7 - - + -
377B ILE 2.9 7.1 + - - +
378B GLY* 3.3 31.9 - - - -
379B GLY* 3.3 17.7 + - - -
389B THR* 2.6 45.1 + - + -
391B TRP* 3.3 19.4 - + - -
411B TYR* 4.6 0.2 - - - -
414B TYR* 4.8 2.9 + - - -
425B MET* 3.4 6.7 - - - +
437B PRO* 1.3 76.2 - - - +
439B GLY* 1.3 59.3 + - - +
464B ILE* 3.0 31.4 - - + +
466B VAL* 3.7 17.7 - - + -
511B TYR* 5.8 2.5 - + + -
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Residues in contact with GLY 439 (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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379B GLY 3.5 7.0 - - - -
414B TYR* 5.0 0.7 - - - -
421B MET* 3.8 21.4 - - - +
425B MET* 3.2 12.9 - - - -
438B TYR* 1.3 75.9 - - - +
440B GLY* 1.3 61.5 + - - -
441B THR 4.2 0.2 + - - -
464B ILE 2.8 8.5 + - - -
465B TRP* 3.4 9.4 - - - +
466B VAL* 2.8 26.0 + - - +
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Residues in contact with GLY 440 (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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379B GLY 2.9 16.8 + - - -
380B SER* 3.8 0.8 - - - +
381B ALA 2.9 27.0 + - - -
387B ASN* 2.8 15.8 - - - +
389B THR* 4.2 4.2 - - - +
421B MET* 3.5 3.8 - - - +
439B GLY* 1.3 74.8 - - - -
441B THR* 1.3 64.0 - - - -
466B VAL* 3.2 17.0 - - - -
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Residues in contact with THR 441 (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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381B ALA* 4.4 4.3 - - - +
383B LEU* 3.9 11.8 - - - +
387B ASN* 2.8 15.3 + - - +
418B GLU* 3.8 26.4 + - + +
421B MET* 4.4 2.5 - - - -
440B GLY* 1.3 77.8 - - - -
442B PHE* 1.3 80.3 + - - +
445B PHE* 4.0 4.9 - - - +
446B VAL* 3.7 24.2 - - + +
465B TRP* 3.9 19.5 - - + -
466B VAL 3.2 2.4 + - - +
467B ALA* 3.2 7.0 - - - -
468B THR 3.2 19.1 + - - -
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Residues in contact with PHE 442 (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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1682A THD 3.6 22.7 - - - -
383B LEU* 3.7 35.4 - - + +
386B SER* 3.8 14.6 - - - -
387B ASN* 4.1 0.4 - - - -
441B THR* 1.3 83.3 + - - +
443B LEU* 1.3 67.4 + - - +
444B ASN* 4.3 5.4 - - + +
445B PHE* 2.8 43.2 + + + -
446B VAL 3.4 6.6 + - - -
468B THR* 3.3 9.6 - - - +
469B HIS* 3.4 52.9 - + + +
477B ASP* 5.1 5.2 - - - -
481B HIS* 4.3 15.0 - + + +
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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