Contacts of the strand formed by residues 436 - 442 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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338A LEU* 4.4 8.7 - - + -
373A LEU* 6.1 1.3 - - + -
375A GLU* 2.8 24.5 + - + +
376A LEU* 3.5 15.8 - - + +
377A ILE* 3.0 18.6 + - - +
434A ASN* 3.4 31.8 + - - +
435A TYR* 1.3 80.3 + - - +
437A PRO* 1.3 63.8 - - - +
462A PRO* 4.0 20.9 - - + +
464A ILE* 5.8 1.6 - - + -
514A SER 4.9 0.4 + - - -
515A LEU* 3.1 47.2 + - + +
516A GLU 4.9 0.4 - - - -
517A SER 3.0 26.5 + - - -
518A LYS* 5.0 2.2 - - - +
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Residues in contact with PRO 437 (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 ILE* 3.1 12.3 - - + +
412A ILE* 6.2 0.2 - - + -
414A TYR* 5.2 1.1 - - - +
425A MET* 3.4 44.6 - - + +
428A ILE* 4.0 29.8 - - + -
429A SER* 4.1 8.7 - - - +
435A TYR 3.4 9.6 - - - +
436A LYS* 1.3 88.5 - - - +
438A TYR* 1.3 60.5 + - - +
462A PRO 4.9 1.9 - - - +
463A VAL* 4.0 11.1 - - + -
464A ILE* 3.3 21.8 + - - +
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Residues in contact with TYR 438 (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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366A LEU* 3.6 26.6 - - + +
376A LEU* 3.6 39.5 - - + -
377A ILE 2.9 7.0 + - - +
378A GLY* 3.4 28.5 - - - -
379A GLY* 3.3 16.7 + - - -
389A THR* 2.6 43.0 + - + -
391A TRP* 3.4 19.4 - + - -
414A TYR* 4.8 3.5 + - - -
425A MET* 3.3 6.7 - - - +
436A LYS 4.9 0.2 - - - +
437A PRO* 1.3 74.5 - - - +
439A GLY* 1.3 62.3 + - - +
464A ILE* 3.0 32.8 - - + +
466A VAL* 3.8 14.1 - - + -
511A TYR* 5.8 1.8 - + + -
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Residues in contact with GLY 439 (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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379A GLY 3.4 6.7 - - - -
414A TYR* 4.9 0.9 - - - -
421A MET* 3.8 20.9 - - - +
425A MET* 3.2 12.7 - - - -
438A TYR* 1.3 76.8 - - - +
440A GLY* 1.3 61.2 + - - -
464A ILE 2.8 8.5 + - - -
465A TRP* 3.4 9.4 - - - +
466A VAL* 2.8 26.0 + - - -
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Residues in contact with GLY 440 (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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379A GLY 2.9 15.4 + - - -
380A SER* 3.2 1.4 + - - +
381A ALA 2.9 27.0 + - - -
387A ASN* 2.8 15.5 - - - +
389A THR* 4.2 5.1 - - - +
421A MET* 3.5 3.0 - - - +
439A GLY* 1.3 74.9 - - - -
441A THR* 1.3 63.5 + - - -
466A VAL* 3.1 16.4 - - - -
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Residues in contact with THR 441 (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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381A ALA* 4.4 6.9 - - - +
383A LEU* 3.8 13.3 - - - +
387A ASN* 2.8 17.1 + - - -
418A GLU* 3.7 26.6 + - + +
421A MET* 4.4 0.7 - - - -
440A GLY* 1.3 75.3 - - - -
442A PHE* 1.3 77.6 + - - +
445A PHE* 4.0 5.0 - - - +
446A VAL* 3.7 25.4 - - + +
465A TRP* 3.9 19.1 - - + -
466A VAL 3.2 4.8 + - - +
467A ALA* 3.3 3.2 - - - -
468A THR 3.2 19.6 + - - -
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Residues in contact with PHE 442 (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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383A LEU* 3.6 33.8 - - + +
386A SER* 3.9 17.0 - - - -
387A ASN* 4.0 0.9 - - - -
441A THR* 1.3 82.9 + - - +
443A LEU* 1.3 67.3 + - - +
444A ASN* 4.3 5.2 - - + +
445A PHE* 2.9 44.0 + + + -
446A VAL 3.4 6.8 + - - -
468A THR* 3.4 8.3 - - - +
469A HIS* 3.3 54.3 - + + +
477A ASP* 5.1 5.4 - - - -
481A HIS* 4.2 14.1 - + + +
191B ILE* 5.9 0.4 - - + -
1682B THD 3.7 21.1 - - - -
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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