Contacts of the helix formed by residues 503 - 517 (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 ASP 503 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358A THR* 4.4 1.3 - - - -
361A LEU* 3.6 12.1 - - - -
501A PRO 3.6 0.4 - - - -
502A ALA* 1.3 80.1 - - - +
504A GLY* 1.3 67.5 + - - +
505A ASN* 3.4 3.4 + - - -
506A GLU* 3.1 23.2 + - - +
507A VAL* 2.9 24.8 + - - +
531A LEU* 5.5 1.8 - - - +
532A PRO 3.6 15.9 - - - +
533A GLN* 3.5 12.0 - - - +
534A LEU* 2.9 28.6 + - + +
537A SER* 2.8 26.3 + - - -
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Residues in contact with GLY 504 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A TYR* 3.6 23.8 - - - -
361A LEU* 3.3 20.8 - - - +
503A ASP* 1.3 77.2 - - - +
505A ASN* 1.3 60.8 + - - +
507A VAL* 3.2 6.1 + - - +
508A SER* 3.2 22.5 + - - -
533A GLN* 2.8 16.7 + - - -
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Residues in contact with ASN 505 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A THR* 3.6 9.9 - - - -
349A TYR* 2.9 49.2 + - - +
350A THR* 5.1 1.0 - - - +
503A ASP* 3.4 3.6 + - - -
504A GLY* 1.3 74.1 - - - +
506A GLU* 1.3 63.0 + - - +
508A SER* 3.2 6.0 + - - -
509A ALA* 3.0 20.0 + - - +
533A GLN* 4.4 0.6 + - - +
534A LEU 5.1 1.0 + - - -
537A SER* 3.0 38.9 + - - +
538A SER* 3.8 22.4 - - - +
539A ILE* 3.7 15.2 - - - +
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Residues in contact with GLU 506 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499A TRP* 4.9 2.6 - - - -
500A ARG 4.3 1.0 - - - +
501A PRO* 3.7 8.1 - - + +
502A ALA* 2.8 45.0 + - - +
503A ASP* 3.1 18.1 + - - +
505A ASN* 1.3 73.4 - - - +
507A VAL* 1.3 60.7 + - - +
509A ALA* 3.2 2.1 + - - +
510A ALA* 2.9 28.8 + - - +
534A LEU* 4.8 2.4 - - - +
537A SER* 4.6 1.8 - - - -
542A ALA* 4.0 15.9 - - + +
547A TYR* 2.6 30.9 + - - +
563A GLY 5.2 0.2 + - - -
587A SER* 2.6 22.1 + - - -
589A PRO* 3.2 23.1 - - + +
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Residues in contact with VAL 507 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358A THR* 3.9 14.1 - - - +
361A LEU* 3.9 23.3 - - + -
362A SER* 4.0 24.7 - - - +
365A VAL* 4.0 8.3 - - + -
501A PRO* 3.6 22.4 - - + -
503A ASP 2.9 20.1 + - - +
504A GLY 3.2 7.8 + - - +
506A GLU* 1.3 76.5 - - - +
508A SER* 1.3 63.0 + - - +
510A ALA* 3.3 2.8 + - + +
511A TYR* 3.1 41.2 + - + -
524A ILE* 5.9 0.4 - - + -
526A LEU* 4.6 3.1 - - + -
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Residues in contact with SER 508 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346A LEU* 3.8 12.1 - - - +
347A PRO* 2.6 45.2 + - - +
349A TYR* 5.1 0.3 - - - -
365A VAL* 4.0 10.3 - - - +
504A GLY 3.2 7.9 + - - -
505A ASN 3.2 8.7 + - - -
507A VAL* 1.3 79.6 - - - +
509A ALA* 1.3 57.1 + - - +
511A TYR* 3.4 2.6 + - - +
512A LYS* 2.8 29.9 + - - +
539A ILE* 3.6 17.0 - - - -
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Residues in contact with ALA 509 (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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499A TRP* 4.6 3.4 - - + -
505A ASN 3.0 10.2 + - - +
506A GLU 3.2 4.7 + - - +
508A SER* 1.3 75.0 - - - +
510A ALA* 1.3 65.6 + - - +
512A LYS* 3.1 1.6 + - - -
513A ASN* 2.9 29.8 + - - +
539A ILE* 3.6 12.1 - - - +
542A ALA* 3.5 33.9 - - + +
543A SER* 3.6 23.1 - - - +
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Residues in contact with ALA 510 (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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499A TRP* 3.6 43.0 + - + -
501A PRO* 3.9 12.3 - - + -
506A GLU 2.9 13.6 + - - +
507A VAL 3.3 8.7 + - - +
509A ALA* 1.3 77.3 - - - +
511A TYR* 1.3 55.1 + - - +
514A SER* 2.6 37.6 + - - -
524A ILE* 4.2 11.0 - - + -
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Residues in contact with TYR 511 (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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342A TRP* 4.6 0.7 - - - -
346A LEU* 4.6 3.8 - - + -
362A SER* 2.6 43.1 + - - -
365A VAL* 3.7 27.4 - - + -
366A LEU* 3.9 25.5 - - + +
369A VAL* 6.3 0.2 - - + -
438A TYR* 5.8 2.2 - + - -
464A ILE* 4.7 13.5 - - + -
466A VAL* 3.5 22.4 - - + +
507A VAL* 3.1 31.7 + - + +
508A SER 3.9 3.8 - - - +
510A ALA* 1.3 74.3 - - + +
512A LYS* 1.3 65.8 + - - +
514A SER* 4.3 1.8 - - - -
515A LEU* 3.0 46.9 + - + +
524A ILE* 3.9 26.4 - - + +
526A LEU* 4.8 0.7 - - - +
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Residues in contact with LYS 512 (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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342A TRP* 4.0 14.3 - - + -
343A GLU* 4.1 24.1 + - + -
346A LEU* 3.7 15.4 - - + +
508A SER 2.8 18.1 + - - +
509A ALA* 3.1 6.9 + - - +
511A TYR* 1.3 77.2 - - - +
513A ASN* 1.3 66.7 + - - +
516A GLU* 3.0 67.7 + - - +
539A ILE* 3.9 23.1 - - + -
543A SER* 4.1 9.7 + - - +
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Residues in contact with ASN 513 (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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497A GLN* 3.9 7.9 + - - +
499A TRP* 3.5 32.6 - - + -
509A ALA 2.9 8.2 + - - +
510A ALA 4.1 0.2 - - - +
512A LYS* 1.3 83.7 + - - +
514A SER* 1.3 62.0 + - - +
516A GLU* 3.5 6.0 + - - +
517A SER* 3.1 24.8 + - - -
543A SER* 3.0 47.7 + - - -
593A THR* 3.7 11.5 + - - +
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Residues in contact with SER 514 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436A LYS* 4.9 0.9 + - - +
462A PRO 4.5 6.2 - - - +
464A ILE* 3.8 26.2 - - - +
497A GLN* 3.9 10.4 + - - +
499A TRP* 3.7 6.4 + - - -
510A ALA 2.6 24.5 + - - -
511A TYR* 3.9 4.9 - - - -
512A LYS 3.3 0.2 - - - -
513A ASN* 1.3 76.0 - - - +
515A LEU* 1.3 61.5 + - - +
517A SER* 3.4 17.2 - - - +
520A THR 5.0 0.5 - - - +
522A SER* 2.8 31.2 + - - -
524A ILE* 3.9 5.8 - - - +
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Residues in contact with LEU 515 (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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338A LEU* 3.6 11.8 - - + +
342A TRP* 3.7 27.4 - - + -
346A LEU* 5.8 0.2 - - + -
365A VAL* 5.9 0.2 - - + -
366A LEU* 6.6 0.2 - - + -
369A VAL* 4.9 7.2 - - + -
373A LEU* 3.8 20.9 - - + -
376A LEU* 4.0 24.5 - - + -
436A LYS* 3.1 52.0 + - + +
464A ILE* 3.6 22.7 - - + -
511A TYR* 3.0 35.9 + - + +
514A SER* 1.3 74.8 - - - +
516A GLU* 1.3 60.6 + - - +
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Residues in contact with GLU 516 (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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338A LEU* 4.1 7.6 - - + -
342A TRP* 3.4 29.6 + - + +
343A GLU* 4.3 7.1 - - - +
436A LYS* 4.9 0.4 - - - -
512A LYS* 3.0 57.7 + - - +
513A ASN* 4.2 6.3 - - - +
514A SER 3.4 0.2 - - - -
515A LEU* 1.3 74.5 - - - +
517A SER* 1.3 64.8 + - - +
518A LYS* 3.4 12.6 + - - +
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Residues in contact with SER 517 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436A LYS* 3.0 24.8 + - - -
462A PRO* 3.4 6.5 - - - +
497A GLN* 3.8 7.9 - - - -
513A ASN 3.1 14.0 + - - -
514A SER 3.4 14.8 - - - +
515A LEU 3.2 0.8 - - - +
516A GLU* 1.3 76.4 - - - +
518A LYS* 1.3 59.9 + - - +
520A THR* 2.8 44.6 + - - -
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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