Contacts of the helix formed by residues 503 - 517 (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 ASP 503 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358B THR* 4.4 1.3 - - - -
361B LEU* 3.7 11.4 - - - -
501B PRO 3.5 0.4 - - - -
502B ALA* 1.3 81.5 - - - +
504B GLY* 1.3 67.7 + - - +
505B ASN* 3.3 3.9 + - - -
506B GLU* 3.1 23.2 + - - +
507B VAL* 2.9 24.8 + - - +
531B LEU* 5.5 2.0 - - - +
532B PRO 3.6 19.7 - - - +
533B GLN* 3.7 7.2 - - - +
534B LEU* 2.9 28.6 + - + +
537B SER* 2.7 25.5 + - - -
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Residues in contact with GLY 504 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349B TYR* 3.6 24.8 - - - -
361B LEU* 3.4 18.8 - - - +
503B ASP* 1.3 79.3 - - - +
505B ASN* 1.3 60.8 + - - +
507B VAL* 3.2 4.2 + - - +
508B SER* 3.2 21.5 + - - -
533B GLN* 2.9 18.4 + - - -
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Residues in contact with ASN 505 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347B PRO 5.2 0.2 - - - -
348B THR* 3.6 10.4 - - - +
349B TYR* 2.8 49.2 + - - +
350B THR* 5.1 1.2 - - - +
503B ASP* 3.3 3.2 + - - -
504B GLY* 1.3 74.4 - - - +
506B GLU* 1.3 63.1 + - - +
508B SER* 3.2 5.6 + - - +
509B ALA* 3.0 21.8 + - - +
533B GLN* 4.6 0.8 + - - +
534B LEU 5.1 1.6 + - - -
537B SER* 3.1 37.4 + - - +
538B SER* 3.8 22.6 - - - +
539B ILE* 3.7 14.0 - - - +
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Residues in contact with GLU 506 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499B TRP* 5.0 1.9 - - - -
500B ARG 4.3 1.4 - - - +
501B PRO* 3.5 8.1 - - + +
502B ALA* 2.8 43.9 + - - +
503B ASP* 3.1 17.2 + - - +
505B ASN* 1.3 76.1 - - - +
507B VAL* 1.3 59.3 + - - +
509B ALA* 3.2 2.1 + - - +
510B ALA* 2.9 29.5 + - - +
534B LEU* 4.9 2.1 - - - +
537B SER* 4.6 2.0 - - - -
542B ALA* 4.0 14.8 - - + -
547B TYR* 2.6 30.9 + - - +
563B GLY 5.2 0.3 + - - -
587B SER* 2.6 26.1 + - - -
589B PRO* 3.3 21.9 - - + +
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Residues in contact with VAL 507 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358B THR* 3.9 22.2 - - + +
361B LEU* 3.9 14.4 - - + -
362B SER* 3.9 19.7 - - - +
365B VAL* 3.9 13.9 - - + -
501B PRO* 3.6 24.7 - - + -
503B ASP 2.9 19.4 + - - +
504B GLY 3.6 8.1 - - - +
506B GLU* 1.3 77.6 - - - +
508B SER* 1.3 61.8 + - - +
510B ALA* 3.3 4.5 + - + +
511B TYR* 3.1 39.8 + - + -
524B ILE* 5.9 0.2 - - + -
526B LEU* 4.5 2.5 - - + -
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Residues in contact with SER 508 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346B LEU* 3.7 11.5 - - - +
347B PRO* 2.7 45.7 + - - +
349B TYR* 5.1 0.2 - - - -
365B VAL* 3.9 10.8 - - - +
504B GLY 3.2 6.1 + - - -
505B ASN 3.2 5.8 + - - -
507B VAL* 1.3 75.2 - - - +
509B ALA* 1.3 59.5 + - - +
511B TYR* 3.3 3.1 + - - +
512B LYS* 2.8 30.8 + - - +
539B ILE* 3.7 20.0 - - - -
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Residues in contact with ALA 509 (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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499B TRP* 4.6 2.9 - - + -
505B ASN 3.0 10.5 + - - +
506B GLU 3.2 4.7 + - - +
508B SER* 1.3 75.4 - - - +
510B ALA* 1.3 64.6 + - - +
512B LYS* 3.1 0.8 + - - -
513B ASN* 2.9 30.5 + - - +
539B ILE* 3.7 25.5 - - - +
542B ALA* 3.5 35.0 - - + +
543B SER* 3.7 9.6 - - - +
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Residues in contact with ALA 510 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499B TRP* 3.7 42.2 + - + -
501B PRO* 4.6 3.4 - - + -
506B GLU 2.9 12.8 + - - +
507B VAL* 3.4 12.6 - - - +
509B ALA* 1.3 77.4 - - - +
511B TYR* 1.3 54.2 + - - +
513B ASN 3.9 0.3 - - - -
514B SER* 2.7 37.7 + - - -
524B ILE* 4.3 17.0 - - + -
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Residues in contact with TYR 511 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342B TRP* 4.6 0.9 - - - -
346B LEU* 4.6 3.1 - - + -
362B SER* 2.6 41.5 + - - -
365B VAL* 3.7 28.9 - - + -
366B LEU* 4.0 24.7 - - + +
369B VAL* 6.3 0.2 - - + -
376B LEU* 6.6 0.2 - - + -
438B TYR* 5.8 2.2 - + - -
464B ILE* 4.7 12.8 - - + -
466B VAL* 3.5 22.7 - - + +
507B VAL* 3.1 30.9 + - + +
508B SER 3.9 3.8 - - - +
510B ALA* 1.3 75.0 - - + +
512B LYS* 1.3 66.3 + - - +
514B SER* 4.3 2.2 - - - -
515B LEU* 2.9 49.1 + - + +
524B ILE* 3.9 26.8 - - + +
526B LEU* 4.8 0.2 - - - +
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Residues in contact with LYS 512 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342B TRP* 3.9 13.8 - - + -
343B GLU* 4.0 30.6 + - + -
346B LEU* 3.6 11.4 - - + +
508B SER 2.8 19.1 + - - +
509B ALA* 3.5 5.6 - - - +
511B TYR* 1.3 77.6 - - - +
513B ASN* 1.3 65.6 + - - +
516B GLU* 2.8 66.5 + - - +
539B ILE* 4.0 21.5 - - + -
543B SER* 4.1 10.7 + - - +
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Residues in contact with ASN 513 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497B GLN* 3.9 7.8 - - - +
499B TRP* 3.5 31.5 - - + -
509B ALA 2.9 10.6 + - - +
512B LYS* 1.3 81.4 + - - +
514B SER* 1.3 62.5 + - - +
516B GLU* 3.6 5.7 + - - +
517B SER* 3.1 23.9 + - - -
543B SER* 3.0 48.4 + - - -
593B THR* 3.7 11.1 + - - +
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Residues in contact with SER 514 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436B LYS* 4.8 0.7 + - - -
462B PRO 4.5 6.1 - - - +
464B ILE* 3.8 26.9 - - - +
497B GLN* 4.0 8.9 + - - +
499B TRP* 3.6 7.3 + - - -
510B ALA 2.7 23.2 + - - -
511B TYR* 3.9 4.7 - - - -
512B LYS 3.3 0.2 - - - -
513B ASN* 1.3 78.1 - - - +
515B LEU* 1.3 61.0 + - - +
517B SER* 3.3 17.5 - - - +
520B THR 5.0 0.5 - - - +
522B SER* 2.8 30.1 + - - -
524B ILE* 3.9 6.2 - - - +
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Residues in contact with LEU 515 (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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338B LEU* 3.7 11.0 - - + +
342B TRP* 3.8 27.6 - - + -
346B LEU* 5.7 0.4 - - + -
366B LEU* 6.5 0.2 - - + -
369B VAL* 4.9 7.4 - - + -
373B LEU* 3.9 19.3 - - + -
376B LEU* 4.0 24.9 - - + -
436B LYS* 3.0 50.0 + - + +
464B ILE* 3.5 22.9 - - + -
511B TYR* 2.9 39.0 + - + +
514B SER* 1.3 72.5 - - - +
516B GLU* 1.3 61.3 + - - +
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Residues in contact with GLU 516 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338B LEU* 4.1 8.3 - - + -
342B TRP* 3.4 29.4 + - + +
343B GLU* 4.4 7.1 - - - +
436B LYS* 4.8 0.2 - - - -
512B LYS* 2.8 61.4 + - - +
513B ASN* 4.2 5.9 + - - +
514B SER 3.4 0.2 - - - -
515B LEU* 1.3 75.0 - - - +
517B SER* 1.3 65.1 + - - +
518B LYS* 3.4 12.5 + - - +
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Residues in contact with SER 517 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436B LYS* 3.0 25.1 + - - -
462B PRO* 3.3 7.1 - - - +
497B GLN* 3.7 7.9 - - - -
513B ASN 3.1 14.6 + - - -
514B SER 3.3 15.0 - - - +
515B LEU 3.2 0.4 - - - -
516B GLU* 1.3 77.0 - - - +
518B LYS* 1.3 57.9 + - - +
519B HIS 3.9 0.2 + - - -
520B THR* 2.7 45.0 + - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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