Contacts of the helix formed by residues 517 - 531 (chain A) in PDB entry 5GJK
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 517 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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472A GLU* 4.7 0.2 - - - +
480A SER* 5.1 5.8 + - - +
481A LYS* 3.2 22.3 + - + -
485A ILE* 5.8 0.2 - - - +
489A TYR* 3.8 4.6 + - + +
516A GLY* 1.3 67.1 - - - -
518A VAL* 1.3 64.7 + - - +
519A CYS* 3.0 19.8 + - - +
520A ALA* 3.1 22.6 + - + +
521A VAL* 3.1 22.7 + - - +
523A ARG* 4.8 0.2 + - - -
184B GLU* 3.0 26.9 - - - +
186B LEU* 3.9 13.2 - - + +
205B THR 4.0 0.2 - - - -
207B ASN* 3.4 20.1 + - - +
210B GLU* 4.0 6.3 - - - +
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Residues in contact with VAL 518 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
511A ARG* 3.5 33.7 - - + +
516A GLY 3.1 4.3 + - - +
517A ASP* 1.3 72.0 + - - +
519A CYS* 1.3 64.3 + - - +
521A VAL* 3.3 9.3 + - - +
522A MET* 3.1 29.5 + - + +
204B PHE* 3.9 19.1 - - + -
205B THR 3.0 24.7 + - - +
206B TRP* 3.7 31.0 - - + -
218B PHE* 3.5 24.2 - - + -
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Residues in contact with CYS 519 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517A ASP* 3.0 3.3 + - - +
518A VAL* 1.3 81.0 - - - +
520A ALA* 1.3 62.4 + - - +
522A MET* 3.1 10.2 + - - +
523A ARG* 2.9 43.9 + - - +
206B TRP* 3.4 44.2 - - - -
207B ASN 6.0 0.9 - - - -
210B GLU* 3.3 31.6 - - - +
213B MET* 3.7 18.3 - - - +
218B PHE* 4.6 0.4 - - - -
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Residues in contact with ALA 520 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472A GLU* 3.6 17.9 - - - +
473A PHE* 3.7 19.2 - - + -
481A LYS* 3.6 19.5 - - + -
489A TYR* 4.7 4.0 - - + -
517A ASP* 3.1 18.0 + - + +
519A CYS* 1.3 77.7 - - - +
521A VAL* 1.3 61.6 + - - +
523A ARG* 3.3 13.3 + - - +
524A VAL* 3.1 27.0 + - - +
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Residues in contact with VAL 521 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489A TYR* 3.4 41.1 - - + +
493A MET* 3.4 25.2 - - + +
507A SER* 5.0 1.8 - - - +
511A ARG* 3.8 35.4 - - + +
514A LEU* 3.9 11.9 - - + -
515A THR 5.0 2.2 - - - +
516A GLY 5.1 1.1 - - - -
517A ASP 3.1 14.7 + - - +
518A VAL* 3.5 9.9 - - - +
519A CYS 3.2 0.2 - - - -
520A ALA* 1.3 76.0 - - - +
522A MET* 1.3 62.5 + - - +
524A VAL* 3.2 2.4 + - - -
525A HIS* 3.2 18.4 + - - +
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Residues in contact with MET 522 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507A SER* 3.6 33.2 - - - +
508A THR* 5.2 4.0 - - - -
511A ARG* 5.1 7.2 - - - -
518A VAL* 3.1 20.5 + - - +
519A CYS* 3.1 11.9 + - - +
521A VAL* 1.3 77.4 - - - +
523A ARG* 1.3 58.4 + - - +
525A HIS* 3.3 8.4 + - - +
526A ALA* 3.0 27.5 + - - +
213B MET* 3.8 26.2 - - + -
218B PHE* 4.2 20.9 - - + -
221B ILE* 4.4 15.9 - - + -
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Residues in contact with ARG 523 (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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470A LEU* 3.8 21.2 - - + +
472A GLU* 2.6 41.0 + - - +
481A LYS* 5.1 0.6 - - - +
517A ASP* 4.6 2.4 + - - -
519A CYS* 2.9 24.1 + - - +
520A ALA* 3.6 15.6 - - - +
521A VAL 3.2 0.2 - - - -
522A MET* 1.3 73.7 - - - +
524A VAL* 1.3 61.2 + - - +
526A ALA* 3.7 7.5 - - - +
527A PHE* 2.9 28.8 + - - +
210B GLU* 2.8 39.3 + - - -
212B LEU* 3.5 31.4 - - - +
213B MET* 3.8 16.6 - - + +
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Residues in contact with VAL 524 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470A LEU* 4.2 6.7 - - + -
473A PHE* 3.8 16.4 - - + -
486A TYR* 3.8 29.4 - - + +
489A TYR* 4.3 10.5 - - + -
490A ARG* 3.8 37.5 - - + +
493A MET* 4.1 13.2 - - + -
520A ALA 3.1 15.2 + - - +
521A VAL 3.2 6.5 + - - +
523A ARG* 1.3 76.9 - - - +
525A HIS* 1.3 62.7 + - - +
527A PHE* 3.2 2.8 + - - +
528A LEU* 3.0 27.0 + - + +
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Residues in contact with HIS 525 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493A MET* 3.6 19.0 - - + -
504A TYR* 4.1 5.6 - - - -
505A LEU* 2.7 28.8 + - + +
506A THR 3.9 3.4 - - - -
507A SER* 3.5 40.1 + - - -
510A CYS* 4.0 14.6 - - - -
521A VAL 3.2 7.6 + - - +
522A MET 3.6 8.1 - - - +
524A VAL* 1.3 80.4 - - - +
526A ALA* 1.3 65.2 + - - +
528A LEU* 3.2 5.1 + - - +
529A GLU* 3.0 47.3 + - - +
534A VAL* 4.3 10.7 - - + +
535A ASN* 3.8 4.0 + - - -
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Residues in contact with ALA 526 (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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522A MET 3.0 16.9 + - - +
523A ARG* 3.7 8.3 - - - +
524A VAL 3.3 0.2 - - - -
525A HIS* 1.3 79.1 + - - +
527A PHE* 1.3 63.3 + - - +
529A GLU* 3.3 4.6 + - - +
530A GLN* 3.0 27.4 + - - +
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Residues in contact with PHE 527 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456A TRP* 3.8 13.7 - + - -
465A ILE* 4.2 4.3 - - + -
466A GLU* 3.6 28.5 - - + -
469A ALA* 3.4 35.0 - - + -
470A LEU* 3.8 15.5 - - + -
486A TYR* 3.6 24.2 - + - -
523A ARG 2.9 17.8 + - - +
524A VAL 3.6 3.8 - - - +
526A ALA* 1.3 76.2 - - - +
528A LEU* 1.3 78.8 + - + +
530A GLN* 3.2 12.4 + - - +
531A TRP* 3.2 60.4 + + - -
533A LEU* 4.9 2.5 - - + -
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Residues in contact with LEU 528 (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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490A ARG* 3.6 51.4 - - + +
493A MET* 3.8 24.9 - - + -
494A ILE* 4.1 5.2 - - + -
524A VAL* 3.0 20.7 + - + +
525A HIS 3.2 4.2 + - - +
527A PHE* 1.3 85.6 - - + +
529A GLU* 1.3 61.6 + - - +
531A TRP* 3.2 3.1 + - - -
532A GLY 3.1 3.8 + - - -
533A LEU* 2.9 55.6 + - + -
534A VAL* 3.9 23.3 - - + +
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Residues in contact with GLU 529 (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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504A TYR* 2.7 33.9 + - - -
525A HIS* 3.0 25.5 + - - +
526A ALA* 3.8 6.5 - - - +
528A LEU* 1.3 76.1 - - - +
530A GLN* 1.3 63.5 + - - +
532A GLY* 3.1 12.6 + - - -
534A VAL* 3.7 21.4 - - + +
535A ASN* 3.0 22.9 + - + -
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Residues in contact with GLN 530 (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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453A TYR* 4.4 10.7 + - - -
526A ALA* 3.0 18.6 + - - +
527A PHE* 3.2 13.4 + - - +
529A GLU* 1.3 76.7 - - - +
531A TRP* 1.3 78.0 + - + +
532A GLY 3.7 0.5 + - - -
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Residues in contact with TRP 531 (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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451A PRO* 3.5 8.0 - - - +
453A TYR* 3.3 48.8 - + + -
454A ALA* 3.3 23.4 - - + +
456A TRP* 3.3 27.4 - + + -
465A ILE* 3.8 22.6 - - + +
527A PHE* 3.2 56.3 + + - +
528A LEU 3.2 2.9 + - - +
529A GLU 3.1 0.6 - - - -
530A GLN* 1.3 95.1 - - + +
532A GLY* 1.3 62.3 + - - +
533A LEU* 3.2 18.2 + - + +
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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