Contacts of the helix formed by residues 491 - 506 (chain A) in PDB entry 3GKL
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 SER 491 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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489A PHE* 3.7 0.8 - - - +
490A LYS* 1.3 91.1 + - - +
492A PHE* 1.3 61.5 + - - +
493A ASP* 2.9 17.6 - - - +
494A ASP* 3.3 10.0 + - - +
495A PHE* 2.9 23.0 + - - +
556A TYR* 3.2 17.2 + - - -
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Residues in contact with PHE 492 (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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491A SER* 1.3 73.9 - - - +
493A ASP* 1.3 58.2 + - - +
495A PHE* 3.5 32.1 - + - +
496A ARG* 2.9 26.6 + - + +
543A LEU* 4.2 36.3 - - + -
545A ALA* 5.2 11.9 - - + -
556A TYR* 3.4 26.9 + + + -
561A ILE* 4.0 20.9 - - + -
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Residues in contact with ASP 493 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491A SER* 3.6 10.1 - - - +
492A PHE* 1.3 77.8 - - - +
494A ASP* 1.3 64.2 + - - +
496A ARG* 3.1 35.4 + - - +
497A LYS* 3.1 31.2 + - - +
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Residues in contact with ASP 494 (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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488A GLU 4.2 3.6 - - - +
489A PHE* 3.6 12.2 - - + +
490A LYS* 3.4 48.3 + - + +
491A SER* 3.3 11.7 + - - +
493A ASP* 1.3 73.8 - - - +
495A PHE* 1.3 65.5 + - - +
497A LYS* 4.0 11.0 - - - +
498A LYS* 3.1 47.7 + - - +
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Residues in contact with PHE 495 (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 ALA* 4.2 15.9 - - + -
476A VAL* 5.7 0.4 - - + -
484A LEU* 4.2 22.7 - - + -
489A PHE* 3.8 23.0 - + + -
491A SER 2.9 14.6 + - - +
492A PHE* 3.5 33.0 - + - +
494A ASP* 1.3 77.6 - - - +
496A ARG* 1.3 60.3 + - - +
498A LYS* 3.9 0.7 - - - +
499A PHE* 3.0 36.2 + + + +
543A LEU* 4.4 11.7 - - + -
556A TYR* 4.0 25.4 - + + -
558A MET* 4.2 11.9 - - + -
561A ILE* 3.9 32.1 - - + -
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Residues in contact with ARG 496 (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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492A PHE* 2.9 20.3 + - + +
493A ASP* 3.1 29.3 + - - +
495A PHE* 1.3 81.7 - - - +
497A LYS* 1.3 86.0 + - - +
499A PHE* 3.3 4.8 + - - +
500A TRP* 3.1 36.2 + - - +
524A GLY 2.8 25.2 + - - -
525A LYS* 4.0 10.1 - - - +
526A ALA* 4.2 9.2 - - - +
541A PHE 6.2 0.2 - - - -
543A LEU* 3.8 26.5 - - + +
1030C GLU* 5.9 0.2 + - - -
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Residues in contact with LYS 497 (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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493A ASP* 3.1 20.1 + - - +
494A ASP* 4.0 12.1 - - - +
496A ARG* 1.3 102.3 - - - +
498A LYS* 1.3 68.5 + - + +
500A TRP 3.4 0.2 + - - -
501A GLU* 3.2 28.8 + - - +
523A VAL 4.5 12.5 + - - +
524A GLY* 3.6 23.4 - - - +
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Residues in contact with LYS 498 (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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484A LEU* 3.8 18.1 - - + +
487A LYS* 4.7 17.0 - - + +
488A GLU 5.4 3.6 - - - +
489A PHE* 4.2 15.9 - - + -
494A ASP* 3.1 36.4 + - - +
497A LYS* 1.3 78.6 - - + +
499A PHE* 1.3 62.5 + - - +
501A GLU* 3.3 38.4 + - - +
502A GLU* 3.2 24.3 + - - +
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Residues in contact with PHE 499 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464A TRP* 4.0 22.4 - + - -
476A VAL* 4.1 28.5 - - + -
477A PRO* 4.7 2.5 - - + -
480A ILE* 4.3 8.2 - - + +
484A LEU* 4.0 27.7 - - + +
495A PHE* 3.0 32.0 + + + +
496A ARG* 3.5 7.2 - - - +
498A LYS* 1.3 76.5 - - - +
500A TRP* 1.3 108.3 + + - +
502A GLU* 3.5 2.9 + - - +
503A VAL* 3.3 28.3 + - + +
543A LEU* 3.9 16.4 - - + -
561A ILE* 5.8 0.4 - - + -
563A VAL* 4.0 11.4 - - + -
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Residues in contact with TRP 500 (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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464A TRP* 4.1 19.1 - + - -
465A LEU* 5.0 1.8 - - + -
496A ARG* 3.1 40.8 + - + +
497A LYS 3.4 2.7 + - - +
499A PHE* 1.3 104.5 - + - +
501A GLU* 1.3 61.9 + - - +
503A VAL* 3.1 10.9 + - + +
504A SER 3.0 17.7 + - - -
513A PHE* 5.1 0.2 - + - -
521A MET* 3.3 26.2 - - + +
524A GLY 4.1 8.3 - - - -
525A LYS 4.0 12.1 - - - +
526A ALA* 3.3 36.9 - - + +
527A PRO* 3.5 30.1 - - + -
541A PHE* 4.2 14.5 + - + -
543A LEU* 4.3 12.0 - - + +
563A VAL* 4.2 19.7 - - + -
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Residues in contact with GLU 501 (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 LYS* 3.2 19.0 + - - +
498A LYS* 3.3 44.0 + - - +
500A TRP* 1.3 72.1 - - - +
502A GLU* 1.3 61.2 + - - +
504A SER* 2.7 19.4 + - - -
505A LYS* 3.1 18.8 + - - +
521A MET 3.0 14.7 + - - +
522A LYS 3.4 23.7 - - - +
523A VAL* 4.3 4.3 - - - -
524A GLY* 4.3 6.7 + - - +
522B LYS* 3.2 25.5 + - - +
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Residues in contact with GLU 502 (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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480A ILE* 3.7 24.6 - - + +
483A LYS* 3.7 29.8 - - + +
484A LEU* 4.4 14.1 - - + -
487A LYS* 3.5 14.2 + - - -
498A LYS 3.2 15.6 + - - +
499A PHE 3.8 4.5 - - - +
501A GLU* 1.3 75.8 - - - +
503A VAL* 1.3 65.8 + - - +
505A LYS* 3.1 18.8 + - - +
506A ASP* 3.3 10.0 + - - +
515B ARG* 2.8 47.4 + - - +
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Residues in contact with VAL 503 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464A TRP* 3.9 28.7 - - + -
480A ILE* 4.0 19.5 - - + -
499A PHE* 3.3 29.6 + - + +
500A TRP* 3.1 23.6 + - + +
502A GLU* 1.3 76.2 - - - +
504A SER* 1.3 62.7 + - - +
505A LYS 3.1 0.9 + - - -
506A ASP 3.4 7.6 + - - -
509A LEU* 4.1 9.8 - - + +
510A SER 3.7 13.7 + - - -
513A PHE* 4.1 11.9 - - + -
521A MET* 3.9 17.9 - - + -
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Residues in contact with SER 504 (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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500A TRP 3.0 5.2 + - - -
501A GLU* 2.7 19.0 + - - -
503A VAL* 1.3 78.1 - - - +
505A LYS* 1.3 56.8 + - - +
506A ASP 3.6 0.2 - - - -
510A SER* 3.3 17.3 - - - -
518A ASN* 4.1 17.3 + - - +
521A MET* 3.9 22.9 - - - +
522A LYS* 3.4 49.4 + - - +
504B SER 4.5 2.8 - - - +
510B SER* 5.2 1.2 - - - -
518B ASN* 5.2 0.7 - - - +
522B LYS* 6.1 0.5 - - - -
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Residues in contact with LYS 505 (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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501A GLU* 3.1 21.8 + - - +
502A GLU* 3.1 15.6 + - - +
503A VAL 3.0 1.0 - - - -
504A SER* 1.3 83.9 - - - +
506A ASP* 1.3 60.0 + - - +
507A PRO* 3.2 4.3 - - - +
510A SER* 4.9 0.4 - - - -
522A LYS* 4.5 7.4 - - - -
515B ARG* 3.6 43.7 - - + +
518B ASN* 3.1 35.2 - - + +
519B ASP* 2.9 42.0 + - + +
522B LYS* 3.2 32.5 - - + +
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Residues in contact with ASP 506 (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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479A ARG* 3.1 37.2 + - - +
480A ILE* 4.1 5.6 - - + +
502A GLU 3.3 12.5 + - - +
503A VAL 3.4 2.5 + - - +
505A LYS* 1.3 76.1 - - - +
507A PRO* 1.3 69.8 - - - +
508A GLU* 2.5 38.1 + - - +
509A LEU* 2.9 30.6 + - + +
510A SER* 2.9 22.2 + - - -
515B ARG* 4.9 5.4 - - + -
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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