Contacts of the helix formed by residues 499 - 511 (chain A) in PDB entry 6CIM
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 PRO 499 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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481A TYR* 4.6 0.4 - - - -
485A TYR* 3.9 29.8 - - + +
495A GLN* 3.8 17.3 - - - +
498A GLN* 1.3 95.7 - - + +
500A LEU* 1.3 68.1 + - - +
501A HIS* 3.3 19.3 - - + +
502A ALA* 3.2 8.5 + - + +
503A LEU* 3.1 14.4 - - - +
30G T 3.3 36.3 - - + +
31G G 4.3 6.1 - - - +
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Residues in contact with LEU 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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471A ARG* 4.6 8.3 - - - +
478A CYS* 3.8 48.5 - - + +
481A TYR* 3.6 29.6 - - + -
482A HIS* 4.1 20.8 + - + +
485A TYR* 5.8 0.2 - - - -
499A PRO* 1.3 76.1 - - - +
501A HIS* 1.3 63.4 + - - +
503A LEU* 3.2 9.5 + - + +
504A ARG* 3.0 39.8 + - - +
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Residues in contact with HIS 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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499A PRO* 3.6 19.0 - - + +
500A LEU* 1.3 77.8 - - - +
502A ALA* 1.3 69.6 + - - +
504A ARG* 3.3 17.7 + - - +
505A ASN* 3.0 25.3 + - + +
29G T 3.4 19.2 + + + +
30G T 3.0 65.4 + + + +
31G G 5.8 1.2 + - - -
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Residues in contact with ALA 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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464A PRO* 3.8 24.2 - - + +
498A GLN* 4.0 12.6 - - + +
499A PRO* 3.2 16.0 + - + +
501A HIS* 1.3 95.3 - - - +
503A LEU* 1.3 58.3 + - - +
505A ASN* 3.4 6.8 + - - +
506A ALA* 3.0 26.7 + - - +
30G T 4.6 3.8 - - - +
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Residues in contact with LEU 503 (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 PRO 3.7 4.5 - - - +
467A CYS* 3.5 29.2 - - + +
468A LEU* 3.5 40.4 - - + +
471A ARG* 4.1 22.4 - - - +
481A TYR* 3.9 14.6 - - + -
498A GLN* 3.8 16.2 - - + +
499A PRO 3.1 17.3 - - - +
500A LEU* 3.2 10.4 + - + +
502A ALA* 1.3 76.4 - - - +
504A ARG* 1.3 60.7 + - - +
506A ALA* 3.2 7.3 + - - +
507A GLU* 2.8 33.4 + - - +
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Residues in contact with ARG 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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478A CYS* 4.4 17.6 - - - -
500A LEU* 3.0 40.0 + - - +
501A HIS* 3.6 15.6 - - - +
503A LEU* 1.3 74.7 - - - +
505A ASN* 1.3 65.5 + - - +
507A GLU* 2.9 30.9 + - - +
508A LYS* 3.1 24.4 + - + +
23J G 4.5 3.8 - - - +
24J A 3.2 42.4 + - - +
25J T 3.2 39.7 + - - +
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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
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501A HIS* 3.0 18.3 + - + +
502A ALA* 3.7 7.2 - - - +
504A ARG* 1.3 75.9 - - - +
506A ALA* 1.3 62.2 + - - +
508A LYS* 3.0 49.4 + - - +
509A VAL* 3.8 8.8 + - - +
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Residues in contact with ALA 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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464A PRO* 4.2 9.6 - - + +
465A ALA* 4.2 31.9 - - + +
468A LEU* 4.1 6.3 - - + -
502A ALA 3.0 17.0 + - - +
503A LEU 3.7 4.7 - - - +
505A ASN* 1.3 72.4 - - - +
507A GLU* 1.3 67.2 + - - +
508A LYS 3.4 0.2 + - - -
509A VAL* 3.5 14.4 + - - +
510A LEU* 3.3 18.4 - - - +
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Residues in contact with GLU 507 (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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468A LEU* 3.5 22.9 - - + +
471A ARG* 2.9 29.6 + - - -
503A LEU* 2.8 19.9 + - - +
504A ARG* 2.9 27.8 + - - +
506A ALA* 1.3 77.2 - - - +
508A LYS* 1.3 62.1 + - - +
510A LEU* 2.8 16.1 + - - +
511A LEU* 3.3 23.4 + - + +
989A LYS* 2.9 30.7 + - - -
993A LEU* 3.6 13.4 - - + +
24J A 4.3 5.1 + - - -
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Residues in contact with LYS 508 (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 ARG* 3.1 20.0 + - + +
505A ASN* 3.0 36.6 + - - +
507A GLU* 1.3 77.7 - - + +
509A VAL* 1.3 62.6 + - + +
511A LEU* 3.6 17.9 + - + +
512A PRO 5.3 0.2 - - - +
514A TYR* 3.4 29.0 - - + +
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Residues in contact with VAL 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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505A ASN* 4.0 13.2 - - - +
506A ALA* 3.9 11.2 - - - +
507A GLU 3.0 1.2 + - - -
508A LYS* 1.3 76.9 - - - +
510A LEU* 1.3 69.3 + - + +
511A LEU 3.5 5.2 + - - +
514A TYR* 3.8 42.2 - - + +
515A HIS* 3.9 23.7 - - + +
565A SER* 4.9 1.4 + - - -
998A TYR* 6.4 1.3 - - + -
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Residues in contact with LEU 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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465A ALA* 5.6 2.5 - - + -
468A LEU* 3.7 18.2 - - + -
506A ALA* 3.3 20.6 - - + +
507A GLU 2.8 5.2 + - - +
509A VAL* 1.3 84.7 - - + +
511A LEU* 1.4 51.6 + - - +
565A SER* 3.2 8.4 + - - +
569A ASP* 4.8 11.9 - - + +
992A TRP* 2.8 28.7 + - - -
993A LEU* 3.9 12.3 - - + -
996A SER* 4.5 10.7 - - - +
998A TYR* 3.5 37.2 - - + -
999A LEU* 3.6 26.5 - - + -
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Residues in contact with LEU 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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507A GLU* 3.5 27.4 - - + +
508A LYS* 3.7 17.2 - - + +
509A VAL 3.3 4.9 - - - +
510A LEU* 1.4 72.3 - - - +
512A PRO* 1.3 79.7 - - + +
513A GLY 3.5 1.2 + - - -
514A TYR* 3.9 5.9 + - - +
515A HIS* 5.9 0.2 + - - -
534A ILE* 6.5 0.2 - - + -
557A PHE* 4.8 3.6 - - + -
565A SER* 3.4 9.2 + - - -
989A LYS* 4.0 40.8 - - + +
992A TRP* 3.5 28.3 - - + -
993A LEU* 4.3 7.6 - - + -
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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