Contacts of the helix formed by residues 499 - 511 (chain B) in PDB entry 6CM9
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 THR 499 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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463B ASP* 3.7 24.2 - - + -
488B ILE 5.6 0.7 - - - -
491B LEU* 3.7 25.6 - - + -
492B PHE* 3.2 28.4 + - - -
495B LYS* 2.9 24.9 + - + +
497B THR 3.3 0.6 - - - -
498B GLU* 1.3 85.4 - - + +
500B GLN* 1.3 64.2 + - - +
501B GLU* 3.5 2.7 - - - -
502B LEU* 3.8 22.4 - - + -
503B VAL* 3.4 13.5 + - - +
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Residues in contact with GLN 500 (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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492B PHE* 3.3 34.6 - - - -
496B PRO* 3.8 16.0 + - - +
497B THR 4.0 7.3 + - - +
498B GLU 3.7 1.6 - - - -
499B THR* 1.3 77.9 - - - +
501B GLU* 1.3 70.2 + - - +
503B VAL* 3.3 16.1 - - - +
504B GLN* 3.6 17.8 + - + +
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Residues in contact with GLU 501 (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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497B THR 5.4 1.0 - - - +
498B GLU 5.1 7.2 - - - +
499B THR* 5.3 0.9 - - - -
500B GLN* 1.3 85.4 + - + +
502B LEU* 1.3 63.0 + - + +
503B VAL 3.4 0.2 - - - -
504B GLN* 3.7 8.6 - - + +
505B GLN* 2.9 32.7 + - - +
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Residues in contact with LEU 502 (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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463B ASP* 4.3 17.5 - - + +
466B LEU* 5.1 6.5 - - + -
467B GLU* 3.2 26.2 - - + +
470B LEU* 4.6 6.3 - - + -
488B ILE* 3.7 35.4 - - + -
491B LEU* 4.5 9.6 - - + -
499B THR* 3.5 36.4 + - + +
500B GLN 3.3 1.0 - - - -
501B GLU* 1.3 80.3 - - + +
503B VAL* 1.3 59.8 + - - +
505B GLN* 3.3 19.5 - - + +
506B VAL* 3.0 26.5 + - - +
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Residues in contact with VAL 503 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488B ILE* 4.1 3.8 - - + -
489B VAL* 4.1 25.8 - - + -
492B PHE* 3.6 46.4 - - + -
499B THR 3.4 1.6 + - - -
500B GLN* 3.3 17.3 - - - +
502B LEU* 1.3 77.4 - - - +
504B GLN* 1.3 64.4 + - - +
506B VAL* 3.3 8.4 - - + +
507B LEU* 2.9 41.3 + - + +
530B LEU* 3.7 24.7 - - + -
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Residues in contact with GLN 504 (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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500B GLN* 3.6 24.7 + - + +
501B GLU* 3.4 11.6 + - + +
502B LEU 3.2 0.4 - - - -
503B VAL* 1.3 84.8 - - - +
505B GLN* 1.3 57.7 + - - +
507B LEU* 3.3 11.9 + - - +
508B SER* 2.9 34.0 + - - +
527B TRP* 4.9 12.2 + - - +
530B LEU* 4.7 11.3 - - - +
531B SER* 5.9 1.4 + - - -
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Residues in contact with GLN 505 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467B GLU* 2.5 40.5 + - - +
470B LEU* 4.7 11.1 - - + +
501B GLU* 2.9 20.1 + - - +
502B LEU* 3.3 25.1 - - + +
504B GLN* 1.3 75.1 - - - +
506B VAL* 1.3 59.0 + - + +
508B SER* 3.5 5.3 + - - +
509B LEU* 2.9 39.8 + - + +
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Residues in contact with VAL 506 (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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470B LEU* 4.2 15.9 - - + -
473B PHE* 4.6 20.2 - - + -
484B LEU 4.9 4.3 - - - +
485B LEU* 4.7 18.8 - - + -
488B ILE* 3.7 41.5 - - + -
489B VAL* 5.2 1.1 - - + -
502B LEU 3.0 16.8 + - - +
503B VAL* 3.3 18.8 - - + +
505B GLN* 1.3 76.2 - - - +
507B LEU* 1.3 61.2 + - + +
509B LEU* 4.3 3.4 - - + +
510B ALA* 2.9 32.1 + - - +
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Residues in contact with LEU 507 (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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485B LEU* 4.4 17.9 - - + -
489B VAL* 5.3 2.0 - - + -
503B VAL* 2.9 35.8 + - + +
504B GLN* 3.8 12.8 - - - +
505B GLN 3.3 0.2 - - - -
506B VAL* 1.3 79.9 - - + +
508B SER* 1.3 54.9 - - - +
510B ALA* 4.4 0.7 - - - -
511B THR* 2.4 42.9 + - + +
523B GLY* 3.5 30.3 - - - +
526B TYR* 4.5 6.3 - - + -
527B TRP* 3.5 41.7 - - + +
530B LEU* 4.7 9.9 - - + -
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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
----------------------------------------------------------
504B GLN* 2.9 18.9 + - - -
505B GLN* 4.1 5.4 - - - -
507B LEU* 1.3 76.6 - - - +
509B LEU* 1.3 61.7 + - - +
511B THR* 4.3 2.9 - - - -
512B GLN* 3.3 39.0 + - - +
513B ASP* 4.2 3.3 + - - +
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Residues in contact with LEU 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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470B LEU* 3.7 38.4 - - + +
473B PHE* 3.8 21.3 - - + -
474B HIS* 3.1 34.6 - - + +
505B GLN* 2.9 26.4 + - + +
506B VAL* 4.1 4.3 - - - +
508B SER* 1.3 83.5 - - - +
510B ALA* 1.3 50.4 + - - +
511B THR 3.6 0.2 - - - -
512B GLN 4.7 1.3 - - - -
513B ASP* 5.9 2.2 - - + +
514B SER* 2.3 27.7 + - - -
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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
----------------------------------------------------------
473B PHE* 4.0 18.4 - - + -
485B LEU* 4.3 20.4 - - + -
506B VAL 2.9 19.5 + - - +
507B LEU* 3.3 3.6 + - - +
509B LEU* 1.3 78.8 - - - +
511B THR* 1.3 63.8 + - + +
514B SER* 3.3 19.7 - - - -
519B LEU* 3.8 22.1 - - + +
520B ARG* 4.2 5.5 - - - +
523B GLY* 4.9 0.7 - - - -
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Residues in contact with THR 511 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507B LEU* 2.4 29.3 + - + +
508B SER* 4.3 2.3 - - - -
510B ALA* 1.3 83.5 - - - +
512B GLN* 1.3 62.1 + - - +
514B SER 4.7 3.7 - - - +
520B ARG* 4.2 13.3 + - - +
523B GLY* 3.6 34.8 - - - +
524B TYR* 3.2 47.9 + - + +
527B TRP* 5.3 3.4 - - + -
587G MET* 5.3 0.5 - - - +
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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