Contacts of the helix formed by residues 493 - 504 (chain B) in PDB entry 3C4C
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 GLN 493 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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491B THR* 2.1 37.0 + - - +
492B PRO* 1.3 78.9 - - + +
494B GLN* 1.3 61.1 + - - +
495B LEU 3.2 2.2 - - - -
496B GLN* 3.7 8.8 + - - +
497B ALA* 3.6 17.0 + - - +
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Residues in contact with GLN 494 (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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468B PHE* 4.4 9.2 - - + +
485B LEU* 3.4 38.8 - - - +
487B VAL* 3.8 23.8 - - - +
490B PRO* 4.0 11.8 - - + +
491B THR* 3.1 39.6 + - + +
493B GLN* 1.3 74.2 + - - +
495B LEU* 1.3 55.5 + - - +
496B GLN 3.1 7.6 + - - -
497B ALA* 3.8 12.7 + - + +
498B PHE* 3.8 17.0 + - - +
525B LEU* 4.8 6.0 - - - +
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Residues in contact with LEU 495 (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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490B PRO* 4.9 12.6 - - + +
491B THR 3.0 11.6 + - - +
492B PRO* 3.3 18.8 - - + +
493B GLN 3.2 0.4 - - - -
494B GLN* 1.3 77.1 - - - +
496B GLN* 1.3 59.8 + - - +
498B PHE* 4.5 9.9 - - + -
499B LYS* 3.1 39.7 + - + +
521B THR* 5.5 6.7 - - + -
525B LEU* 4.6 18.2 - - + -
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Residues in contact with GLN 496 (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 PRO 3.9 9.6 + - - +
493B GLN* 3.7 10.5 + - - +
494B GLN 3.1 0.4 - - - -
495B LEU* 1.3 81.3 - - - +
497B ALA* 1.3 65.4 + - - +
498B PHE 3.2 1.6 - - - -
499B LYS* 3.6 34.6 - - - +
500B ASN* 3.1 52.5 + - - +
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Residues in contact with ALA 497 (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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467B SER 5.7 2.2 - - - +
468B PHE* 5.1 10.8 - - + -
493B GLN 3.6 10.9 + - - +
494B GLN* 3.8 14.8 + - + +
496B GLN* 1.3 78.1 - - - +
498B PHE* 1.3 62.3 + - - +
500B ASN* 4.6 0.8 - - - +
501B GLU* 2.7 48.4 + - - +
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Residues in contact with PHE 498 (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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468B PHE* 5.0 14.7 - + + -
485B LEU* 6.2 0.2 - - + -
494B GLN 3.8 15.6 + - - +
495B LEU* 4.5 9.2 - - + -
497B ALA* 1.3 78.0 - - - +
499B LYS* 1.3 81.9 + - + +
501B GLU* 3.2 4.7 + - - +
502B VAL* 3.0 29.1 + - + +
519B TYR* 3.8 31.0 - + + -
520B SER 3.5 21.8 - - - -
521B THR* 4.4 12.8 - - + -
525B LEU* 3.6 28.5 - - + -
526B ALA 3.2 29.4 - - - -
527B ILE* 5.1 8.9 - - + +
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Residues in contact with LYS 499 (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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495B LEU* 3.1 31.5 + - + +
496B GLN* 3.3 35.8 + - - +
498B PHE* 1.3 86.5 - - + +
500B ASN* 1.3 58.2 + - - +
502B VAL* 2.6 32.3 + - - +
503B GLY* 2.9 10.6 + - - -
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Residues in contact with ASN 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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496B GLN* 3.1 30.5 + - - +
497B ALA* 4.6 1.3 - - - +
499B LYS* 1.3 78.5 - - - +
501B GLU* 1.3 59.2 + - + +
503B GLY* 3.0 18.3 + - - +
504B VAL* 3.0 23.4 + - + +
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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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3B 324 3.1 37.7 - - + +
467B SER* 3.9 13.5 + - - -
468B PHE* 4.1 11.1 - - - -
497B ALA* 2.7 40.4 + - - +
498B PHE 3.2 4.2 + - - +
500B ASN* 1.3 79.0 - - + +
502B VAL* 1.3 56.2 + - - +
504B VAL* 3.6 13.7 - - + +
505B LEU* 3.1 33.5 + - - +
527B ILE* 4.6 4.0 - - + -
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Residues in contact with VAL 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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498B PHE* 3.0 20.4 + - + +
499B LYS* 2.6 22.3 + - - +
501B GLU* 1.3 73.5 - - - +
503B GLY* 1.3 60.6 + - - +
504B VAL 3.4 0.4 - - - -
505B LEU* 4.0 3.4 - - + +
506B ARG* 3.1 29.7 + - - +
516B PHE* 3.8 19.0 - - + -
519B TYR* 3.8 46.0 - - + -
527B ILE* 4.9 12.3 - - + -
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Residues in contact with GLY 503 (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 LYS 2.9 10.2 + - - -
500B ASN* 3.0 3.8 + - - -
502B VAL* 1.3 77.7 - - - +
504B VAL* 1.3 62.8 + - - +
506B ARG* 3.0 29.6 + - - +
507B LYS* 3.2 17.7 - - - +
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Residues in contact with VAL 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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3B 324 5.7 1.1 - - + -
500B ASN* 3.0 20.7 + - + +
501B GLU* 3.6 18.4 - - + +
503B GLY* 1.3 77.2 - - - +
505B LEU* 1.3 67.3 + - + +
507B LYS* 3.6 20.0 + - + +
508B THR* 3.3 21.8 - - - +
572B ILE* 4.1 18.8 - - + +
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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