Contacts of the helix formed by residues 476 - 484 (chain B) in PDB entry 4G3D
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 476 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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474B GLY 4.6 1.0 - - - +
475B GLY* 1.3 75.7 - - - -
477B LEU* 1.3 63.2 + - - +
478B GLY* 3.1 6.5 + - - -
479B GLN* 2.9 46.9 + - - +
480B LEU* 3.4 11.3 + - - +
519B ASP* 3.7 26.6 + - - -
521B VAL 3.4 10.1 - - - -
522B LEU* 3.8 12.2 - - - +
523B LEU* 4.1 4.3 - - - +
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Residues in contact with LEU 477 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476B SER* 1.3 73.1 - - - +
478B GLY* 1.3 60.1 + - - +
480B LEU* 3.4 8.1 + - + +
481B VAL* 3.2 28.2 + - - +
487B LEU* 4.0 15.0 - - + -
495B TYR* 3.5 42.6 - - + -
518B ALA* 3.2 19.1 - - + +
521B VAL* 2.7 27.9 + - + +
523B LEU* 4.3 11.9 - - + +
585B MET* 3.9 25.1 - - + -
589B MET* 3.6 22.9 - - + -
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Residues in contact with GLY 478 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476B SER* 3.1 1.2 + - - -
477B LEU* 1.3 74.9 - - - +
479B GLN* 1.3 63.2 + - - +
481B VAL* 3.5 5.2 + - - +
482B LYS* 3.1 31.7 + - - +
518B ALA* 3.1 24.0 + - - -
519B ASP* 3.5 23.3 - - - -
588B HIS* 5.1 4.7 + - - -
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Residues in contact with GLN 479 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384A GLU* 4.0 17.0 - - - +
408B ARG* 3.5 35.8 + - - +
474B GLY 5.8 0.4 - - - +
475B GLY* 3.8 9.3 - - - -
476B SER* 2.9 52.7 + - - +
478B GLY* 1.3 75.4 - - - +
480B LEU* 1.3 57.5 + - - +
482B LYS* 3.2 9.9 + - - +
483B GLU* 2.8 44.3 + - + +
519B ASP* 4.4 0.9 + - - +
522B LEU* 5.8 0.2 - - - +
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Residues in contact with LEU 480 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476B SER 3.4 8.6 + - - +
477B LEU* 3.6 9.9 - - + +
478B GLY 3.3 0.4 - - - -
479B GLN* 1.3 76.8 - - - +
481B VAL* 1.3 56.7 + - - +
483B GLU* 3.1 11.3 + - + +
484B GLN* 2.7 53.5 + - + +
487B LEU* 3.9 31.6 - - + -
491B ARG* 5.6 2.0 - - - -
495B TYR* 4.1 8.1 - - + -
523B LEU* 3.9 17.3 - - + -
665B TRP* 3.6 40.2 - - + -
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Residues in contact with VAL 481 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477B LEU 3.2 18.9 + - - +
478B GLY 3.8 4.5 - - - +
480B LEU* 1.3 75.5 - - - +
482B LYS* 1.3 59.8 + - - +
484B GLN 2.6 23.8 - - - +
485B GLY* 3.4 17.2 - - - +
486B CYS* 5.3 0.2 - - - -
487B LEU* 4.1 16.2 - - + -
518B ALA* 4.7 6.3 - - + -
588B HIS* 3.6 42.8 - - + +
589B MET* 3.8 30.5 - - + +
592B GLY* 4.2 4.7 - - - +
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Residues in contact with LYS 482 (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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384A GLU* 3.3 45.7 + - + +
478B GLY* 3.1 18.4 + - - +
479B GLN* 3.3 8.7 - - - +
480B LEU 3.1 0.2 - - - -
481B VAL* 1.3 76.1 - - - +
483B GLU* 1.3 67.9 + - + +
484B GLN 4.2 1.9 - - - -
485B GLY* 4.3 2.9 + - - -
519B ASP* 3.5 30.5 + - - -
588B HIS* 6.0 5.0 + - + -
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Residues in contact with GLU 483 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479B GLN* 2.8 44.2 + - + +
480B LEU* 3.1 12.8 + - + +
482B LYS* 1.3 76.5 - - - +
484B GLN* 1.3 64.5 + - + +
485B GLY 3.8 2.1 + - - -
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Residues in contact with GLN 484 (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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480B LEU* 2.7 32.3 + - - +
481B VAL* 2.6 24.4 - - - +
483B GLU* 1.3 77.1 - - + +
485B GLY* 1.3 62.7 + - - +
486B CYS 2.9 18.5 + - - +
487B LEU* 3.8 15.7 - - + +
488B PRO* 4.6 8.5 - - - +
491B ARG* 5.9 1.9 - - - -
665B TRP* 4.1 7.9 + - - +
666B ARG* 4.0 33.5 - - - +
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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