Contacts of the helix formed by residues 479 - 485 (chain A) in PDB entry 3H0G
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 479 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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367A LEU* 3.5 12.6 - - - +
477A ASN* 2.9 5.2 + - - +
478A LEU* 1.3 78.0 - - - +
480A VAL* 1.3 54.9 + - - +
481A THR 3.3 1.9 + - - -
482A SER* 4.6 2.5 + - - -
483A PRO* 4.3 2.8 - - - +
527A MET* 3.3 23.7 - - - +
528A GLY 3.7 21.5 + - - +
529A ILE* 5.0 3.6 - - - -
530A VAL* 5.3 4.3 - - - +
652A PHE* 3.1 28.6 - - - -
656A GLN* 3.6 21.4 - - - +
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Residues in contact with VAL 480 (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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367A LEU* 3.1 38.8 - - + +
462A MET* 4.7 2.2 - - - -
464A HIS* 4.4 5.8 - - - +
476A LEU* 5.2 5.8 - - + -
477A ASN* 2.7 25.9 + - + +
479A SER* 1.3 79.4 - - - +
481A THR* 1.3 60.4 + - - +
483A PRO* 3.3 16.5 - - + +
484A TYR* 2.9 41.0 - - + -
513A VAL* 4.3 17.7 - - + -
527A MET* 4.5 5.4 - - - -
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Residues in contact with THR 481 (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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476A LEU* 4.3 6.9 - - - +
477A ASN 4.1 1.7 + - - -
478A LEU* 3.0 25.8 + - - +
480A VAL* 1.3 78.9 - - - +
482A SER* 1.3 66.6 + - - +
484A TYR* 3.0 17.8 + - + +
485A ASN* 3.3 9.5 + - - -
486A ALA 3.1 28.0 - - - +
487A ASP* 4.6 8.1 - - - +
488A PHE* 4.2 19.7 - - + -
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Residues in contact with SER 482 (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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457A HIS* 5.7 2.6 - - - -
478A LEU 4.7 0.8 + - - -
479A SER 4.6 4.6 + - - -
481A THR* 1.3 77.1 - - - +
483A PRO* 1.3 69.7 - - - +
485A ASN* 3.1 17.7 + - - +
526A VAL* 3.9 14.7 - - - +
527A MET* 5.2 2.2 - - - -
528A GLY 5.8 0.7 - - - -
530A VAL* 4.6 17.6 - - - +
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Residues in contact with PRO 483 (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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457A HIS* 4.4 16.0 + - + +
459A MET* 4.1 30.2 - - + +
460A SER* 3.9 14.0 + - - -
462A MET* 4.7 2.5 - - - -
479A SER 4.3 0.9 - - - +
480A VAL* 3.3 21.3 - - + +
482A SER* 1.3 97.1 - - - +
484A TYR* 1.3 61.4 + - + +
485A ASN* 3.3 3.1 + - - -
526A VAL* 3.8 16.6 - - + +
527A MET* 3.6 37.5 - - + -
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Residues in contact with TYR 484 (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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450A PHE* 3.7 6.5 + + - -
452A ARG* 4.0 14.5 - - + +
459A MET 4.2 2.5 - - - -
460A SER* 3.3 36.6 - - - -
462A MET* 2.7 34.5 - - + +
464A HIS* 3.2 16.7 - + - -
476A LEU* 4.6 12.1 - - + -
480A VAL* 2.9 44.9 - - + -
481A THR* 3.0 9.3 + - - +
483A PRO* 1.3 76.4 - - + +
485A ASN* 1.3 77.8 + - - +
486A ALA* 2.5 19.2 + - + +
493A MET* 3.4 36.3 - - + -
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Residues in contact with ASN 485 (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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452A ARG* 4.5 6.6 + - - +
454A PRO* 4.9 16.1 + - - +
456A LEU* 5.3 8.7 - - - +
457A HIS* 4.2 24.5 + - + -
460A SER* 5.6 3.2 + - - -
481A THR 3.3 3.2 + - - -
482A SER* 3.1 16.9 + - - +
483A PRO 3.3 1.9 + - - -
484A TYR* 1.3 85.6 - - - +
486A ALA* 1.3 57.4 + - - +
487A ASP* 5.2 0.2 - - - -
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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