Contacts of the helix formed by residues 474 - 479 (chain A) in PDB entry 3HOU
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 VAL 474 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361A LEU* 4.1 14.4 - - + +
363A GLN 6.0 0.2 - - - +
456A MET* 3.3 29.6 - - + -
458A HIS* 4.0 10.8 - - + -
470A LEU* 4.0 20.9 - - + -
471A ASN 3.0 20.0 + - - +
473A SER* 1.3 76.4 - - - +
475A THR* 1.3 59.9 + - - +
477A PRO* 3.4 8.7 - - - +
478A TYR* 2.9 43.9 - - + -
507A VAL* 3.8 21.3 - - + -
521A MET* 4.2 6.3 - - - -
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Residues in contact with THR 475 (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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470A LEU* 5.5 5.2 - - - +
471A ASN 3.8 0.6 + - - -
472A LEU* 2.6 25.2 + - - +
473A SER 2.9 1.0 - - - -
474A VAL* 1.3 79.9 - - - +
476A SER* 1.3 90.6 + - - +
478A TYR* 3.5 3.0 + - - +
479A ASN* 3.0 17.7 + - - -
480A ALA* 3.1 33.1 + - - +
482A PHE* 4.3 12.4 - - - -
524A VAL* 4.8 9.0 - - + -
836B GLU* 4.1 29.1 + - + +
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Residues in contact with SER 476 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473A SER 4.2 4.4 + - - -
475A THR* 1.3 90.3 - - - +
477A PRO* 1.3 74.4 - - - +
479A ASN* 2.8 19.7 + - - +
520A CYS 4.2 10.3 - - - -
521A MET* 5.1 4.0 - - - -
522A GLY 5.1 1.9 + - - -
524A VAL* 4.8 8.7 - - - +
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Residues in contact with PRO 477 (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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451A HIS* 3.2 28.8 - - + +
453A MET* 3.3 30.1 - - + +
454A SER* 4.0 1.7 + - - -
456A MET* 3.5 14.1 - - + -
473A SER 3.9 5.6 - - - +
474A VAL 3.4 14.4 - - - +
476A SER* 1.3 95.2 - - - +
478A TYR* 1.3 59.1 + - - +
479A ASN* 4.9 0.9 - - - +
520A CYS* 3.7 13.7 - - + +
521A MET* 3.3 33.7 - - + -
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Residues in contact with TYR 478 (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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444A PHE* 3.4 24.6 + + - -
446A ARG* 3.4 41.0 + - + +
448A PRO 4.9 1.9 - - - +
453A MET 3.9 1.1 - - - -
454A SER* 3.4 33.1 + - - +
456A MET* 3.2 34.3 + - + +
458A HIS* 2.4 34.5 + - - -
470A LEU* 4.5 2.9 - - + -
474A VAL* 2.9 41.5 - - + -
475A THR* 3.5 4.8 + - - +
476A SER 3.2 0.6 - - - -
477A PRO* 1.3 75.8 - - - +
479A ASN* 1.3 70.5 - - - +
480A ALA* 4.2 5.4 - - + +
487A MET* 3.9 19.5 - - + -
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Residues in contact with ASN 479 (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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446A ARG* 3.1 26.6 + - - +
450A LEU* 6.0 1.6 - - - +
475A THR 3.0 2.7 + - - -
476A SER* 2.8 16.9 + - - +
477A PRO 4.9 0.9 - - - +
478A TYR* 1.3 84.0 - - - +
480A ALA* 1.3 60.1 + - - +
481A ASP* 3.6 10.6 + - - +
1078A GLN* 4.1 23.1 + - - +
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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