Contacts of the strand formed by residues 474 - 477 (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 PHE 474 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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355A ALA 4.6 0.4 - - - -
356A ARG* 3.7 5.4 - - - -
357A THR* 3.3 51.6 - - + -
358A VAL 3.2 4.4 + - - -
359A ILE* 3.7 12.0 - - + +
360A THR 3.2 18.5 + - - +
370A LEU* 4.5 8.1 - - + -
371A GLY 3.6 13.0 - - - -
372A VAL* 4.9 2.0 - - + -
373A PRO* 4.6 7.4 - - + -
376A ILE* 4.1 15.5 - - + -
450A PHE* 3.7 33.0 - + + -
473A THR* 1.3 75.3 + - - +
475A ARG* 1.3 62.8 + - - +
476A LEU* 3.3 1.7 + - - -
493A MET 3.5 13.7 - - - -
495A MET* 3.2 41.3 - - + -
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Residues in contact with ARG 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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360A THR* 3.7 20.2 - - - -
361A GLY 3.9 4.0 - - - +
362A ASP* 3.6 29.2 - - + +
365A LEU* 4.0 6.2 - - + +
370A LEU* 3.0 9.5 - - - +
371A GLY* 2.9 41.8 + - - +
373A PRO 4.8 2.4 - - - -
469A MET* 3.6 28.4 + - + +
470A PRO 2.7 30.7 + - - -
471A TYR* 3.0 25.5 + - - +
473A THR* 3.0 35.9 + - - +
474A PHE* 1.3 70.7 - - - +
476A LEU* 1.3 57.8 + - - +
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Residues in contact with LEU 476 (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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359A ILE* 4.5 11.2 - - + -
360A THR 3.3 5.4 + - - +
361A GLY* 4.0 1.7 - - - -
362A ASP* 3.3 25.1 + - - +
365A LEU* 4.9 3.4 - - - -
369A GLU 4.6 6.1 - - - +
370A LEU* 3.5 13.5 - - + -
450A PHE* 3.5 31.0 - - + -
464A HIS* 5.2 5.4 - - + +
474A PHE 3.3 2.2 + - - +
475A ARG* 1.3 75.2 - - - +
477A ASN* 1.3 70.9 + - - +
478A LEU 3.7 0.9 + - - -
480A VAL* 5.2 5.8 - - + -
481A THR* 4.3 13.2 - - + +
484A TYR* 4.6 17.3 - - + -
488A PHE* 4.3 16.4 - - + -
493A MET* 3.9 14.4 - - - -
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Residues in contact with ASN 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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362A ASP 3.9 10.1 + - - -
365A LEU* 4.2 13.4 + - + +
366A SER 4.2 4.9 - - - +
367A LEU* 3.2 45.6 + - - +
369A GLU 4.7 3.9 + - - +
464A HIS* 6.2 0.4 - - - -
476A LEU* 1.3 77.9 - - - +
478A LEU* 1.3 60.0 + - - +
479A SER 4.0 1.6 - - - -
480A VAL* 2.7 47.6 + - + +
481A THR* 4.1 0.9 + - - -
652A PHE* 5.0 0.5 - - - +
653A ASN* 4.8 1.2 - - - +
656A GLN* 2.5 42.1 + - - +
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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