Contacts of the strand formed by residues 476 - 480 (chain A) in PDB entry 3I7H
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 476 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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469A ILE* 4.3 17.0 - - + -
470A GLN 4.0 4.9 - - - -
471A ILE* 4.0 24.2 - - + +
475A SER* 1.3 68.2 - - - +
477A ARG* 1.3 59.7 + - - +
489A GLU* 3.9 0.9 - - - -
490A TRP* 3.0 58.4 + - + +
498A ILE* 3.8 13.1 - - + +
508A VAL* 4.9 6.1 - - + -
510A VAL* 4.8 7.2 - - + -
519A LEU* 3.7 14.4 - - + -
526A LEU* 3.8 25.3 - - + +
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Residues in contact with ARG 477 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450A GLY* 2.7 38.4 + - - -
451A PHE 4.1 0.2 - - - -
452A VAL* 3.1 41.3 - - - +
468A LEU 5.3 0.2 - - - -
469A ILE* 3.5 6.9 - - - +
470A GLN* 2.7 63.0 + - + +
472A THR* 4.3 1.6 - - - -
475A SER* 3.1 24.2 - - - +
476A VAL* 1.3 72.9 - - - +
478A LEU* 1.3 72.9 + - - +
479A VAL* 5.1 0.9 - - + +
486A LEU* 4.1 15.8 - - + +
488A SER 4.0 4.3 - - - -
489A GLU* 3.1 32.1 + - + +
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Residues in contact with LEU 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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463A VAL* 5.3 4.7 - - + -
467A GLN* 3.5 28.0 - - + +
468A LEU 4.4 3.4 - - - +
469A ILE* 5.3 1.8 - - + -
476A VAL* 4.8 1.6 - - + -
477A ARG* 1.3 85.9 - - - +
479A VAL* 1.3 63.2 + - - +
480A SER 4.3 0.2 - - - -
486A LEU* 3.1 27.2 - - - +
487A VAL* 3.1 23.6 + - + -
488A SER* 3.2 19.9 + - - +
521A ILE* 3.6 28.9 - - + -
525A GLU* 4.5 9.0 - - - +
526A LEU* 3.4 43.3 - - + -
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Residues in contact with VAL 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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448A LEU* 5.6 1.6 - - + -
449A MET 3.4 16.8 - - - +
450A GLY* 3.0 38.1 - - - +
451A PHE* 4.7 11.0 - - + -
467A GLN* 4.5 2.0 - - - +
468A LEU* 2.7 60.3 + - + +
477A ARG* 5.1 1.1 - - + +
478A LEU* 1.3 81.2 - - - +
480A SER* 1.3 71.1 + - - +
484A LYS* 4.8 4.5 - - + -
485A ALA 3.3 7.6 - - - +
486A LEU* 4.0 11.9 - - + +
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Residues in contact with SER 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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465A HIS 4.6 1.6 - - - -
466A GLN 3.2 13.0 - - - -
467A GLN* 3.7 17.8 - - - +
468A LEU* 4.6 0.2 - - - +
478A LEU 4.3 0.4 - - - -
479A VAL* 1.3 83.3 - - - +
481A GLN* 1.3 60.0 + - - +
483A PRO* 3.0 35.8 - - - +
484A LYS* 3.0 21.7 - - - +
485A ALA 3.0 12.1 + - - -
487A VAL* 3.3 19.8 - - - +
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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