Contacts of the strand formed by residues 489 - 493 (chain A) in PDB entry 4IQJ
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 489 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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477A ILE* 4.9 3.4 - - + +
480A VAL* 3.7 40.2 - - + +
481A ARG* 3.6 28.9 - - + -
484A TYR* 4.0 13.9 - - + -
485A GLY 2.8 15.9 + - - +
486A GLU 3.0 16.3 - - - +
487A ASP 3.5 0.4 - - - -
488A LYS* 1.3 82.8 - - - +
490A ALA* 1.3 66.9 + - - +
579A VAL* 4.2 12.3 - - + -
580A VAL 3.4 13.2 - - - +
581A ILE* 4.2 5.8 - - + -
586A LEU* 3.8 0.4 - - - -
600A PRO* 4.0 9.2 - - - +
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Residues in contact with ALA 490 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481A ARG* 5.8 0.4 - - - +
489A VAL* 1.3 80.6 - - - +
491A GLN* 1.3 64.5 + - - +
579A VAL* 4.7 0.9 - - - -
580A VAL* 2.9 33.5 + - - +
586A LEU* 3.4 21.9 - - + +
592A LEU* 4.4 10.5 - - + -
600A PRO* 3.2 28.7 - - + +
601A VAL 4.8 0.2 - - - -
602A THR* 4.1 8.5 - - - +
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Residues in contact with GLN 491 (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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473A ARG* 4.4 5.5 - - - +
477A ILE* 4.0 27.2 - - + +
490A ALA* 1.3 75.3 - - - +
492A ILE* 1.3 55.8 + - - +
574A VAL* 4.0 15.7 - - + +
575A HIS 3.6 21.0 + - - -
576A ALA 4.5 1.8 + - - -
578A GLY 3.2 16.8 + - - +
579A VAL* 4.2 8.5 - - + +
599A ARG* 2.7 48.0 + - + +
600A PRO* 2.8 16.8 + - + +
601A VAL* 3.4 3.8 - - + -
602A THR* 2.6 37.4 + - - -
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Residues in contact with ILE 492 (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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491A GLN* 1.3 74.6 - - - +
493A GLY* 1.3 68.7 + - - +
574A VAL* 3.6 3.8 - - - +
575A HIS* 2.7 37.6 + - + +
578A GLY* 3.3 24.6 + - - -
579A VAL 4.4 0.2 - - - +
580A VAL* 3.3 28.0 - - + -
601A VAL* 4.0 2.0 - - - -
602A THR* 4.0 3.8 - - - +
604A TYR 3.9 4.0 - - - +
605A ASP 3.8 5.6 - - - +
606A MET* 3.7 29.2 - - + +
609A VAL* 4.3 11.9 - - + -
616A LYS* 3.4 40.4 - - + -
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Residues in contact with GLY 493 (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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492A ILE* 1.3 88.8 - - - +
494A THR* 1.3 63.1 + - - -
495A PHE* 4.6 9.4 - - - -
573A SER 2.9 15.3 - - - -
575A HIS* 5.1 0.2 + - - -
601A VAL* 3.6 6.3 - - - +
602A THR 3.3 23.3 + - - -
604A TYR 3.8 2.8 + - - -
605A ASP* 3.8 12.7 - - - +
606A MET* 4.4 1.4 + - - +
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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