Contacts of the strand formed by residues 457 - 462 (chain A) in PDB entry 2IHU
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 THR 457 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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405A THR* 3.4 11.5 + - - +
407A VAL* 4.3 6.3 - - + -
445A ALA* 3.9 34.8 - - + +
448A ALA* 4.1 16.2 + - + -
449A GLN* 3.1 40.0 + - - -
452A ARG* 4.9 1.6 + - - +
455A GLN 3.7 1.3 + - - -
456A PRO* 1.3 75.8 + - - +
458A PHE* 1.3 65.1 + - - +
482A PRO 4.4 2.5 + - - +
483A ILE* 3.5 8.2 - - + +
484A VAL* 3.0 23.7 + - - +
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Residues in contact with PHE 458 (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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391A MET* 3.6 51.8 - - + -
394A VAL* 4.1 20.4 - - + -
395A MET* 3.6 40.8 - - + -
398A ALA* 4.7 1.6 - - + -
405A THR 2.9 7.5 + - - +
406A ILE* 3.4 6.0 - - + -
407A VAL* 2.7 35.2 + - - +
456A PRO* 4.3 10.3 - - + -
457A THR* 1.3 84.2 - - - +
459A LEU* 1.3 54.5 + - - +
483A ILE* 5.0 0.2 - - - -
484A VAL* 3.2 30.7 - - + +
543A LEU* 4.3 14.4 - - + -
547A ALA* 4.2 14.4 - - + -
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Residues in contact with LEU 459 (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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391A MET* 4.1 4.7 - - - +
407A VAL* 3.4 16.2 - - + +
409A ASP 4.2 0.7 - - - +
441A GLY* 3.4 45.8 - - - +
442A ILE* 3.7 17.7 - - + +
445A ALA* 4.4 7.6 - - + -
458A PHE* 1.3 74.3 - - - +
460A ILE* 1.3 78.3 + - - +
461A ALA* 4.5 1.8 - - + +
466A PHE* 4.4 6.7 - - + -
476A ILE* 5.9 0.7 - - + -
483A ILE* 4.4 8.5 - - + -
484A VAL 2.8 7.2 + - - +
485A THR* 3.4 32.7 - - + +
486A VAL* 2.7 34.7 + - - +
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Residues in contact with ILE 460 (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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384A VAL* 4.4 8.5 - - + -
387A VAL* 4.3 4.7 - - + -
388A ILE* 4.2 27.8 - - + -
391A MET* 4.0 23.1 - - + +
406A ILE* 4.9 5.8 - - + -
407A VAL 2.9 17.2 + - - +
408A SER* 3.4 18.2 - - - +
409A ASP 3.0 24.1 + - - -
413A PHE* 3.5 19.9 - - + +
417A GLY* 5.8 2.9 - - - -
429A PHE* 5.6 1.3 - - + -
459A LEU* 1.3 77.7 - - - +
461A ALA* 1.3 64.9 + - - +
486A VAL* 3.3 9.2 - - + +
488A VAL* 4.1 24.5 - - + -
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Residues in contact with ALA 461 (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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409A ASP* 3.5 19.1 - - + +
413A PHE* 3.5 9.9 - - - -
459A LEU* 4.2 8.0 - - + -
460A ILE* 1.3 77.1 - - - +
462A GLY* 1.3 55.8 + - - +
466A PHE* 3.8 33.9 - - + -
485A THR* 5.5 0.2 - - + -
486A VAL 2.9 7.3 + - - +
487A VAL* 3.2 6.4 - - + -
488A VAL* 2.8 34.3 + - - +
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Residues in contact with GLY 462 (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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409A ASP* 4.8 0.4 - - - +
413A PHE* 3.1 19.9 - - - -
461A ALA* 1.3 74.9 - - - +
463A ASP* 1.3 61.2 + - - -
464A GLY 3.3 2.5 - - - -
466A PHE* 2.8 31.6 + - - +
487A VAL* 4.3 1.1 - - - -
488A VAL* 3.2 15.3 - - - -
600A TP9 3.4 16.5 + - - -
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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