Contacts of the strand formed by residues 457 - 462 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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405D THR* 3.4 13.1 + - - +
407D VAL* 4.3 7.0 - - + -
445D ALA* 3.8 37.0 - - + +
448D ALA* 4.2 13.6 + - + -
449D GLN* 3.1 40.0 + - - -
452D ARG* 4.8 0.9 + - - +
455D GLN* 3.6 2.7 + - - +
456D PRO* 1.3 74.6 + - - +
458D PHE* 1.3 66.6 + - - +
482D PRO 4.3 2.5 + - - +
483D ILE* 3.6 8.5 - - + +
484D VAL 3.1 23.0 + - - -
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Residues in contact with PHE 458 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391D MET* 3.7 35.4 - - + -
394D VAL* 4.0 23.1 - - + -
395D MET* 3.5 48.0 - - + -
398D ALA* 4.7 2.7 - - + -
405D THR 2.9 8.3 + - - +
406D ILE* 3.4 5.9 - - + -
407D VAL* 2.8 35.2 + - - +
456D PRO* 4.3 11.0 - - + -
457D THR* 1.3 84.8 - - - +
459D LEU* 1.3 55.4 + - - +
483D ILE* 5.0 0.2 - - - -
484D VAL* 3.2 31.0 - - + +
543D LEU* 4.4 18.4 - - + -
547D ALA* 4.2 12.6 - - + -
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Residues in contact with LEU 459 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391D MET* 4.0 4.8 - - - +
407D VAL* 3.4 17.5 - - + +
409D ASP 4.2 0.9 - - - +
441D GLY* 3.4 46.4 - - - +
442D ILE* 3.8 16.8 - - + +
445D ALA* 4.4 13.7 - - + -
457D THR 4.3 0.2 + - - -
458D PHE* 1.3 74.4 - - - +
460D ILE* 1.3 76.0 + - - +
461D ALA* 4.6 2.0 - - + -
466D PHE* 4.4 7.0 - - + -
483D ILE* 4.4 2.4 - - + +
484D VAL 2.8 9.8 + - - +
485D THR* 3.4 33.6 - - + +
486D VAL* 2.6 35.5 + - - +
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Residues in contact with ILE 460 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384D VAL* 4.6 5.4 - - + -
387D VAL* 4.0 25.6 - - + -
388D ILE* 4.1 27.8 - - + -
391D MET* 4.0 19.0 - - + +
406D ILE* 4.9 6.1 - - + -
407D VAL 2.9 16.5 + - - +
408D SER* 3.4 17.8 - - - +
409D ASP 2.9 25.1 + - - -
413D PHE* 3.4 19.2 - - + -
417D GLY* 5.7 2.2 - - - -
429D PHE* 5.7 0.9 - - + -
459D LEU* 1.3 76.5 - - - +
461D ALA* 1.3 64.5 + - - +
486D VAL* 3.4 9.4 - - + +
488D VAL* 4.0 16.2 - - + -
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Residues in contact with ALA 461 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409D ASP* 3.6 17.5 - - + +
413D PHE* 3.5 10.8 - - - -
459D LEU* 4.6 8.7 - - + -
460D ILE* 1.3 75.3 - - - +
462D GLY* 1.3 54.8 + - - +
466D PHE* 3.8 35.2 - - + -
485D THR* 5.3 0.2 - - + -
486D VAL 3.0 7.0 + - - +
487D VAL* 3.3 5.2 - - - -
488D VAL* 2.8 34.9 + - - +
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Residues in contact with GLY 462 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409D ASP* 4.8 0.4 - - - +
413D PHE* 3.2 18.9 - - - -
461D ALA* 1.3 74.5 - - - +
463D ASP* 1.3 61.3 + - - -
464D GLY 3.3 2.7 - - - -
466D PHE* 2.8 32.4 + - - +
487D VAL* 4.2 1.3 - - - -
488D VAL* 3.3 14.8 - - - -
600D TP9 3.4 16.2 + - - -
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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