Contacts of the strand formed by residues 457 - 462 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405C THR* 3.4 12.2 + - - +
407C VAL* 4.3 6.3 - - + -
445C ALA* 3.8 34.8 - - + +
448C ALA* 4.0 17.5 + - + -
449C GLN* 3.2 40.0 + - - -
452C ARG* 4.9 2.1 + - - +
455C GLN 3.6 2.2 + - - -
456C PRO* 1.3 77.3 + - - +
458C PHE* 1.3 66.2 + - - +
482C PRO 4.4 2.8 + - - +
483C ILE* 3.6 8.2 - - + +
484C VAL* 3.1 23.4 + - - +
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Residues in contact with PHE 458 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391C MET* 3.8 32.8 - - + -
394C VAL* 4.1 21.1 - - + -
395C MET* 3.6 47.3 - - + -
398C ALA* 4.9 1.6 - - + -
405C THR 2.9 8.0 + - - +
406C ILE* 3.4 6.2 - - + -
407C VAL* 2.7 36.3 + - - +
456C PRO* 4.4 8.5 - - + -
457C THR* 1.3 83.7 - - - +
459C LEU* 1.3 54.5 + - - +
460C ILE 4.3 0.2 - - - -
484C VAL* 3.3 32.3 - - + +
543C LEU* 4.1 25.1 - - + -
547C ALA* 4.1 15.5 - - + -
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Residues in contact with LEU 459 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391C MET* 4.0 4.9 - - - +
407C VAL* 3.4 16.4 - - + +
409C ASP 4.2 0.7 - - - +
441C GLY* 3.4 44.9 - - - +
442C ILE* 3.7 16.6 - - + +
445C ALA* 4.3 15.0 - - + -
457C THR 4.3 0.2 + - - -
458C PHE* 1.3 76.0 - - - +
460C ILE* 1.3 80.0 + - - +
461C ALA* 4.5 2.7 - - + -
466C PHE* 4.5 5.6 - - + -
476C ILE* 5.8 0.9 - - + -
483C ILE* 4.5 2.2 - - + -
484C VAL 2.8 12.4 + - - +
485C THR* 3.4 28.4 - - + +
486C VAL* 2.7 35.3 + - - +
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Residues in contact with ILE 460 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384C VAL* 4.5 7.2 - - + -
387C VAL* 3.9 18.2 - - + -
388C ILE* 4.0 28.3 - - + -
391C MET* 4.0 15.8 - - + +
406C ILE* 5.1 3.6 - - + -
407C VAL 2.8 20.2 + - - +
408C SER* 3.4 17.2 - - - +
409C ASP 3.0 25.1 + - - -
413C PHE* 3.4 19.1 - - + +
417C GLY* 5.6 1.8 - - - -
429C PHE* 5.8 0.2 - - + -
459C LEU* 1.3 77.7 - - - +
461C ALA* 1.3 64.8 + - - +
486C VAL* 3.3 10.1 - - + +
488C VAL* 3.8 26.9 - - + -
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Residues in contact with ALA 461 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409C ASP* 3.6 17.7 - - + +
413C PHE* 3.5 11.4 - - - -
459C LEU* 4.5 8.3 - - + -
460C ILE* 1.3 76.6 - - - +
462C GLY* 1.3 54.5 + - - +
466C PHE* 3.8 34.3 - - + -
485C THR* 5.4 0.2 - - + -
486C VAL 3.0 7.3 + - - +
487C VAL* 3.2 7.5 - - - -
488C VAL* 2.8 32.0 + - - +
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Residues in contact with GLY 462 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409C ASP* 4.8 0.4 - - - +
413C PHE* 3.2 19.8 - - - -
461C ALA* 1.3 73.2 - - - +
463C ASP* 1.3 61.5 + - - -
464C GLY 3.3 2.7 - - - -
466C PHE* 2.8 32.0 + - - +
487C VAL* 4.2 0.9 - - - -
488C VAL* 3.3 14.8 - - - -
600C TP8 3.5 17.8 + - - -
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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