Contacts of the strand formed by residues 484 - 489 (chain B) 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 VAL 484 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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457B THR 3.0 6.2 + - - +
458B PHE* 3.2 27.0 - - + +
459B LEU 2.8 30.3 + - - +
482B PRO 4.1 7.0 - - - +
483B ILE* 1.3 75.6 - - - +
485B THR* 1.3 57.5 + - - +
486B VAL* 5.3 1.2 - - + +
543B LEU* 4.2 16.8 - - + +
546B GLY* 3.5 41.1 - - - +
547B ALA* 3.7 5.4 - - - +
551B ARG 5.6 0.2 - - - +
553B PHE* 3.4 9.9 - - + +
555B ILE* 4.0 25.1 - - + -
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Residues in contact with THR 485 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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442B ILE* 5.5 0.2 - - - +
459B LEU* 3.4 27.9 - - + +
461B ALA* 5.3 0.2 - - + -
466B PHE* 3.8 28.6 - - + -
473B LEU* 5.3 3.7 - - - +
476B ILE* 5.0 6.9 - - - +
483B ILE* 3.8 11.4 + - - +
484B VAL* 1.3 74.8 - - - +
486B VAL* 1.3 61.6 + - - +
487B VAL* 4.0 14.4 - - + -
553B PHE 2.8 15.5 + - - -
554B LEU* 3.4 12.6 - - + -
555B ILE* 2.8 35.7 + - - +
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Residues in contact with VAL 486 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387B VAL* 3.9 20.9 - - + -
391B MET* 4.0 21.3 - - + -
458B PHE* 6.3 0.2 - - + -
459B LEU 2.7 14.2 + - - +
460B ILE* 3.3 3.6 - - + +
461B ALA* 3.0 26.2 + - - +
484B VAL* 5.3 1.6 - - + +
485B THR* 1.3 77.0 - - - +
487B VAL* 1.3 62.9 + - - +
488B VAL* 3.8 9.4 + - + -
539B LEU* 4.6 3.8 - - + -
543B LEU* 3.9 27.8 - - + -
555B ILE* 3.3 11.9 - - + +
557B VAL* 3.8 26.2 - - + -
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Residues in contact with VAL 487 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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461B ALA 3.2 8.7 - - - +
462B GLY 4.3 2.7 - - - +
463B ASP* 4.3 14.1 - - - +
466B PHE* 3.9 21.5 - - + -
485B THR* 4.0 7.4 - - + -
486B VAL* 1.3 73.9 - - - +
488B VAL* 1.3 65.0 + - - +
489B ASN* 3.6 1.8 + - + +
519B PHE* 4.0 35.2 - - + -
554B LEU* 3.9 31.6 - - + -
555B ILE 2.8 11.2 + - - +
556B GLU* 3.5 6.8 - - - +
557B VAL 2.8 28.2 + - - +
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Residues in contact with VAL 488 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384B VAL* 4.7 3.8 - - + -
387B VAL* 4.0 28.5 - - + -
413B PHE* 4.0 28.5 - - + -
460B ILE* 4.0 13.0 - - + -
461B ALA 2.8 20.0 + - - +
462B GLY* 3.4 6.5 - - - -
463B ASP* 3.3 20.5 + - - +
486B VAL* 3.8 5.6 + - + -
487B VAL* 1.3 72.1 - - - +
489B ASN* 1.3 59.1 + - - +
490B ASN* 4.0 0.3 + - - +
557B VAL* 3.4 5.4 - - + -
559B VAL* 3.7 30.6 - - + +
561B TYR* 4.4 9.0 + - - +
600B TP9 5.7 0.2 + - - -
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Residues in contact with ASN 489 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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463B ASP* 3.1 21.8 - - + +
487B VAL* 4.5 0.9 - - + +
488B VAL* 1.3 72.5 - - - +
490B ASN* 1.3 58.9 + - - +
491B ASP* 2.8 44.4 + - - +
516B GLY* 5.9 0.2 - - - -
517B VAL 3.8 7.5 + - - +
519B PHE* 3.6 16.1 - - + -
556B GLU* 2.9 34.4 + - + +
557B VAL 2.9 15.1 + - - +
558B PRO* 3.5 5.9 - - + +
559B VAL* 2.9 27.6 + - - +
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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