Contacts of the strand formed by residues 457 - 462 (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 THR 457 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405B THR* 3.4 11.6 + - - +
407B VAL* 4.2 7.9 - - + -
445B ALA* 3.9 36.1 - - + +
448B ALA* 4.2 14.1 - - + -
449B GLN* 3.0 41.5 + - - -
452B ARG* 4.9 1.4 + - - +
455B GLN* 3.6 1.8 + - - +
456B PRO* 1.3 74.1 + - - +
458B PHE* 1.3 66.4 + - - +
482B PRO 4.5 3.1 + - - +
483B ILE* 3.5 8.1 - - + +
484B VAL* 3.0 24.4 + - - +
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Residues in contact with PHE 458 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391B MET* 3.6 52.3 - - + -
394B VAL* 4.0 22.0 - - + -
395B MET* 3.6 37.0 - - + -
398B ALA* 4.9 1.3 - - + -
405B THR 2.9 7.5 + - - +
406B ILE* 3.4 6.1 - - + -
407B VAL* 2.7 34.9 + - - +
456B PRO* 4.3 12.3 - - + -
457B THR* 1.3 83.0 - - - +
459B LEU* 1.3 54.9 + - - +
484B VAL* 3.2 29.2 - - + +
543B LEU* 4.2 21.1 - - + -
547B ALA* 4.3 12.1 - - + -
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Residues in contact with LEU 459 (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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391B MET* 4.0 4.6 - - - +
407B VAL* 3.4 17.0 - - + +
409B ASP 4.2 0.4 - - - +
441B GLY* 3.3 45.8 - - - +
442B ILE* 3.8 17.3 - - + +
445B ALA* 4.3 14.6 - - + -
458B PHE* 1.3 75.0 - - - +
460B ILE* 1.3 76.4 + - - +
461B ALA* 4.6 2.7 - - + -
466B PHE* 4.4 6.1 - - + -
483B ILE* 4.4 1.3 - - + -
484B VAL 2.8 10.3 + - - +
485B THR* 3.4 32.5 - - + +
486B VAL* 2.7 35.3 + - - +
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Residues in contact with ILE 460 (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* 4.5 7.4 - - + -
387B VAL* 4.0 16.6 - - + -
388B ILE* 4.2 19.5 - - + -
391B MET* 3.9 21.1 - - + +
406B ILE* 4.7 6.1 - - + -
407B VAL 2.8 19.1 + - - +
408B SER* 3.4 17.6 - - - +
409B ASP 3.0 25.3 + - - -
413B PHE* 3.5 20.9 - - + -
417B GLY* 5.8 2.7 - - - -
429B PHE* 5.5 1.3 - - + -
459B LEU* 1.3 74.9 - - - +
461B ALA* 1.3 63.1 + - - +
486B VAL* 3.3 8.3 - - + +
488B VAL* 4.0 26.2 - - + -
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Residues in contact with ALA 461 (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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409B ASP* 3.7 17.0 - - + +
413B PHE* 3.6 9.6 - - - -
459B LEU* 4.6 8.3 - - + -
460B ILE* 1.3 75.9 - - - +
462B GLY* 1.3 61.1 + - - +
466B PHE* 3.7 35.9 - - + -
485B THR* 5.3 0.2 - - + -
486B VAL 3.0 8.0 + - - +
487B VAL* 3.2 7.0 - - + -
488B VAL* 2.8 27.5 + - - +
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Residues in contact with GLY 462 (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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409B ASP* 4.8 0.4 - - - +
413B PHE* 3.2 22.5 - - - -
461B ALA* 1.3 73.0 - - - +
463B ASP* 1.3 60.2 + - - -
464B GLY 3.4 2.2 - - - -
466B PHE* 2.8 32.6 + - - +
487B VAL* 4.3 1.1 - - - -
488B VAL* 3.4 11.7 - - - -
600B TP9 3.3 19.2 + - - -
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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