Contacts of the strand formed by residues 436 - 442 (chain B) in PDB entry 1EOB
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 TYR 436 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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381B HIS* 2.8 42.0 + + + +
382B GLY 3.3 20.2 - - - -
383B TYR* 3.6 36.8 - + + -
430B LEU 4.4 0.7 - - - +
431B THR* 3.3 4.6 - - - -
432B ASP* 3.0 48.3 + - - +
434B ASN* 3.1 4.5 + - + +
435B GLY* 1.3 78.6 - - - +
437B TYR* 1.3 66.2 + - - +
438B VAL* 4.1 20.5 - - + +
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Residues in contact with TYR 437 (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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380B VAL* 3.8 5.2 - - + +
381B HIS* 3.2 34.0 + - - +
382B GLY 3.0 33.0 + - - -
383B TYR 4.0 1.8 - - - -
384B VAL* 4.0 17.7 - - + -
397B VAL* 4.9 13.0 - - + -
429B MET* 4.4 12.6 - - + -
430B LEU 5.2 3.8 - - - +
431B THR* 4.1 16.4 - - + +
436B TYR* 1.3 78.6 - - - +
438B VAL* 1.3 70.0 + - - +
439B PHE* 3.8 28.9 - + - -
478B PHE* 5.0 0.9 - + - -
523B PHE* 2.6 52.2 + + - +
525B ILE* 4.5 15.3 - - + -
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Residues in contact with VAL 438 (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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361B ASN* 2.9 29.4 + - - +
379B ILE* 3.9 20.2 - - + -
380B VAL 3.4 12.1 - - - +
381B HIS* 3.9 9.2 - - + -
429B MET* 4.0 7.9 - - - +
436B TYR* 4.1 19.7 - - + +
437B TYR* 1.3 80.7 - - - +
439B PHE* 1.3 67.8 + - - +
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Residues in contact with PHE 439 (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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361B ASN* 3.1 22.9 - - + +
363B LEU* 3.9 10.8 - - + -
379B ILE* 3.6 5.0 - - - +
380B VAL* 2.9 68.4 + - + +
397B VAL* 5.9 0.2 - - + -
399B VAL* 4.2 27.4 - - + -
401B GLN* 5.0 1.1 - - - -
429B MET* 3.6 28.3 - - + -
437B TYR* 3.8 14.4 - + - -
438B VAL* 1.3 78.3 - - - +
440B ARG* 1.3 68.7 + - - +
441B THR* 4.1 20.2 - - + -
461B ILE* 4.3 7.6 - - + -
478B PHE* 4.1 18.8 - + - -
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Residues in contact with ARG 440 (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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361B ASN 3.0 8.1 + - - +
362B ASP* 2.6 39.9 + - - +
363B LEU* 2.9 29.2 + - - +
364B ILE* 3.3 24.7 - - + +
365B LEU* 3.4 21.4 - - - +
377B ARG* 3.8 19.6 - - - +
378B VAL 3.7 10.3 - - - +
379B ILE* 4.2 19.7 - - + +
439B PHE* 1.3 75.3 - - - +
441B THR* 1.3 69.3 + - - +
517B ASP* 5.1 4.8 + - - -
518B SER* 4.7 6.9 + - - +
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Residues in contact with THR 441 (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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363B LEU* 3.4 19.3 - - - +
364B ILE* 3.8 19.2 - - - +
376B GLU 3.6 0.5 - - - +
378B VAL* 2.9 51.9 + - + +
380B VAL* 4.8 2.7 - - + -
401B GLN* 2.7 34.5 + - - +
423B PHE* 3.8 0.9 - - - -
439B PHE* 4.1 10.3 - - + -
440B ARG* 1.3 79.6 - - - +
442B ILE* 1.3 68.2 + - - +
461B ILE* 4.0 15.0 - - + -
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Residues in contact with ILE 442 (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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364B ILE* 4.6 9.9 - - + -
373B PRO* 3.9 32.5 - - + +
374B ILE 3.7 6.3 - - - +
375B GLY* 3.6 46.4 - - - +
376B GLU 3.4 7.2 - - - +
377B ARG* 4.1 10.8 - - + +
401B GLN* 2.6 32.4 + - - -
403B ASN* 4.9 0.9 - - + -
404B ALA* 3.9 13.0 - - + +
423B PHE* 3.8 18.5 - - + -
441B THR* 1.3 85.2 + - - +
443B LYS* 1.3 70.8 + - - +
444B PRO* 3.4 0.9 - - - +
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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