Contacts of the strand formed by residues 528 - 534 (chain B) in PDB entry 1EQR
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 HIS 528 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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199B GLN* 3.7 19.4 + - + -
202B MET* 4.1 16.8 - - + -
203B MET* 3.5 31.1 - - + +
235B GLU* 3.6 9.9 - - - +
236B THR 3.1 13.5 - - - +
237B SER* 4.1 2.7 - - - +
238B PHE 4.7 0.4 - - - +
239B MET 5.2 3.1 - - - -
488B VAL* 3.9 7.1 - - - +
489B ARG* 3.2 54.6 + - + +
490B ILE 3.7 24.4 + - - -
491B HIS* 4.7 0.4 - - + +
521B LEU* 4.9 3.4 - - + +
525B THR* 3.9 4.7 - - - -
526B PRO 2.9 14.9 + - - +
527B PRO* 1.3 74.2 - - - +
529B ALA* 1.3 64.4 + - - +
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Residues in contact with ALA 529 (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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235B GLU* 3.5 8.0 + - - -
236B THR* 2.5 50.4 + - - +
239B MET 4.5 6.2 + - - +
244B VAL* 4.1 14.6 - - + -
474B TYR* 3.8 7.0 - - - +
487B SER 3.5 15.5 - - - +
488B VAL* 3.6 22.7 - - + -
489B ARG* 4.0 1.8 - - - +
528B HIS* 1.3 77.5 - - - +
530B GLY* 1.3 54.3 + - - +
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Residues in contact with GLY 530 (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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234B VAL* 3.2 7.0 - - - -
235B GLU* 3.1 18.6 - - - -
236B THR* 5.7 0.4 - - - -
244B VAL* 4.9 4.7 - - - -
474B TYR* 2.9 19.0 + - - -
487B SER 3.1 18.4 + - - -
489B ARG* 3.2 12.3 - - - +
529B ALA* 1.3 76.6 - - - +
531B LEU* 1.3 64.2 + - - +
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Residues in contact with LEU 531 (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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198B LYS* 3.7 7.3 + - - +
234B VAL* 2.7 43.8 + - + +
244B VAL* 4.8 2.2 - - + -
248B MET* 3.6 23.8 - - + -
429B TRP* 4.1 20.9 - - + -
474B TYR* 3.8 21.5 - - + -
484B GLY* 4.5 2.0 - - - -
485B GLY* 3.1 33.7 - - - +
486B GLY* 3.8 1.3 - - - -
489B ARG* 5.0 0.2 - - - +
530B GLY* 1.3 76.8 - - - +
532B ALA* 1.3 63.0 + - - +
533B PHE* 3.5 39.0 - - + -
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Residues in contact with ALA 532 (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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198B LYS* 4.8 2.0 - - - +
231B GLN* 3.6 34.4 + - + +
232B ILE 3.2 10.3 - - - +
233B ASP* 3.9 11.0 - - - +
484B GLY* 3.2 4.3 - - - -
485B GLY 2.8 29.2 + - - +
531B LEU* 1.3 77.8 - - - +
533B PHE* 1.3 61.0 + - - +
534B GLY 4.1 0.3 + - - -
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Residues in contact with PHE 533 (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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231B GLN* 3.3 6.2 - - - +
232B ILE* 2.8 57.4 + - + -
234B VAL* 5.2 0.4 - - + -
248B MET* 3.7 39.3 - - + -
251B LEU* 3.9 15.9 - - + -
252B VAL* 3.8 7.0 - - + -
476B MET* 3.5 33.0 - - + -
483B VAL* 3.1 20.4 - - + -
484B GLY* 3.9 6.3 - - - -
531B LEU* 3.5 27.4 - - + -
532B ALA* 1.3 72.3 - - - +
534B GLY* 1.3 61.9 + - - +
535B LEU 3.3 0.2 + - - -
538B LEU* 3.4 24.9 - - + -
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Residues in contact with GLY 534 (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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229B PHE* 5.6 3.4 - - - -
230B THR 3.9 5.6 - - - -
231B GLN* 4.6 9.5 - - - +
483B VAL 3.0 13.3 + - - +
532B ALA 4.1 1.0 + - - -
533B PHE* 1.3 69.9 - - - +
535B LEU* 1.3 65.3 + - - -
536B ASP* 3.3 3.8 - - - -
537B ARG* 3.6 10.4 + - - +
538B LEU* 3.3 24.1 + - - +
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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