Contacts of the strand formed by residues 473 - 478 (chain A) 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 ALA 473 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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431A ILE* 3.4 2.9 - - - +
432A ASP 3.3 23.7 + - - -
433A PHE* 3.8 7.6 - - + -
448A HIS* 3.4 35.9 - - + +
452A THR* 4.3 1.1 - - + -
471A ALA* 3.1 19.5 + - + -
472A ASN* 1.3 78.4 - - - +
474A TYR* 1.3 67.3 + - - +
486A GLY 3.5 7.4 - - - +
487A SER* 4.0 4.7 - - - -
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Residues in contact with TYR 474 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241A ALA* 3.9 25.1 - - + -
244A VAL* 3.8 14.3 - - + +
245A ARG* 3.9 24.7 - - + +
429A TRP* 3.9 21.8 - + + -
430A VAL 3.3 9.0 - - - +
431A ILE* 4.1 6.7 - - + -
433A PHE* 4.4 1.3 - - - -
448A HIS* 4.3 0.2 + - - -
472A ASN* 3.8 4.5 - - - -
473A ALA* 1.3 84.0 - - - +
475A ASP* 1.3 64.7 + - - +
485A GLY* 3.2 1.4 - - - -
486A GLY 2.9 34.0 + - - +
487A SER* 3.2 33.5 + - - -
488A VAL 3.9 1.6 - - - -
529A ALA* 3.6 12.5 - - - +
530A GLY 2.6 29.6 + - - -
531A LEU* 3.9 12.8 - - + -
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Residues in contact with ASP 475 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A ASP* 4.7 4.2 - - - +
429A TRP* 3.3 10.6 - - - -
430A VAL* 2.7 35.9 + - + +
433A PHE* 3.6 29.8 - - + -
448A HIS* 3.1 19.3 + - - -
474A TYR* 1.3 82.0 - - - +
476A MET* 1.3 60.2 + - - +
477A VAL* 3.9 7.4 + - + -
482A GLU* 3.0 33.9 - - + +
484A GLY 3.3 9.2 - - - +
485A GLY* 3.7 7.5 - - - -
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Residues in contact with MET 476 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248A MET 3.6 16.4 - - - +
249A GLU* 4.0 1.3 - - - -
252A VAL* 3.5 35.7 - - + -
267A PHE* 3.9 25.6 - - + -
428A LEU 3.4 10.8 - - - +
429A TRP* 3.6 32.5 - - + -
475A ASP* 1.3 72.3 - - - +
477A VAL* 1.3 65.1 + - - +
478A ILE* 4.4 2.9 - - + -
482A GLU* 3.9 1.6 - - - -
483A VAL* 2.9 52.8 + - + +
484A GLY 2.8 16.8 + - - +
531A LEU* 5.4 0.2 - - + -
533A PHE* 3.6 13.5 - - + -
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Residues in contact with VAL 477 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282A ASP 4.0 3.6 - - - +
283A LYS* 3.6 29.2 - - + -
284A PRO 3.4 24.9 - - - +
427A PRO* 3.3 2.4 - - - +
428A LEU* 2.8 46.8 + - + +
430A VAL* 4.0 20.4 - - + -
475A ASP* 4.7 7.4 - - + -
476A MET* 1.3 79.6 - - - +
478A ILE* 1.3 64.6 + - - +
480A GLY 3.7 0.9 - - - +
481A TYR 3.1 28.0 - - - +
482A GLU* 4.7 3.6 - - + -
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Residues in contact with ILE 478 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252A VAL* 3.9 21.8 - - + -
256A TRP* 3.8 27.4 - - + -
264A LEU* 5.3 2.5 - - + -
267A PHE* 5.3 0.2 - - + -
425A TRP* 4.1 18.6 - - + -
426A ALA 3.5 6.3 - - - +
427A PRO* 4.1 18.6 - - + -
476A MET* 4.2 5.1 + - + -
477A VAL* 1.3 80.3 - - - +
479A ASN* 1.3 85.6 + - - +
481A TYR* 2.9 27.8 + - - +
483A VAL* 4.0 24.0 - - + -
538A LEU* 4.9 0.7 - - + -
541A LEU* 4.1 17.1 - - + +
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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