Contacts of the strand formed by residues 473 - 478 (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 ALA 473 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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431B ILE* 3.4 4.5 - - - +
432B ASP 3.2 23.9 + - - -
433B PHE* 3.6 8.1 - - + -
448B HIS* 3.4 40.4 - - + +
452B THR* 4.8 0.7 - - + -
471B ALA* 3.1 10.0 + - + -
472B ASN* 1.3 77.3 - - - +
474B TYR* 1.3 64.2 + - - +
486B GLY 3.5 12.3 - - - +
487B SER* 3.8 5.8 - - - -
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Residues in contact with TYR 474 (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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241B ALA* 3.9 26.7 - - + -
244B VAL* 3.7 24.9 - - + +
245B ARG* 4.1 16.8 - - + -
429B TRP* 4.2 8.3 - + + -
430B VAL 3.5 5.6 - - - -
431B ILE* 4.1 16.4 - - + -
433B PHE* 4.0 1.8 - - - -
472B ASN* 3.9 6.1 - - - -
473B ALA* 1.3 81.6 - - - +
475B ASP* 1.3 67.9 + - - +
485B GLY* 3.0 1.4 - - - -
486B GLY* 2.9 41.0 + - - +
487B SER* 3.2 32.1 + - - -
488B VAL 3.9 0.9 - - - -
529B ALA* 3.8 8.0 - - - +
530B GLY 2.9 20.8 + - - -
531B LEU* 3.8 20.4 - - + -
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Residues in contact with ASP 475 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B ASP* 5.1 4.4 - - - +
429B TRP* 3.1 15.3 - - - -
430B VAL* 2.8 38.8 + - + +
433B PHE* 3.4 30.8 - - + -
448B HIS* 5.9 2.1 + - - -
474B TYR* 1.3 82.7 - - - +
476B MET* 1.3 59.2 - - - +
477B VAL* 4.0 7.4 - - + +
482B GLU* 2.4 35.8 - - + +
484B GLY 3.2 9.9 - - - +
485B GLY* 3.4 10.1 - - - -
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Residues in contact with MET 476 (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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248B MET 3.9 7.9 - - - +
249B GLU* 4.2 0.9 - - - -
252B VAL* 3.2 39.3 - - + -
267B PHE* 3.6 24.0 - - + -
428B LEU 3.4 10.3 - - - +
429B TRP* 3.3 40.3 - - + -
475B ASP* 1.3 72.3 - - - +
477B VAL* 1.3 67.9 + - - +
478B ILE* 4.7 2.2 - - + -
482B GLU* 3.7 2.1 - - - -
483B VAL* 2.8 47.1 + - + +
484B GLY* 2.8 13.8 + - - +
533B PHE* 3.5 17.0 - - + -
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Residues in contact with VAL 477 (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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282B ASP 4.3 1.8 - - - +
283B LYS* 4.0 18.8 - - + -
284B PRO 3.6 22.9 - - - +
427B PRO* 3.2 2.8 - - - +
428B LEU* 2.8 44.3 + - + +
430B VAL* 3.8 28.9 - - + -
475B ASP* 4.5 8.7 - - + +
476B MET* 1.3 80.3 - - - +
478B ILE* 1.3 66.5 + - - +
480B GLY* 3.7 3.8 - - - +
481B TYR 3.4 27.1 - - - +
482B GLU* 4.9 3.1 - - - -
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Residues in contact with ILE 478 (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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252B VAL* 3.8 22.9 - - + -
256B TRP* 3.7 35.2 - - + -
264B LEU* 5.1 2.7 - - + -
425B TRP* 4.3 7.2 - - + -
426B ALA 3.7 4.9 - - - +
427B PRO* 4.0 17.0 - - + -
476B MET* 4.7 3.8 - - + -
477B VAL* 1.3 77.7 - - - +
479B ASN* 1.3 86.5 + - - +
480B GLY 3.3 0.6 + - - -
481B TYR* 3.3 25.3 + - - +
483B VAL* 4.1 18.1 - - + +
538B LEU* 4.7 2.5 - - + -
541B LEU* 3.4 24.7 - - + +
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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