Contacts of the strand formed by residues 284 - 288 (chain B) in PDB entry 2EIT
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 ARG 284 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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269A TYR* 4.5 4.0 - - - +
493A THR 3.9 20.0 + - - -
494A ASN* 4.1 7.3 + - - +
174B LEU* 3.8 19.5 - - + +
254B ARG* 3.5 20.6 + - - +
255B PHE* 3.1 11.4 - - + +
256B ILE* 2.9 24.8 + - - +
282B PHE 4.4 2.7 - - - +
283B LYS* 1.3 76.9 - - - +
285B ALA* 1.3 61.4 + - - +
286B TYR* 3.4 29.4 + - + +
504B ARG* 3.9 6.6 + - - +
505B LEU* 2.9 24.2 + - - +
507B LEU 2.8 31.5 + - - -
508B GLU* 3.9 16.4 + - - +
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Residues in contact with ALA 285 (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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269A TYR* 5.4 0.2 + - - -
256B ILE* 3.4 15.5 - - + +
268B ILE* 4.6 9.2 - - + -
269B TYR* 3.7 33.3 - - + -
272B ALA* 3.5 28.0 - - + -
283B LYS 4.0 1.8 + - - -
284B ARG* 1.3 76.4 - - - +
286B TYR* 1.3 69.2 + - - +
287B VAL* 4.0 3.0 + - + -
493B THR* 4.1 2.8 - - - +
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Residues in contact with TYR 286 (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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255B PHE* 5.3 1.8 - - + -
256B ILE 3.0 12.1 + - - +
257B ASN* 3.7 14.8 - - - +
258B PHE* 2.8 29.5 + - - +
284B ARG* 3.4 31.1 + - + -
285B ALA* 1.3 76.8 - - - +
287B VAL* 1.3 63.8 + - - +
288B GLU* 4.9 2.0 - - + -
493B THR* 3.5 15.0 - - - +
495B ALA* 4.3 12.1 - - + -
505B LEU* 2.9 70.1 + - + +
506B PHE* 3.7 27.1 - + + -
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Residues in contact with VAL 287 (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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282A PHE* 3.7 36.1 - - + -
258B PHE* 3.5 22.9 - - + -
265B GLY* 4.0 15.9 - - - +
268B ILE* 4.1 19.5 - - + -
269B TYR* 4.1 10.8 - - + -
285B ALA* 4.6 0.9 - - + -
286B TYR* 1.3 81.9 - - - +
288B GLU* 1.3 64.1 + - - +
289B THR* 4.0 2.0 - - + -
492B GLY* 3.0 6.1 - - - -
493B THR* 2.9 51.8 + - + -
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Residues in contact with GLU 288 (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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257B ASN* 6.0 1.3 - - - +
258B PHE* 3.0 13.2 + - - +
259B THR* 3.3 10.6 - - - +
260B GLY 3.0 25.1 + - - +
286B TYR* 5.1 1.3 - - + -
287B VAL* 1.3 76.9 - - - +
289B THR* 1.3 60.0 + - - +
485B PHE 5.9 0.2 - - - +
486B GLY* 3.8 23.7 - - - -
487B GLY 3.9 4.0 + - - -
491B SER 3.7 5.2 - - - +
493B THR* 3.1 19.7 + - - -
494B ASN 3.3 7.9 + - - -
495B ALA* 3.0 42.7 + - + +
497B THR* 5.6 7.0 - - + -
502B TYR* 6.4 0.2 - - + -
2518B NAD 3.2 28.7 + - - +
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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