Contacts of the strand formed by residues 284 - 288 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174A LEU* 3.8 19.0 - - + +
254A ARG* 3.5 19.4 + - - +
255A PHE* 3.1 11.2 - - + +
256A ILE* 2.8 26.9 + - - +
282A PHE 3.5 3.8 + - - +
283A LYS* 1.3 75.0 - - - +
285A ALA* 1.3 61.1 + - - +
286A TYR* 3.4 30.2 + - + +
504A ARG* 4.0 5.9 + - - +
505A LEU* 3.0 24.0 + - - +
507A LEU 2.8 30.2 + - - -
508A GLU* 4.0 16.8 + - - +
269B TYR* 4.5 4.7 - - - +
493B THR 3.9 20.2 + - - -
494B ASN* 4.1 7.3 + - - +
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Residues in contact with ALA 285 (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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256A ILE* 3.4 15.0 - - + +
268A ILE* 4.6 10.3 - - + -
269A TYR* 3.7 34.6 - - + -
272A ALA* 3.5 27.1 - - + -
283A LYS 4.1 1.6 + - - -
284A ARG* 1.3 74.7 - - - +
286A TYR* 1.3 70.6 + - - +
287A VAL* 4.0 1.7 + - + -
493A THR* 4.1 2.8 - - - +
269B TYR* 5.5 0.2 + - - -
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Residues in contact with TYR 286 (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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255A PHE* 5.4 2.0 - - + -
256A ILE 2.9 13.2 + - - +
257A ASN* 3.7 14.4 - - - +
258A PHE* 2.8 30.2 + - - +
284A ARG* 3.4 31.3 + - + -
285A ALA* 1.3 80.1 - - - +
287A VAL* 1.3 63.6 + - - +
288A GLU* 5.0 1.3 - - + -
493A THR* 3.6 14.6 - - - +
495A ALA* 4.3 12.3 - - + -
505A LEU* 2.7 69.7 + - + +
506A PHE* 3.6 28.3 - + - -
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Residues in contact with VAL 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A PHE* 3.4 21.3 - - + -
265A GLY* 4.0 13.9 - - - +
268A ILE* 4.1 19.5 - - + -
269A TYR* 4.3 10.3 - - + -
285A ALA* 4.6 0.4 - - + -
286A TYR* 1.3 82.2 - - - +
288A GLU* 1.3 66.6 + - - +
289A THR* 4.0 5.8 - - + -
492A GLY* 3.2 1.4 - - - -
493A THR* 2.9 49.5 + - + -
282B PHE* 3.7 37.0 - - + -
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Residues in contact with GLU 288 (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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257A ASN* 5.9 2.0 - - - +
258A PHE 2.9 10.9 + - - +
259A THR* 3.3 12.8 - - - +
260A GLY 3.0 25.8 + - - +
286A TYR* 5.1 1.1 - - + -
287A VAL* 1.3 85.9 - - - +
289A THR* 1.3 59.2 + - - +
486A GLY* 3.8 23.9 - - - -
487A GLY 4.0 5.7 + - - -
491A SER 3.8 5.4 - - - +
493A THR* 3.1 10.2 + - - -
494A ASN 3.3 4.9 + - - -
495A ALA* 3.0 42.7 + - + +
497A THR* 5.5 6.7 - - + -
502A TYR* 6.3 0.4 - - + -
1518A NAD 3.3 32.3 + - - +
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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