Contacts of the helix formed by residues 500 - 505 (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 LEU 500 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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157A VAL* 6.2 1.9 - - + +
158A GLU* 3.7 48.1 + - + +
1530A MPD 4.0 13.5 - - + -
1533A MPD 6.5 0.4 - - + -
144B TYR* 3.2 15.8 + - - +
148B ALA* 3.8 28.7 - - + +
151B ARG* 4.0 15.5 - - + +
152B TYR* 2.7 27.7 + - - -
499B ALA* 1.3 73.8 - - - +
501B ASP* 1.3 60.9 + - - +
502B TYR 3.2 1.7 + - - -
503B LEU* 3.4 8.5 + - - +
2534B MPD 3.8 29.4 - - + +
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Residues in contact with ASP 501 (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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157A VAL* 6.1 0.4 - - - -
171A TYR* 2.5 28.5 + - - -
504A ARG* 2.8 37.7 + - - +
509A MET* 3.2 16.8 - - + +
1533A MPD 5.7 2.4 + - - -
152B TYR* 3.9 5.8 + - - -
496B LYS* 5.2 4.5 - - + +
499B ALA* 3.1 4.0 - - + +
500B LEU* 1.3 78.6 - - - +
502B TYR* 1.3 65.6 + - - +
503B LEU 3.2 1.0 + - - -
504B ARG* 3.3 19.2 + - + +
505B LEU* 3.8 9.7 + - - +
2534B MPD 5.5 2.9 + - - +
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Residues in contact with TYR 502 (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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145B TYR* 3.1 41.3 - + + -
192B GLY 4.1 7.8 - - - -
193B MET* 3.7 14.4 + - - +
196B GLY* 4.5 4.3 - - - -
197B PRO* 4.7 0.2 - - + -
257B ASN* 3.0 28.7 + - - -
288B GLU* 6.4 0.2 - - + -
495B ALA* 4.1 15.3 - - + -
496B LYS 3.3 30.4 + - - +
497B THR* 3.6 22.3 - - + +
499B ALA 3.0 13.2 + - - +
501B ASP* 1.3 78.4 - - - +
503B LEU* 1.3 68.2 + - + +
505B LEU* 3.2 34.2 + - + +
506B PHE* 3.4 27.7 - + - -
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Residues in contact with LEU 503 (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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145B TYR* 3.8 24.0 - - + +
148B ALA* 3.7 15.3 - - + -
149B ALA* 3.3 45.3 - - + +
152B TYR* 3.8 13.7 - - + -
196B GLY* 3.4 40.8 - - - +
199B ALA* 5.0 0.2 - - + -
200B VAL* 4.0 12.4 - - + +
499B ALA 5.2 0.4 - - - +
500B LEU 3.4 4.6 + - - +
501B ASP 3.2 0.6 - - - -
502B TYR* 1.3 78.4 - - + +
504B ARG* 1.3 59.2 + - - +
506B PHE* 2.9 26.7 + - - +
507B LEU* 3.7 12.8 - - - +
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Residues in contact with ARG 504 (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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494A ASN* 4.6 12.3 + - - -
496A LYS* 5.2 2.0 - - - +
501A ASP* 2.8 41.4 + - - +
504A ARG* 6.0 6.1 - - + -
152B TYR* 3.6 29.8 + - - +
171B TYR* 3.3 26.1 - - - -
284B ARG* 3.9 6.8 + - - +
501B ASP* 3.3 15.4 + - + +
502B TYR 3.2 0.4 - - - -
503B LEU* 1.3 77.3 - - - +
505B LEU* 1.3 63.4 + - + +
506B PHE 3.2 1.0 + - - -
507B LEU* 3.0 39.9 + - - +
508B GLU* 4.4 2.0 - - - +
509B MET* 4.2 12.7 - - - +
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Residues in contact with LEU 505 (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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174B LEU* 3.9 1.0 - - - +
284B ARG* 2.9 16.6 + - - +
286B TYR* 2.9 57.9 + - + +
495B ALA* 3.4 38.8 - - + -
496B LYS 4.9 0.4 - - - +
501B ASP 3.9 8.3 - - - +
502B TYR* 3.3 28.5 - - + +
503B LEU 3.1 0.6 - - - -
504B ARG* 1.3 80.1 - - + +
506B PHE* 1.3 60.1 + - + +
507B LEU 3.4 0.9 - - - -
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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