Contacts of the strand formed by residues 233 - 237 (chain J) in PDB entry 3EXG
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 CYS 233 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202J ARG* 2.7 33.1 + - - +
203J GLN 3.3 1.9 - - - +
204J GLY* 3.2 7.9 - - - -
207J ILE* 3.4 28.0 - - + +
209J VAL* 4.4 4.3 - - + -
223J ALA* 4.4 17.9 - - + +
226J LEU* 4.1 16.2 - - - -
231J VAL* 3.8 6.8 + - - -
232J GLU* 1.3 74.3 - - - +
234J GLU* 1.3 60.3 + - - +
235J VAL* 3.7 17.9 - - + -
323J ILE* 3.9 18.8 - - - -
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Residues in contact with GLU 234 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200J ILE* 3.7 24.5 - - + +
202J ARG 3.1 12.1 - - - +
203J GLN* 3.8 7.4 - - - +
204J GLY 2.8 23.2 + - - +
207J ILE 2.9 14.6 + - - +
208J THR* 3.8 3.3 - - - +
209J VAL 3.1 21.7 + - - +
233J CYS* 1.3 72.7 - - - +
235J VAL* 1.3 58.8 + - - +
236J ILE* 3.6 5.0 + - + +
252J SER* 2.8 40.8 + - - +
255J LYS* 2.6 35.5 + - - -
256J THR* 4.8 2.2 - - + -
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Residues in contact with VAL 235 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200J ILE* 3.5 3.0 - - - +
201J GLU* 2.7 37.0 + - + -
202J ARG* 3.0 36.0 + - + -
209J VAL* 3.6 11.2 - - + +
211J SER* 6.2 0.4 - - - -
216J VAL* 4.8 7.9 - - + +
219J CYS* 4.1 29.4 - - + +
220J LEU* 3.9 23.3 - - + -
223J ALA* 4.3 6.5 - - + -
233J CYS* 3.7 13.2 + - + -
234J GLU* 1.3 70.6 - - - +
236J ILE* 1.3 63.3 + - - +
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Residues in contact with ILE 236 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198J ALA* 3.8 22.7 - - + -
199J LYS 3.6 11.2 - - - +
200J ILE* 4.5 10.8 - - + -
208J THR* 3.8 11.0 - - + -
209J VAL 2.8 15.5 + - - +
210J VAL* 3.4 10.3 - - + +
211J SER* 2.9 30.1 + - - +
216J VAL* 4.8 0.3 - - - +
234J GLU* 4.0 11.9 - - + +
235J VAL* 1.3 81.4 - - - +
237J ASN* 1.3 61.6 + - - +
238J MET 3.8 0.8 + - - +
248J THR* 4.1 20.9 - - + +
249J ILE* 4.2 17.5 - - + -
252J SER* 3.7 30.3 - - - -
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Residues in contact with ASN 237 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146J SER 4.5 2.0 + - - -
148J TRP* 3.8 9.0 - - - +
152J ASP* 2.8 28.5 + - - +
198J ALA* 3.6 1.1 - - - -
199J LYS* 2.9 29.7 + - + +
201J GLU* 2.9 37.2 - - + +
211J SER 3.5 3.4 + - - -
212J HIS* 4.3 4.6 - - - +
216J VAL* 3.8 27.2 - - + +
235J VAL 4.0 0.4 + - - -
236J ILE* 1.3 70.6 - - - +
238J MET* 1.3 68.8 + - - +
239J ARG* 3.3 18.3 + - - +
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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