Contacts of the strand formed by residues 233 - 237 (chain T) 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 T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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202T ARG* 3.0 32.5 + - - +
203T GLN 3.3 3.5 - - - +
204T GLY* 3.7 3.6 - - - -
207T ILE* 3.7 20.9 - - + -
209T VAL* 3.9 16.6 - - + -
223T ALA* 4.0 29.5 + - + +
226T LEU* 4.4 11.0 - - - -
231T VAL* 3.9 5.3 + - - -
232T GLU* 1.3 73.8 - - - +
234T GLU* 1.3 59.9 + - - +
235T VAL* 4.3 3.6 - - + -
323T ILE* 3.9 21.5 - - - -
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Residues in contact with GLU 234 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200T ILE* 4.1 30.0 - - + +
202T ARG 3.1 11.9 - - - +
203T GLN* 3.6 5.4 - - - +
204T GLY* 2.9 24.9 + - - +
207T ILE 3.0 14.0 + - - +
208T THR* 3.5 4.9 - - - +
209T VAL 2.9 23.5 + - - +
233T CYS* 1.3 71.0 - - - +
235T VAL* 1.3 58.7 + - - +
236T ILE* 4.6 2.5 - - + -
252T SER* 2.9 42.4 + - - +
255T LYS* 2.5 33.7 + - - -
256T THR* 4.5 0.7 - - + -
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Residues in contact with VAL 235 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200T ILE* 3.6 5.0 - - - +
201T GLU* 3.0 31.2 + - + -
202T ARG* 3.0 15.1 + - + +
209T VAL* 3.3 11.0 - - + +
211T SER* 6.3 0.4 - - - -
216T VAL* 4.6 8.3 - - + +
219T CYS* 4.2 27.6 - - + +
220T LEU* 3.7 34.5 - - + -
223T ALA* 4.1 22.9 - - + -
233T CYS* 3.5 7.4 + - + -
234T GLU* 1.3 72.4 - - - +
236T ILE* 1.3 67.5 + - - +
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Residues in contact with ILE 236 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198T ALA* 3.8 25.4 - - + -
199T LYS 3.5 5.4 - - - +
200T ILE* 4.1 14.4 - - + -
208T THR* 3.8 26.2 - - + -
209T VAL 2.7 14.3 + - - +
210T VAL* 4.2 13.5 - - + -
211T SER* 3.0 28.6 + - - +
216T VAL* 4.7 0.9 - - - +
234T GLU* 4.3 3.6 - - + +
235T VAL* 1.3 84.6 - - - +
237T ASN* 1.3 65.5 + - - +
238T MET* 3.6 2.4 + - - +
248T THR* 4.1 20.4 - - + +
249T ILE* 4.1 12.1 - - + -
252T SER* 4.0 17.5 - - - -
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Residues in contact with ASN 237 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146T SER 4.8 1.2 + - - -
148T TRP* 3.9 7.2 - - - +
152T ASP* 3.1 26.1 + - - +
198T ALA* 3.4 0.5 - - - -
199T LYS* 2.8 35.4 + - + +
201T GLU* 3.1 37.0 - - + +
211T SER 3.6 2.8 + - - -
212T HIS* 4.5 3.4 - - - +
213T SER 4.6 1.4 - - - +
216T VAL* 3.9 23.5 - - + +
235T VAL 4.2 0.4 + - - -
236T ILE* 1.3 74.2 - - - +
238T MET* 1.3 66.4 + - - +
239T ARG* 3.2 23.7 + - - +
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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