Contacts of the strand formed by residues 251 - 256 (chain U) 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 ILE 251 (chain U).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17U LEU* 4.2 17.7 - - + -
189U CYS 3.0 7.1 + - - +
190U ILE* 3.4 27.4 - - + +
191U PHE* 3.0 25.3 + - - +
220U ILE* 3.8 5.4 - - - -
221U PRO* 3.3 21.1 - - + +
223U LEU* 3.6 22.4 - - + -
239U PHE* 4.3 11.9 - - + -
240U ALA* 4.0 15.3 - - + -
243U TYR* 4.3 20.4 - - + -
244U CYS* 4.4 5.4 - - - -
250U PRO* 1.3 74.7 - - - +
252U LEU* 1.3 67.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 252 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165U TYR* 3.9 7.6 - - - +
179U TYR* 3.8 27.6 - - + +
191U PHE* 3.4 16.4 - - + +
193U CYS* 5.7 3.1 - - + -
213U TYR 3.2 27.4 - - - +
214U TYR* 3.9 9.2 - - - +
217U GLY* 3.6 30.3 - - - +
220U ILE* 3.8 23.1 - - + +
221U PRO 2.7 13.6 + - - +
222U GLY* 3.0 7.9 - - - -
223U LEU* 3.0 27.1 + - - +
251U ILE* 1.3 71.1 - - - +
253U MET* 1.3 63.6 + - - +
254U GLU 4.1 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 253 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75U LEU* 4.1 5.4 - - + -
162U LEU* 5.7 0.2 - - + -
190U ILE* 4.3 7.4 - - + -
191U PHE 2.9 9.2 + - - +
192U ILE* 3.3 41.3 - - + +
193U CYS* 3.0 21.9 + - - -
223U LEU* 3.6 15.5 - - + -
225U VAL* 4.2 9.2 - - + -
233U VAL 5.2 0.7 - - - +
236U ALA* 3.9 33.4 - - + +
237U THR* 3.4 24.0 - - + +
240U ALA* 4.3 10.3 - - + -
251U ILE 4.2 0.2 + - - -
252U LEU* 1.3 77.2 - - - +
254U GLU* 1.3 57.7 + - - +
255U LEU* 3.7 25.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 254 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193U CYS* 3.4 12.8 - - + +
195U ASN* 2.9 32.5 + - + +
211U THR 4.7 2.9 - - - +
212U ASP* 4.0 0.3 - - - -
213U TYR* 3.1 27.8 + - + -
214U TYR* 3.0 38.6 + - + +
223U LEU 3.0 9.8 + - - +
224U ARG* 3.4 24.3 - - + -
225U VAL* 2.8 30.0 + - - +
252U LEU 4.1 0.4 - - - -
253U MET* 1.3 69.7 - - - +
255U LEU* 1.3 63.6 + - - +
256U GLN* 3.1 14.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 255 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71U CYS* 3.7 30.3 - - + -
75U LEU* 3.6 30.1 - - + -
164U LEU* 5.6 2.2 - - + -
192U ILE* 4.1 13.9 - - + -
193U CYS 2.8 13.6 + - - +
194U GLU* 3.8 9.0 - - + -
195U ASN 3.1 24.4 + - - +
225U VAL* 4.0 16.6 - - + -
227U GLY* 4.6 3.1 - - - -
233U VAL* 4.1 15.3 - - + -
253U MET* 3.7 33.4 - - + +
254U GLU* 1.3 75.8 - - - +
256U GLN* 1.3 62.2 + - - +
257U THR* 3.4 3.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 256 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10U LYS* 5.4 6.4 - - - -
195U ASN* 3.7 19.0 - - - +
197U ARG* 4.3 29.2 + - - +
224U ARG* 3.3 35.1 + - - +
225U VAL 3.1 19.4 + - - +
226U ASP* 3.9 6.9 - - - +
227U GLY* 2.8 22.7 + - - +
228U MET* 4.0 3.5 + - - +
254U GLU* 3.1 22.8 + - - +
255U LEU* 1.3 67.0 - - - +
257U THR* 1.3 61.5 + - - +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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