Contacts of the strand formed by residues 266 - 273 (chain C) in PDB entry 3GUT
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 VAL 266 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257C TYR* 3.6 33.4 - - + +
262C LEU* 3.2 28.9 - - + -
264C ALA 4.4 1.6 - - - +
265C PRO* 1.3 76.2 - - - +
267C ARG* 1.3 75.0 + - - +
268C VAL* 3.5 4.5 + - + +
287C GLN* 4.4 2.9 - - - -
288C TYR* 3.1 35.1 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 267 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265C PRO* 4.3 6.9 + - - +
266C VAL* 1.3 81.0 - - - +
268C VAL* 1.3 63.7 + - - +
285C GLU* 5.6 13.9 - - + -
286C PHE 3.7 5.8 - - - +
287C GLN* 3.4 42.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 268 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228C PHE* 4.6 5.2 - - + -
229C THR 2.9 17.3 - - - +
230C GLY* 4.4 5.2 - - - -
231C PRO* 5.8 1.1 - - + -
233C TRP* 3.4 22.7 - - + -
257C TYR* 4.0 18.6 - - + +
266C VAL* 3.8 9.0 - - + +
267C ARG* 1.3 80.5 - - - +
269C SER* 1.3 78.0 + - - +
285C GLU* 3.9 5.2 - - - +
286C PHE* 2.6 41.8 + - + +
288C TYR* 3.7 27.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 269 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228C PHE* 3.2 3.5 - - - -
229C THR* 2.5 69.8 + - - +
230C GLY* 5.0 0.8 - - - -
268C VAL* 1.3 73.5 - - - +
270C MET* 1.3 55.4 + - - +
271C GLN* 4.6 1.6 - - - -
283C PRO* 3.2 28.1 - - - +
284C MET 4.5 2.2 - - - -
285C GLU* 5.4 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 270 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196C ILE* 4.6 1.3 - - + +
199C VAL* 4.3 29.2 - - + -
201C ARG 4.9 0.4 - - - +
202C ASN* 5.1 1.1 - - + -
212C ILE* 5.6 1.6 - - - -
214C LEU* 5.7 4.0 - - + -
226C VAL* 4.0 19.1 - - + -
227C TYR 3.6 3.8 - - - -
228C PHE* 4.2 23.6 - - + +
252C PHE* 4.6 9.4 - - - -
254C THR* 5.9 0.2 - - - -
269C SER* 1.3 73.8 + - - +
271C GLN* 1.3 66.8 + - - +
283C PRO* 3.5 0.2 - - - +
284C MET* 2.7 73.0 + - + +
285C GLU 4.6 3.8 - - - +
286C PHE* 3.9 37.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 271 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196C ILE* 4.1 7.2 - - - -
226C VAL* 3.5 3.6 - - - -
227C TYR* 2.6 73.0 + - + +
229C THR* 3.7 17.3 - - + +
269C SER* 4.8 0.2 - - - +
270C MET* 1.3 84.1 - - - +
272C LEU* 1.3 66.2 + - - +
280C LEU* 3.5 25.9 - - + +
281C SER* 3.0 28.8 + - - +
283C PRO* 3.9 20.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 272 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194C LEU* 3.4 13.4 - - + +
195C LYS 3.6 24.2 - - - +
196C ILE* 3.1 29.6 - - + +
214C LEU* 3.9 30.5 - - + -
216C CYS* 4.2 13.2 - - + -
219C VAL* 5.3 4.5 - - + -
224C ILE* 4.5 15.5 - - + -
225C GLU 3.7 5.4 - - - +
226C VAL* 4.8 9.0 - - + -
250C ILE* 5.6 3.6 - - + -
271C GLN* 1.3 76.2 - - - +
273C ARG* 1.3 58.8 + - - +
280C LEU* 3.3 8.1 - - - +
281C SER* 3.0 34.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 273 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224C ILE* 3.5 4.5 - - - +
225C GLU* 2.6 69.1 + - + +
227C TYR* 3.8 34.3 - - + -
236C ARG* 3.1 13.3 - - - +
272C LEU* 1.3 75.1 - - - +
274C ARG* 1.3 61.9 + - - +
275C PRO* 3.0 27.5 + - - +
278C ARG* 3.8 35.1 + - - +
279C GLU 3.6 4.9 - - - +
280C LEU* 3.5 26.2 - - + +
----------------------------------------------------------
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