Contacts of the strand formed by residues 264 - 269 (chain C) in PDB entry 2Q7N
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 THR 264 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234C ILE* 3.6 30.7 - - + -
235C GLY* 4.6 7.0 - - - +
256C ILE* 5.5 5.8 - - + -
257C PRO* 4.6 13.2 - - + +
259C SER* 2.5 37.0 - - - -
260C GLU* 4.4 3.9 + - - -
263C GLY* 1.3 70.1 - - - -
265C ASN* 1.3 67.4 + - - +
266C ILE* 3.7 3.6 + - + +
278C VAL* 3.5 1.7 - - - -
279C VAL* 2.9 40.9 + - + +
50D GLU 5.5 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 265 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233C GLN 3.8 0.7 - - - +
234C ILE* 3.7 2.3 - - - -
235C GLY 3.3 24.1 + - - -
263C GLY 3.7 1.2 + - - +
264C THR* 1.3 74.5 - - - +
266C ILE* 1.3 59.2 + - - +
267C ILE* 4.6 9.0 - - + -
277C THR 4.1 4.0 - - - -
278C VAL* 3.7 8.0 - - - +
48D GLN 3.0 12.3 + - - -
49D GLY* 2.9 29.7 + - - -
50D GLU 3.3 10.8 + - - +
51D PRO* 3.9 13.5 - - + +
52D PHE* 3.5 15.5 - - + -
156D PHE* 5.0 6.0 - - + -
159D LYS* 2.6 32.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 266 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206C VAL* 5.3 3.7 - - + +
219C MET* 4.6 5.6 - - + -
221C ILE* 3.7 47.3 - - + -
233C GLN 2.7 24.7 - - - +
234C ILE* 3.5 27.6 - - + -
251C ILE* 4.8 3.8 - - + -
253C ILE* 4.9 1.8 - - + -
264C THR* 4.6 5.6 - - + +
265C ASN* 1.3 74.9 - - - +
267C ILE* 1.3 64.2 + - - +
268C PHE* 5.7 0.7 - - + -
276C GLY* 3.5 0.9 - - - -
277C THR* 2.9 46.5 + - + +
279C VAL* 4.1 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 267 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232C GLY* 2.7 32.6 - - - -
233C GLN* 3.0 42.9 + - + +
265C ASN* 4.6 10.1 - - + -
266C ILE* 1.3 79.6 - - - +
268C PHE* 1.3 59.8 + - - +
269C ILE* 3.9 18.4 - - + -
274C VAL* 4.0 14.4 - - + -
275C TYR 3.6 5.6 - - - +
51D PRO* 4.3 13.7 - - + -
52D PHE* 5.8 0.4 - - + -
55D ASN* 4.8 9.6 - - - +
59D LEU* 5.3 8.7 - - + -
156D PHE* 3.5 33.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 268 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206C VAL* 3.4 20.0 - - + -
221C ILE* 3.2 27.8 - - + -
222C CYS* 3.2 19.3 - - - -
223C CYS* 3.1 39.0 - - + -
229C VAL* 5.1 9.6 - - + -
231C SER 3.1 6.1 - - - +
232C GLY* 3.6 9.6 - - - -
249C VAL* 4.8 7.9 - - + -
250C ALA* 4.7 4.7 - - - -
251C ILE* 3.9 27.1 - - + -
266C ILE* 5.7 1.1 - - + -
267C ILE* 1.3 77.9 - - - +
269C ILE* 1.3 58.8 - - - +
270C THR* 6.4 0.4 - - + -
274C VAL* 2.7 34.3 - - - +
275C TYR* 2.5 30.7 + - + +
276C GLY* 5.9 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 269 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229C VAL* 4.1 2.0 - - - +
230C LEU* 3.0 32.0 + - + +
231C SER* 2.7 51.3 + - - +
232C GLY* 3.6 5.8 - - - +
233C GLN* 4.2 14.6 - - - +
267C ILE* 3.9 16.4 - - + -
268C PHE* 1.3 79.0 - - - +
270C THR* 1.3 73.1 + - - +
273C ASP 3.9 6.5 - - - +
274C VAL* 4.8 9.6 - - + -
58D LYS* 4.6 24.0 - - + -
----------------------------------------------------------
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