Contacts of the strand formed by residues 255 - 260 (chain C) in PDB entry 3TQI
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 LEU 255 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230C VAL 3.5 13.2 - - - +
232C VAL* 3.3 37.0 - - + +
244C ALA 3.3 24.7 - - - +
247C VAL* 3.6 17.5 - - + -
248C HIS* 3.6 24.6 - - + -
251C ILE* 4.0 4.5 - - + +
252C GLY 2.9 16.4 + - - +
253C ASP* 3.5 11.9 - - - +
254C GLN* 1.3 76.0 - - - +
256C VAL* 1.3 62.0 + - - +
257C CYS* 3.6 25.9 + - - +
277C PHE* 6.2 0.7 - - + -
283C ALA* 5.7 2.0 - - + -
284C LYS* 4.0 15.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 256 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229C GLN* 4.4 13.9 - - + +
230C VAL 2.9 16.1 + - - +
231C ILE* 3.2 41.7 - - + +
232C VAL 3.3 0.5 + - - -
253C ASP 5.8 0.4 - - - +
254C GLN 4.2 5.4 - - - +
255C LEU* 1.3 76.5 - - - +
257C CYS* 1.3 64.4 + - - +
258C VAL* 3.8 2.1 + - + -
284C LYS* 4.0 15.9 - - + -
286C ILE* 3.7 31.2 - - + -
326C LEU* 4.4 9.4 - - + -
328C VAL* 4.3 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 257 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232C VAL 3.4 6.7 - - - +
234C LEU* 3.5 37.7 - - + -
244C ALA* 4.5 6.5 - - - -
255C LEU* 3.6 27.8 - - - -
256C VAL* 1.3 76.5 - - - +
258C VAL* 1.3 63.3 + - - +
277C PHE* 4.7 4.7 - - - -
283C ALA* 4.7 9.4 - - - -
284C LYS 2.9 17.5 + - - +
285C VAL* 3.4 11.1 - - + -
286C ILE 3.0 23.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 258 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231C ILE* 3.9 26.9 - - + -
232C VAL 2.9 7.7 + - - -
233C GLY* 3.4 4.3 - - - -
234C LEU* 2.8 29.2 + - - -
256C VAL* 4.4 7.0 - - + +
257C CYS* 1.3 79.1 - - - +
259C LEU* 1.3 63.6 + - - +
260C VAL* 3.9 23.1 - - + -
286C ILE* 3.4 21.8 - - + +
288C VAL* 4.0 13.5 - - + -
319C PHE* 3.9 19.2 - - + -
322C GLN* 4.6 15.3 - - + -
326C LEU* 5.7 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 259 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234C LEU* 4.1 7.6 - - + -
235C SER* 3.7 30.5 - - - +
258C VAL* 1.3 73.4 - - - +
260C VAL* 1.3 68.2 + - - +
261C ASP 3.8 0.7 + - - +
265C LEU* 5.1 4.0 - - + -
269C GLU 6.1 0.2 - - - -
270C VAL* 4.0 29.2 - - + +
273C VAL* 3.3 37.2 - - + -
274C LEU* 4.1 19.5 - - + -
285C VAL* 4.4 8.7 - - + +
286C ILE 2.9 12.4 + - - +
287C CYS* 3.3 11.5 - - - +
288C VAL 3.0 22.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 260 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235C SER* 3.6 21.4 + - - +
258C VAL* 3.9 15.2 - - + -
259C LEU* 1.3 74.8 - - - +
261C ASP* 1.3 61.2 + - - +
262C THR* 3.1 27.3 + - + +
265C LEU* 3.7 11.7 - - - +
288C VAL* 3.5 18.2 - - + +
290C ALA* 4.7 5.6 - - + -
294C PHE* 5.4 0.9 - - + -
315C PHE* 3.7 14.6 - - + -
318C VAL* 3.6 31.9 - - + -
319C PHE* 4.4 10.8 - - + -
----------------------------------------------------------
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