Contacts of the strand formed by residues 334 - 341 (chain C) in PDB entry 2G4C
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 334 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241C TRP 3.0 16.6 - - - +
242C PHE* 3.5 1.7 - - - -
243C THR* 2.6 29.4 + - - +
245C PRO* 4.4 16.2 - - - -
248C SER* 3.4 32.5 - - - +
305C ASN* 4.0 2.7 - - - +
307C GLY* 3.3 30.1 - - - -
308C ASP* 3.7 5.6 - - - -
333C PRO* 1.3 74.8 - - - +
335C VAL* 1.3 61.9 + - - +
336C LEU* 3.3 2.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 335 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186C LEU* 5.6 1.3 - - + -
190C LEU* 3.5 17.7 - - + -
240C VAL* 5.0 4.5 - - + -
241C TRP 3.9 2.5 - - - -
242C PHE* 3.4 33.7 - - + -
305C ASN* 3.7 0.7 - - - -
306C LEU* 2.9 57.4 + - + +
307C GLY 2.9 27.0 + - - +
310C GLU* 3.8 12.1 - - + -
311C LEU* 4.1 17.7 - - + +
333C PRO 4.1 0.9 - - - +
334C CYS* 1.3 69.8 - - - +
336C LEU* 1.3 60.8 + - - +
337C SER 3.7 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 336 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239C LEU 3.6 2.4 - - - +
240C VAL* 4.6 0.9 - - - -
241C TRP* 3.0 48.6 + - + +
243C THR* 5.2 4.5 - - + +
248C SER* 4.1 6.1 - - - +
251C TRP* 3.6 17.3 - - + -
252C LEU* 3.1 53.8 - - + +
255C TRP* 4.0 13.2 - - + -
304C TRP 3.1 10.3 - - - +
305C ASN* 4.5 7.0 - - - +
334C CYS* 3.3 4.0 + - + +
335C VAL* 1.3 70.9 - - - +
337C SER* 1.3 60.0 + - - +
338C VAL* 3.9 22.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 337 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186C LEU* 3.1 38.6 - - - +
238C SER* 5.7 1.0 - - - -
239C LEU 3.6 3.5 + - - -
240C VAL* 4.6 1.8 - - - +
302C THR 3.7 2.1 - - - +
303C LEU* 3.5 1.7 - - - -
304C TRP* 2.8 43.4 + - - +
306C LEU* 4.3 13.9 - - - -
335C VAL 3.7 2.0 - - - -
336C LEU* 1.3 72.7 - - - +
338C VAL* 1.3 67.7 + - - +
339C ASN* 4.9 5.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 338 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114C TRP* 6.3 2.0 - - + -
238C SER* 3.3 6.5 - - - -
239C LEU* 2.7 55.8 + - + +
255C TRP* 4.5 10.8 - - + -
259C ARG* 3.9 14.1 - - - +
301C GLU* 3.4 26.7 - - - +
302C THR 3.7 2.2 - - - +
303C LEU* 3.7 24.5 - - + +
336C LEU* 3.9 21.5 - - + +
337C SER* 1.3 78.7 + - - +
339C ASN* 1.3 65.2 + - - +
340C GLY 5.3 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 339 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184C ASN* 4.9 5.5 - - - +
185C LEU* 4.7 10.7 - - - +
186C LEU* 5.5 1.8 - - - +
236C GLU* 3.7 33.7 + - - +
237C ALA 3.7 5.4 - - - -
238C SER* 3.7 18.2 - - - -
301C GLU* 3.3 5.4 - - - -
302C THR* 2.9 42.8 + - - +
337C SER* 4.9 6.7 + - - +
338C VAL* 1.3 76.7 - - - +
340C GLY* 1.3 70.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 340 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114C TRP* 5.8 2.5 - - - +
236C GLU* 3.6 4.9 - - - -
237C ALA* 3.1 36.6 + - - +
259C ARG* 5.7 0.7 - - - -
263C TRP* 4.9 2.7 - - - -
300C ILE 3.5 8.1 - - - -
301C GLU* 3.6 19.9 - - - +
338C VAL* 5.3 0.4 - - - +
339C ASN* 1.3 79.0 - - - +
341C ASP* 1.3 60.3 + - - -
342C LEU* 3.5 2.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 341 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234C LYS* 2.7 54.2 + - - +
235C THR 4.1 5.9 - - - +
236C GLU* 4.7 8.4 - - + +
263C TRP* 4.2 5.6 - - - -
299C LEU* 5.2 1.8 - - + +
300C ILE* 2.7 22.8 + - - +
340C GLY* 1.3 68.9 - - - -
342C LEU* 1.3 64.1 + - - +
343C ASP* 3.2 6.2 + - - +
344C ARG* 3.3 22.6 + - + +
345C GLY* 3.0 18.4 + - - -
----------------------------------------------------------
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