Contacts of the strand formed by residues 294 - 301 (chain C) in PDB entry 2Z43
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 ARG 294 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290C SER* 2.9 43.9 + - - +
291C ARG* 2.9 33.9 + - - +
292C GLY 3.1 1.8 - - - -
293C ASN* 1.3 90.7 - - - +
295C ARG* 1.3 68.1 + - - +
311C VAL* 3.9 31.6 - - + +
312C PHE 3.5 8.1 - - - +
313C ALA* 4.3 0.7 - - - +
322C ALA* 4.0 23.6 - - + +
323C GLU 5.9 4.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 295 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117C GLY* 2.7 28.0 + - - -
118C SER 3.3 21.8 - - - +
287C LEU* 5.8 0.2 - - + -
288C LYS 3.5 11.7 - - - +
289C LYS* 3.5 31.7 - - - +
290C SER* 4.1 2.7 + - - +
292C GLY 3.0 23.0 + - - -
293C ASN* 3.4 15.2 - - - +
294C ARG* 1.3 90.2 + - - +
296C ILE* 1.3 63.8 + - - +
311C VAL* 3.4 5.5 - - - +
312C PHE* 2.7 61.1 + - + +
314C LEU* 3.7 27.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 296 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286C GLN 3.5 1.7 - - - +
287C LEU* 3.3 5.7 - - - -
288C LYS* 2.9 54.0 + - + +
289C LYS 5.7 0.9 - - - +
290C SER* 4.2 17.5 - - - +
295C ARG* 1.3 79.1 - - - +
297C ALA* 1.3 62.0 + - - +
298C ARG* 4.8 2.2 - - + +
309C GLU* 3.8 37.0 - - + +
310C VAL 3.5 9.4 - - - +
311C VAL* 3.8 20.0 - - + -
312C PHE* 4.5 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 297 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96C LEU* 3.6 31.6 - - + -
99C LEU* 3.5 8.5 - - + +
285C ILE* 4.2 2.7 - - + -
286C GLN 3.5 4.5 - - - -
287C LEU* 3.7 17.0 - - + -
295C ARG 4.2 1.0 + - - -
296C ILE* 1.3 72.1 - - - +
298C ARG* 1.3 60.0 + - - +
309C GLU* 2.9 4.9 - - - +
310C VAL* 2.8 42.4 + - + -
312C PHE* 3.8 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 298 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B LYS* 5.2 9.5 - - - +
298B ARG* 3.2 26.1 - - - +
309B GLU* 2.3 45.4 + - - -
99C LEU* 4.3 0.4 - - - -
285C ILE* 3.5 5.1 - - - +
286C GLN* 3.0 52.8 + - - +
288C LYS* 5.8 2.7 - - - +
296C ILE* 4.1 3.1 + - + +
297C ALA* 1.3 73.2 - - - +
299C VAL* 1.3 79.7 + - - +
300C VAL* 3.2 9.6 + - + +
307C GLU* 6.0 2.4 - - - +
308C GLY* 3.5 21.0 - - - +
309C GLU* 2.6 37.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 299 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99C LEU* 3.8 32.3 - - + +
284C ARG 4.0 5.2 - - - +
285C ILE* 4.1 10.8 - - + -
298C ARG* 1.3 83.4 + - - +
300C VAL* 1.3 62.6 + - - +
301C ASP 3.8 4.5 - - - +
302C ALA* 3.6 28.9 - - + +
305C LEU* 4.4 7.0 - - + -
306C PRO 3.7 18.6 - - - +
307C GLU* 3.4 28.1 - - - +
308C GLY 3.2 14.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 300 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113C PHE* 4.2 11.7 - - + -
284C ARG* 2.9 29.2 + - + +
286C GLN* 3.9 25.1 - - + +
298C ARG* 3.8 19.7 - - + +
299C VAL* 1.3 76.4 - - - +
301C ASP* 1.3 66.2 + - + +
307C GLU* 5.0 3.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 301 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282C GLY 4.0 4.6 - - - +
283C ILE* 3.4 4.3 - - - -
284C ARG* 2.9 53.8 + - + +
299C VAL* 3.7 0.6 - - - +
300C VAL* 1.3 85.0 - - + +
302C ALA* 1.3 63.2 + - - +
303C PRO* 3.8 14.4 - - - +
307C GLU* 5.5 0.4 - - - -
----------------------------------------------------------
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