Contacts of the strand formed by residues 301 - 308 (chain C) in PDB entry 4PAR
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 GLY 301 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247C GLU 3.2 11.7 - - - -
248C LYS* 4.2 11.1 - - - +
258C LYS* 4.7 10.8 - - - -
262C TRP* 4.7 0.4 - - - -
296C ALA* 4.7 2.5 - - - -
297C ASP 2.9 26.6 + - - +
298C LEU* 4.0 6.0 + - - -
299C LYS 3.5 3.4 - - - -
300C ASP* 1.3 82.1 - - - +
302C ALA* 1.3 65.3 + - - -
303C VAL* 3.7 5.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 302 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245C ILE 3.8 0.5 - - - +
246C THR* 3.3 6.6 - - - -
247C GLU* 2.9 32.0 + - + +
262C TRP* 3.4 38.7 - - + -
293C PHE* 4.2 5.8 - - + -
295C LYS 3.4 11.7 - - - +
296C ALA* 4.5 1.6 - - - +
301C GLY* 1.3 73.0 - - - -
303C VAL* 1.3 60.3 + - - +
304C TRP* 3.6 23.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 303 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244C THR* 4.5 11.7 - - + -
245C ILE 3.8 2.5 - - - -
246C THR* 4.5 13.7 - - + -
293C PHE* 3.8 2.3 - - - -
294C GLN* 2.9 50.7 + - + +
295C LYS* 2.9 34.1 + - + +
297C ASP* 5.5 2.0 - - - +
300C ASP* 5.4 5.8 - - + +
301C GLY 3.7 7.2 + - - +
302C ALA* 1.3 75.6 - - - +
304C TRP* 1.3 58.1 + - - +
305C LYS* 4.2 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 304 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224C TRP* 4.5 12.6 - + + -
244C THR* 3.8 0.3 - - - -
245C ILE* 2.9 50.7 + - + +
247C GLU* 3.5 23.1 + - + -
262C TRP* 4.2 12.8 - + - -
266C PRO 4.2 10.1 - - - -
267C GLN 3.7 10.3 - - - -
269C ARG* 3.2 64.8 - - + +
291C TYR* 3.3 20.1 - - + -
292C GLU* 3.9 7.4 - - - -
293C PHE* 3.5 53.8 - + + -
302C ALA* 3.6 16.6 - - + +
303C VAL* 1.3 76.0 - - - +
305C LYS* 1.3 60.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 305 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243C LEU* 3.5 12.9 + - + +
244C THR* 3.5 24.7 + - - +
291C TYR* 3.3 3.1 - - - -
292C GLU* 2.9 34.7 + - + +
294C GLN* 3.5 47.1 - - + +
303C VAL* 3.9 12.7 + - + -
304C TRP* 1.3 74.2 - - - +
306C ARG* 1.3 64.4 + - - +
307C VAL* 3.5 2.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 306 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185C LEU* 4.3 13.5 - - - +
241C ASP 4.0 12.3 + - - -
242C GLY 3.5 11.1 + - - -
243C LEU* 2.9 51.6 + - + +
288C MET 3.7 22.6 + - - -
289C GLY* 4.4 0.9 - - - -
290C LEU 4.3 2.0 - - - +
291C TYR* 3.4 27.9 - - + -
305C LYS* 1.3 74.9 - - - +
307C VAL* 1.3 64.9 + - - +
308C LYS 4.2 15.7 - - - +
309C SER* 3.1 26.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 307 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268C LYS* 5.6 6.3 - - + +
290C LEU* 3.3 11.9 + - + +
291C TYR 4.0 0.4 - - - -
292C GLU* 3.4 58.3 - - + +
305C LYS 3.7 1.1 - - - +
306C ARG* 1.3 77.8 + - - +
308C LYS* 1.3 93.6 + - + +
309C SER* 4.0 4.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 308 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268C LYS* 5.8 3.8 - - - +
289C GLY* 3.8 1.7 - - - -
290C LEU* 2.9 62.9 + - + +
306C ARG* 4.2 4.7 - - - +
307C VAL* 1.3 99.7 - - + +
309C SER* 1.3 61.5 + - - +
310C GLU* 3.4 16.2 - - + +
----------------------------------------------------------
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