Contacts of the strand formed by residues 303 - 311 (chain D) in PDB entry 6CP3
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 SER 303 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149D ARG* 4.6 9.0 - - - +
150D GLY* 3.9 19.1 + - - -
249D GLN 3.4 9.3 + - - +
250D ASP* 3.3 25.0 + - - +
251D VAL* 2.8 34.4 + - - +
298D THR* 3.7 9.0 - - - +
302D GLY* 1.3 72.5 - - - -
304D VAL* 1.3 57.0 + - - +
305D THR* 4.2 3.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 304 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150D GLY* 3.3 9.9 - - - +
151D GLY 3.8 2.6 - - - +
152D LYS* 5.9 0.5 - - - +
240D ALA* 5.0 6.5 - - + +
244D ARG* 3.6 39.0 - - + +
251D VAL* 3.4 18.4 - - + +
253D LEU* 5.0 7.6 - - + -
296D ILE* 3.9 29.2 - - + -
297D THR* 3.8 18.2 - - - +
298D THR* 2.9 25.0 + - - -
302D GLY 3.9 0.8 + - - -
303D SER* 1.3 78.3 + - - +
305D THR* 1.3 67.1 + - - +
306D SER* 4.0 1.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 305 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134D LEU* 4.9 9.9 - - + -
148D ALA 4.1 13.7 - - - +
149D ARG* 3.4 17.7 - - - -
150D GLY* 2.7 22.5 + - - -
151D GLY 3.7 3.4 - - - +
153D ILE* 4.2 17.5 - - + -
251D VAL 2.8 10.0 + - - +
252D LEU* 3.4 26.6 - - + +
253D LEU* 2.9 26.3 + - - +
303D SER* 4.2 1.6 + - - -
304D VAL* 1.3 71.7 - - - +
306D SER* 1.3 62.9 + - - +
307D VAL* 5.0 3.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 306 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151D GLY 3.2 5.9 + - - -
152D LYS* 3.7 24.9 - - - +
153D ILE* 3.0 31.7 + - - +
253D LEU* 3.5 10.2 + - - +
296D ILE* 3.7 19.5 - - - +
304D VAL* 4.0 1.7 - - - -
305D THR* 1.3 72.3 - - - +
307D VAL* 1.3 63.6 + - - +
308D GLN* 3.2 31.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 307 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147D TYR* 5.6 0.2 - - + -
153D ILE* 3.4 29.4 - - + +
155D LEU* 4.3 16.6 - - + -
167D ILE* 3.7 25.5 - - + +
170D LEU* 4.4 15.3 - - + -
252D LEU* 5.8 0.7 - - + -
253D LEU 2.8 9.3 + - - +
254D PHE* 3.5 28.8 - - + -
255D ILE 3.0 27.2 + - - +
305D THR* 5.0 6.3 - - + +
306D SER* 1.3 77.1 - - - +
308D GLN* 1.3 61.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 308 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152D LYS* 4.8 1.4 - - - +
153D ILE 2.8 12.5 + - - +
154D GLY* 3.4 3.7 - - - -
155D LEU 3.3 19.1 + - - -
255D ILE* 3.3 24.9 - - + +
258D ILE* 4.5 10.0 - - + +
293D GLN* 2.6 45.9 + - - +
296D ILE* 3.5 24.5 - - - +
306D SER* 3.2 24.0 + - - +
307D VAL* 1.3 72.7 - - - +
309D ALA* 1.3 65.5 + - - +
310D VAL* 3.3 16.2 - - + +
325D THR* 5.0 1.6 - - - +
329D LEU* 4.2 12.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 309 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155D LEU* 4.0 16.1 - - + +
163D LYS* 4.5 19.5 - - + -
167D ILE* 4.2 13.8 - - + +
255D ILE 3.0 7.1 + - - +
256D ASP* 3.3 31.9 - - + +
257D ASN* 2.8 16.8 - - - +
258D ILE* 3.2 13.0 + - - +
307D VAL* 3.9 1.8 + - - +
308D GLN* 1.3 72.6 - - - +
310D VAL* 1.3 60.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 310 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155D LEU 3.2 7.4 + - - +
156D PHE* 3.5 36.3 - - + -
157D GLY 3.3 22.9 + - - +
163D LYS* 3.7 4.2 - - - +
257D ASN* 3.3 2.0 - - - -
258D ILE* 3.6 26.0 - - + -
259D PHE* 5.0 2.9 - - + +
308D GLN* 3.3 22.0 - - + +
309D ALA* 1.3 75.2 - - - +
311D TYR* 1.3 74.7 + - - +
312D VAL* 4.2 0.2 - - - +
321D ALA 5.5 0.7 - - - +
322D PRO* 4.7 9.4 - - + -
325D THR* 4.1 16.8 - - + +
329D LEU* 4.8 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 311 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342C THR* 3.3 26.7 + - + +
346C SER* 2.9 29.6 + - - -
157D GLY 3.7 0.7 - - - -
158D GLY 4.2 0.7 - - - -
159D ALA* 3.6 33.0 - - - +
163D LYS* 3.3 19.5 - - - +
257D ASN* 3.1 27.0 + - - +
259D PHE* 3.4 43.5 - + + +
260D ARG* 4.5 7.2 - - - +
310D VAL* 1.3 82.2 - - - +
312D VAL* 1.3 84.6 + - - +
313D PRO* 3.6 11.8 - - + +
314D ALA 4.1 1.4 + - - -
322D PRO* 3.5 15.1 - - - +
600D ADP 5.1 1.3 - - - -
----------------------------------------------------------
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