Contacts of the strand formed by residues 294 - 303 (chain A) in PDB entry 6M85
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 GLU 294 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A ARG* 5.7 0.4 - - - +
43A ASN 4.5 2.6 - - - +
44A ARG* 3.9 8.3 - - - +
45A PHE* 2.9 33.9 + - - +
46A VAL* 3.0 27.7 + - - +
232A LEU* 3.5 2.9 - - - +
233A ILE* 2.6 49.6 + - + +
293A PHE* 1.3 76.8 - - - +
295A ILE* 1.3 64.5 + - - +
296A VAL* 4.5 7.0 - - + -
315A SER* 2.6 32.2 + - - +
316A TYR 3.5 4.7 - - - +
317A LEU* 4.2 11.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 295 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A ALA* 6.1 0.4 - - + -
211A LEU* 3.3 32.1 - - + -
213A TRP* 5.4 0.7 - - + -
230A ALA* 4.7 1.6 - - + -
231A GLN 3.1 3.6 - - - +
232A LEU* 4.6 4.0 - - + -
251A ILE* 3.3 30.3 - - + -
280A LEU* 4.2 7.9 - - + -
293A PHE* 3.9 17.9 - - + -
294A GLU* 1.3 75.9 - - - +
296A VAL* 1.3 69.2 + - - +
297A VAL* 3.9 14.2 + - + -
315A SER* 3.4 1.7 - - - -
316A TYR* 2.7 51.6 + - + +
321A ILE* 3.8 23.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 296 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A PHE* 5.0 1.3 - - + -
46A VAL* 3.9 35.2 - - + -
230A ALA* 3.2 4.9 - - - +
231A GLN* 2.8 43.4 + - + +
233A ILE* 3.5 28.0 - - + -
294A GLU* 4.0 9.2 - - - +
295A ILE* 1.3 73.8 - - - +
297A VAL* 1.3 69.1 + - - +
298A ILE* 4.3 18.8 - - + +
313A ARG* 5.0 5.4 - - + -
314A SER 3.6 11.9 - - - +
315A SER* 5.0 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 297 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A PHE* 3.6 27.3 - - + -
213A TRP* 3.5 44.4 - - + +
229A ARG 3.7 2.9 - - - +
230A ALA* 4.2 0.9 - - + -
295A ILE* 4.2 9.2 - - + -
296A VAL* 1.3 77.3 - - - +
298A ILE* 1.3 66.0 + - - +
313A ARG* 3.5 4.3 - - - -
314A SER* 3.0 43.1 + - - +
316A TYR* 3.7 29.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 298 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A PHE* 4.1 4.1 - - - -
213A TRP* 5.6 0.5 + - - -
227A HIS 5.6 0.2 - - - +
228A VAL* 3.3 8.3 - - - +
229A ARG* 2.9 65.1 + - + +
230A ALA 5.6 0.2 - - - +
231A GLN* 5.3 13.9 - - + +
296A VAL* 4.3 15.3 - - + +
297A VAL* 1.3 80.0 - - - +
299A LEU* 1.3 64.5 + - - +
300A GLU* 3.7 33.0 - - + +
311A GLN* 4.1 13.9 - - + +
312A ALA 3.5 7.6 - - - +
313A ARG* 4.1 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 299 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A LEU* 3.6 39.2 - - + +
196A PHE* 3.8 16.0 - - + -
215A VAL* 4.2 18.8 - - + -
223A ILE* 4.7 2.9 - - + -
226A ALA* 4.4 6.1 - - + -
227A HIS 3.3 23.3 - - - +
228A VAL* 3.7 15.5 - - + -
262A ILE* 4.2 9.0 - - + -
264A LEU* 4.0 16.8 - - + -
298A ILE* 1.3 73.9 - - - +
300A GLU* 1.3 72.4 + - - +
310A THR 3.9 0.5 - - - +
311A GLN* 3.6 1.2 - - - -
312A ALA* 2.9 38.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 300 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A LEU* 6.2 0.9 - - - -
223A ILE* 5.0 0.9 - - - -
226A ALA* 3.1 3.2 - - - -
227A HIS* 2.8 67.3 + - + +
229A ARG* 3.7 22.3 + - - -
298A ILE* 3.7 15.6 - - + +
299A LEU* 1.3 82.8 - - - +
301A GLY* 1.3 60.1 + - - +
309A THR* 5.7 2.9 - - + -
310A THR 3.3 11.4 - - - +
311A GLN* 2.7 33.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 301 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A LEU* 6.2 0.6 - - - +
223A ILE* 3.8 11.8 - - - +
224A VAL 3.6 10.5 - - - -
225A GLU 3.7 7.0 - - - -
227A HIS* 5.5 0.2 - - - -
300A GLU* 1.3 77.0 - - - +
302A MET* 1.3 63.1 + - - -
303A VAL* 3.5 2.4 + - - +
309A THR* 4.2 9.0 - - - +
310A THR* 2.8 34.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 302 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A ILE* 3.4 2.0 - - - -
224A VAL* 2.7 61.3 + - + +
225A GLU* 5.5 3.5 - - + +
301A GLY* 1.3 70.0 - - - -
303A VAL* 1.3 76.8 + - - +
304A GLU* 3.6 11.5 + - + +
307A ALA* 3.6 11.9 - - - +
308A MET* 3.6 25.4 - - - -
309A THR* 4.1 19.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 303 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A THR* 3.9 30.7 - - + +
194A LEU* 4.8 3.4 - - + -
221A SER* 5.3 0.9 - - - +
222A HIS 4.0 7.6 - - - +
223A ILE* 4.3 20.0 - - + +
301A GLY 4.0 2.9 - - - +
302A MET* 1.3 74.3 - - - +
304A GLU* 1.3 54.9 + - - +
305A ALA* 3.7 20.4 - - + +
306A THR* 3.2 16.1 + - + +
307A ALA* 2.8 34.1 + - - -
308A MET 3.2 6.3 + - - -
310A THR* 3.3 27.1 - - + +
----------------------------------------------------------
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