Contacts of the helix formed by residues 326 - 347 (chain A) in PDB entry 2OME
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 326 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A GLU* 2.7 32.0 + - - -
324A TRP 3.5 3.2 + - - -
325A TYR* 1.3 81.7 - - - +
327A GLU* 1.3 65.7 + - - +
328A GLN* 3.3 15.0 + - - -
329A ALA* 2.9 17.3 + - - +
330A SER* 2.9 23.4 + - - +
147B ARG* 4.0 0.2 - - - -
175B ALA 3.3 14.4 - - - -
176B ALA 3.9 2.5 - - - -
177B ARG 3.8 7.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 327 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A TYR* 3.9 18.2 - - - +
326A SER* 1.3 74.3 - - - +
328A GLN* 1.3 76.0 + - + +
330A SER* 3.5 3.4 + - - -
331A LEU* 3.2 23.1 + - + +
175B ALA 3.4 10.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 328 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326A SER* 3.3 9.1 + - - +
327A GLU* 1.3 88.2 + - + +
329A ALA* 1.3 60.2 + - - +
331A LEU* 3.6 5.9 + - - +
332A GLU* 3.1 28.2 + - - +
176B ALA* 3.8 9.5 - - - +
177B ARG* 3.0 63.8 + - + +
181B GLU* 5.8 2.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 329 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A ALA* 3.6 19.5 - - - +
130A ALA* 4.2 4.0 - - + -
133A GLU* 3.6 14.6 - - - +
324A TRP* 3.8 17.0 - - + +
326A SER* 2.9 21.0 + - - +
328A GLN* 1.3 74.8 - - - +
330A SER* 1.3 63.4 + - - +
332A GLU* 3.3 3.0 + - - +
333A MET* 3.1 29.1 + - + +
177B ARG* 3.6 9.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 330 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A TRP* 4.0 11.4 - - - -
325A TYR* 3.9 14.8 - - - -
326A SER 2.9 18.0 + - - +
327A GLU* 3.8 4.7 - - - -
329A ALA* 1.3 76.3 - - - +
331A LEU* 1.3 61.2 + - - +
333A MET* 3.4 8.0 - - - +
334A ARG* 3.2 30.8 + - - +
169B ARG* 3.2 35.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 331 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A VAL* 3.8 33.7 - - + -
327A GLU* 3.2 15.9 + - + +
328A GLN* 3.9 5.8 - - - +
330A SER* 1.3 78.1 - - - +
332A GLU* 1.3 67.3 + - - +
334A ARG* 3.4 3.9 + - - +
335A GLU* 3.0 41.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 332 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A SER* 4.4 1.2 + - - -
129A ALA* 3.3 20.0 - - + +
328A GLN 3.1 16.7 + - - +
329A ALA 3.3 5.6 + - - +
331A LEU* 1.3 76.2 - - - +
333A MET* 1.3 58.6 + - - +
335A GLU* 3.4 9.3 + - - +
336A ALA* 2.9 28.7 + - + +
177B ARG* 3.1 28.9 + - - -
219D ARG* 3.1 30.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 333 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A TYR* 5.8 0.4 - - - -
104A ILE* 3.9 36.0 - - + +
105A GLY* 4.1 9.4 - - - -
126A ILE* 4.0 19.5 - - + +
129A ALA* 3.5 18.6 - - + -
130A ALA* 3.8 24.7 - - + +
324A TRP* 3.8 35.2 - - + -
329A ALA 3.1 11.4 + - - +
330A SER* 3.4 13.5 - - - +
332A GLU* 1.3 77.7 - - - +
334A ARG* 1.3 65.1 + - + +
336A ALA* 3.4 1.2 + - - +
337A ALA* 2.9 30.1 + - - +
169B ARG* 6.1 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 334 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A ASP* 3.1 37.6 + - - -
45A THR 3.4 19.4 - - - +
46A VAL* 3.5 31.5 - - + +
47A GLU* 2.9 44.6 + - - +
82A TYR* 3.9 14.2 + - - +
104A ILE* 4.2 12.1 - - + -
330A SER* 3.2 22.0 + - - +
331A LEU 3.9 2.7 - - - +
333A MET* 1.3 77.6 - - + +
335A GLU* 1.3 55.6 + - - +
337A ALA* 3.2 4.6 + - - +
338A ALA* 2.9 28.9 + - - +
169B ARG* 3.6 33.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 335 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A VAL* 3.8 13.2 - - + +
50A ILE* 3.8 26.6 - - + +
331A LEU* 3.0 38.5 + - + +
332A GLU* 3.7 7.1 - - - +
334A ARG* 1.3 76.7 - - - +
336A ALA* 1.3 63.4 + - - +
338A ALA* 3.5 2.8 + - - +
339A THR* 3.1 26.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 336 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A ILE* 4.0 27.5 - - + +
332A GLU* 2.9 19.9 + - + +
333A MET 3.8 4.7 - - - +
334A ARG 3.2 0.2 - - - -
335A GLU* 1.3 78.4 - - - +
337A ALA* 1.3 56.3 + - - +
339A THR* 3.2 8.1 + - - +
340A GLU* 3.0 27.5 + - - +
343A ARG* 5.0 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 337 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A GLU* 5.9 0.2 - - + -
80A MET* 4.2 10.0 - - - +
102A VAL* 3.8 25.8 - - + +
104A ILE* 4.0 24.0 - - + -
126A ILE* 4.0 7.8 - - + +
333A MET 2.9 17.6 + - - +
334A ARG 3.7 4.3 - - - +
336A ALA* 1.3 74.9 - - - +
338A ALA* 1.3 65.0 + - - +
340A GLU* 3.4 3.4 + - - +
341A ILE* 3.2 25.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 338 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A GLU* 4.1 20.0 - - + -
50A ILE* 3.7 33.2 - - + -
51A LEU* 3.7 16.2 - - + +
80A MET* 4.4 6.3 - - - -
334A ARG 2.9 15.4 + - - +
335A GLU 3.8 3.6 - - - +
337A ALA* 1.3 77.3 - - - +
339A THR* 1.3 61.0 + - - +
341A ILE* 3.4 4.0 + - - +
342A ARG* 3.0 20.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 339 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A ILE* 4.5 11.6 - - - +
335A GLU* 3.1 15.3 + - - +
336A ALA* 3.2 11.6 + - - -
338A ALA* 1.3 76.5 - - - +
340A GLU* 1.3 57.2 + - - +
342A ARG* 3.3 13.5 + - + +
343A ARG* 3.0 61.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 340 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A VAL* 3.9 17.7 - - + -
124A CYS* 3.5 34.4 - - + +
125A ASN 5.2 2.5 - - - -
126A ILE* 5.1 3.5 - - + +
336A ALA 3.0 12.8 + - - +
337A ALA* 3.7 8.7 - - - +
339A THR* 1.3 74.9 - - - +
341A ILE* 1.3 65.7 + - - +
343A ARG* 2.8 39.0 + - - +
344A ALA* 3.0 20.3 + - - +
353A LEU* 4.1 7.1 - - + +
354A ARG* 3.2 15.1 + - - +
355A ASN* 2.9 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 341 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A VAL* 3.8 32.5 - - + -
51A LEU* 3.9 13.7 - - + -
78A GLY* 4.3 4.9 - - - -
79A ALA 4.0 14.8 - - - +
80A MET* 3.9 20.9 - - + -
100A VAL* 4.0 20.0 - - + -
102A VAL* 3.9 19.1 - - + -
337A ALA 3.2 12.8 + - - +
338A ALA 3.7 6.5 - - - +
340A GLU* 1.3 76.6 - - - +
342A ARG* 1.3 64.3 + - - +
344A ALA* 3.0 15.2 + - - +
345A ILE* 3.1 24.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 342 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A ILE* 3.0 31.1 + - + -
51A LEU* 3.8 18.1 - - + +
53A ASP* 3.0 34.4 + - - -
54A LEU* 3.8 29.2 - - + +
338A ALA 3.0 14.2 + - - +
339A THR* 3.3 15.5 - - - +
340A GLU 3.2 0.4 - - - -
341A ILE* 1.3 77.2 - - - +
343A ARG* 1.3 65.4 + - + +
345A ILE* 3.4 1.9 + - - +
346A THR* 3.1 33.8 + - + +
224E GLN* 5.5 4.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 343 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A ALA 5.0 1.4 + - - -
339A THR* 3.0 43.9 + - + +
340A GLU* 2.8 43.1 + - - +
342A ARG* 1.3 78.3 - - + +
344A ALA* 1.3 58.8 + - - +
346A THR* 3.6 6.0 + - - -
347A GLY* 2.8 31.7 + - - -
352A SER* 3.4 32.0 - - - +
353A LEU* 4.6 5.2 - - + -
354A ARG* 3.5 37.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 344 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A ARG* 4.6 4.0 + - - -
100A VAL* 3.7 32.3 - - + -
340A GLU 3.0 10.2 + - - +
341A ILE 3.0 9.9 + - - +
343A ARG* 1.3 80.0 - - - +
345A ILE* 1.3 61.8 + - + +
347A GLY 3.6 11.5 - - - +
348A ARG 5.8 0.4 - - - -
349A ILE* 3.6 23.3 - - + +
353A LEU* 3.9 17.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 345 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A PRO* 4.6 20.6 - - + -
36A VAL* 4.4 5.4 - - + -
51A LEU* 5.2 1.8 - - + -
54A LEU* 4.3 28.9 - - + +
55A ALA* 3.9 27.1 - - + -
77A VAL* 5.0 14.8 - - + -
100A VAL* 6.4 0.4 - - + -
341A ILE* 3.1 29.6 + - + +
342A ARG* 4.0 4.7 - - - +
343A ARG 3.3 0.2 - - - -
344A ALA* 1.3 81.6 - - + +
346A THR* 1.3 63.3 + - - +
347A GLY 3.6 3.6 + - - +
262E ARG* 4.7 3.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 346 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A LEU* 3.3 31.6 - - + -
342A ARG* 3.1 28.2 + - + +
343A ARG* 3.6 7.8 + - - -
345A ILE* 1.3 76.6 - - + +
347A GLY* 1.3 61.2 + - - +
224E GLN* 6.1 0.7 - - - +
235E GLN* 3.3 37.8 + - - +
262E ARG* 3.1 15.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 347 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A ARG* 5.5 1.9 + - - -
343A ARG 2.8 16.8 + - - -
344A ALA 3.6 11.5 - - - +
345A ILE 3.9 2.8 - - - +
346A THR* 1.3 79.4 + - - +
348A ARG* 1.3 60.8 + - - -
349A ILE* 4.2 0.5 + - - +
352A SER* 3.8 13.2 - - - -
234E TYR 3.9 8.3 - - - -
235E GLN* 4.2 5.8 - - - -
262E ARG* 3.4 15.4 + - - -
----------------------------------------------------------
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