Contacts of the helix formed by residues 326 - 347 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147G ARG* 4.1 0.2 - - - -
175G ALA 3.4 16.8 - - - -
176G ALA 4.0 2.0 - - - -
177G ARG 3.9 13.0 - - - -
133H GLU* 2.7 33.1 + - - -
324H TRP 3.6 3.0 + - - -
325H TYR* 1.3 81.7 - - - +
327H GLU* 1.3 65.9 + - - +
328H GLN* 3.4 6.9 + - - +
329H ALA* 2.8 22.7 + - - +
330H SER* 3.0 23.2 + - - -
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Residues in contact with GLU 327 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174G GLY 6.3 0.4 - - - +
175G ALA 3.5 10.5 + - - +
325H TYR* 3.8 18.1 + - - +
326H SER* 1.3 73.8 - - - +
328H GLN* 1.3 85.9 + - + +
330H SER* 3.5 2.8 + - - -
331H LEU* 3.2 34.8 + - - +
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Residues in contact with GLN 328 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176G ALA* 4.3 5.1 - - - +
177G ARG* 3.3 58.2 + - - +
326H SER* 3.1 3.8 + - - +
327H GLU* 1.3 97.9 + - + +
329H ALA* 1.3 64.3 + - - +
331H LEU* 3.5 5.7 + - - +
332H GLU* 3.0 24.6 + - - +
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Residues in contact with ALA 329 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177G ARG* 3.5 8.5 - - - +
129H ALA* 3.5 18.7 - - - +
130H ALA* 4.2 4.7 - - + -
133H GLU* 3.5 15.3 - - - +
324H TRP 3.8 17.3 - - - +
326H SER* 2.8 19.7 + - - +
328H GLN* 1.3 77.0 - - - +
330H SER* 1.3 63.9 + - - +
332H GLU* 3.2 3.1 + - - +
333H MET* 3.1 29.5 + - + +
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Residues in contact with SER 330 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169G ARG* 2.9 33.7 + - - -
324H TRP* 3.8 13.0 - - - -
325H TYR* 3.9 14.4 - - - -
326H SER 3.0 18.1 + - - -
327H GLU* 3.8 3.6 - - - -
329H ALA* 1.3 77.7 - - - +
331H LEU* 1.3 62.1 + - - +
333H MET* 3.4 7.8 - - - +
334H ARG* 3.3 31.5 + - - +
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Residues in contact with LEU 331 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46H VAL* 3.8 31.4 - - + -
327H GLU* 3.2 26.2 + - - +
328H GLN* 3.9 5.4 - - - +
330H SER* 1.3 77.8 - - - +
332H GLU* 1.3 65.9 + - - +
334H ARG* 3.4 4.6 + - - +
335H GLU* 3.0 42.2 + - - +
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Residues in contact with GLU 332 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219E ARG* 2.9 42.2 + - - -
177G ARG* 3.3 18.0 + - - +
128H SER* 4.1 1.6 + - - +
129H ALA* 3.8 17.5 - - + +
328H GLN 3.0 17.4 + - - +
329H ALA 3.2 4.7 + - - +
331H LEU* 1.3 76.8 - - - +
333H MET* 1.3 58.3 + - - +
335H GLU* 3.5 10.3 + - - +
336H ALA* 2.9 28.6 + - + +
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Residues in contact with MET 333 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82H TYR* 5.8 1.8 - - - -
104H ILE* 3.9 33.5 - - + +
105H GLY* 4.4 9.4 - - - -
126H ILE* 3.9 19.5 - - + +
129H ALA* 3.6 20.9 - - + +
130H ALA* 3.7 30.3 - - + +
324H TRP* 3.9 31.6 - - + -
329H ALA 3.1 17.4 + - - +
330H SER* 3.4 8.5 - - - +
332H GLU* 1.3 74.7 - - - +
334H ARG* 1.3 65.9 + - + +
336H ALA* 3.8 1.0 - - - +
337H ALA* 2.9 29.8 + - - +
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Residues in contact with ARG 334 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169G ARG* 3.8 34.2 - - - +
43H ASP* 3.4 45.5 + - - -
45H THR 3.6 3.8 - - - +
46H VAL* 3.4 36.5 - - + +
47H GLU* 3.0 42.8 + - - +
82H TYR* 3.9 8.4 + - - +
104H ILE* 4.1 18.4 - - + -
330H SER* 3.3 22.6 + - - +
331H LEU* 3.9 1.6 - - - +
333H MET* 1.3 78.7 - - + +
335H GLU* 1.3 61.9 + - - +
337H ALA* 3.1 4.6 + - - +
338H ALA* 2.9 24.3 + - - +
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Residues in contact with GLU 335 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46H VAL* 3.9 4.7 - - + -
50H ILE* 3.7 27.2 - - + +
331H LEU* 3.0 45.7 + - + +
332H GLU* 3.7 7.2 - - - +
334H ARG* 1.3 76.0 - - - +
336H ALA* 1.3 62.7 + - - +
338H ALA* 3.4 2.9 + - - +
339H THR* 3.1 24.9 + - - -
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Residues in contact with ALA 336 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126H ILE* 4.1 25.2 - - + +
332H GLU* 2.9 21.1 + - + +
333H MET 3.8 4.5 - - - +
335H GLU* 1.3 76.9 - - - +
337H ALA* 1.3 57.1 + - - +
339H THR* 3.3 9.3 + - - +
340H GLU* 3.0 27.7 + - - +
343H ARG* 5.5 0.2 + - - -
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Residues in contact with ALA 337 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80H MET* 4.2 9.8 - - - +
102H VAL* 4.0 16.8 - - + +
104H ILE* 3.9 27.1 - - + -
126H ILE* 3.9 10.9 - - + +
333H MET 2.9 18.6 + - - +
334H ARG* 3.1 5.4 + - - +
336H ALA* 1.3 73.6 - - - +
338H ALA* 1.3 66.4 + - - +
340H GLU* 3.3 3.5 + - - +
341H ILE* 3.2 25.5 + - - +
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Residues in contact with ALA 338 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47H GLU* 4.2 17.7 - - + -
50H ILE* 3.6 40.2 - - + -
51H LEU* 3.6 23.9 - - + +
80H MET* 4.3 5.9 - - - -
334H ARG 2.9 13.1 + - - +
335H GLU 3.7 0.2 - - - +
337H ALA* 1.3 77.2 - - - +
339H THR* 1.3 55.6 + - - +
341H ILE* 3.4 1.8 + - - +
342H ARG* 3.0 22.0 + - - +
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Residues in contact with THR 339 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50H ILE* 4.5 11.2 - - - +
335H GLU 3.1 18.6 + - - -
336H ALA* 3.6 8.7 - - - +
337H ALA 3.2 0.2 - - - -
338H ALA* 1.3 73.4 - - - +
340H GLU* 1.3 61.0 + - - +
342H ARG* 3.2 11.9 + - + +
343H ARG* 3.0 57.3 + - + +
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Residues in contact with GLU 340 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100H VAL* 5.7 0.2 - - + -
102H VAL* 4.1 14.6 - - + -
124H CYS* 3.5 36.7 - - + +
125H ASN 5.5 2.0 - - - +
126H ILE* 5.3 3.1 - - + -
336H ALA 3.0 13.5 + - - +
337H ALA 3.3 8.0 + - - +
339H THR* 1.3 74.8 - - - +
341H ILE* 1.3 65.3 + - - +
343H ARG* 2.7 38.7 + - - +
344H ALA* 3.0 20.8 + - - +
353H LEU* 3.6 7.4 - - + +
354H ARG* 2.8 31.7 + - - +
355H ASN* 2.9 15.4 + - - -
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Residues in contact with ILE 341 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36H VAL* 3.8 17.9 - - + -
51H LEU* 3.9 16.8 - - + -
78H GLY* 4.2 14.8 - - - -
79H ALA 4.4 7.9 - - - +
80H MET* 4.0 21.3 - - + -
100H VAL* 3.6 28.3 - - + -
102H VAL* 3.9 13.9 - - + -
337H ALA 3.2 11.6 + - - +
338H ALA 3.6 7.2 - - - +
340H GLU* 1.3 75.9 - - - +
342H ARG* 1.3 65.0 + - - +
344H ALA* 3.0 13.8 + - - +
345H ILE* 3.1 32.2 + - + +
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Residues in contact with ARG 342 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224D GLN* 4.8 11.9 + - - -
50H ILE* 3.2 25.2 + - + -
51H LEU* 3.8 14.4 - - + +
53H ASP* 2.9 41.0 + - - -
54H LEU* 4.2 26.8 - - + +
338H ALA 3.0 14.9 + - - +
339H THR* 3.3 15.7 - - + +
340H GLU 3.2 0.2 - - - -
341H ILE* 1.3 77.0 - - - +
343H ARG* 1.3 62.4 + - + +
345H ILE* 3.4 5.6 + - - +
346H THR* 2.7 36.7 + - - +
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Residues in contact with ARG 343 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336H ALA 5.5 0.2 + - - -
339H THR* 3.0 40.9 + - + +
340H GLU* 2.7 39.1 + - - +
342H ARG* 1.3 78.8 - - + +
344H ALA* 1.3 56.5 + - - +
346H THR* 3.7 5.8 - - - -
347H GLY* 2.8 31.9 + - - -
352H SER* 3.2 35.0 + - - +
353H LEU* 4.7 5.2 - - + -
354H ARG* 3.4 38.9 - - - +
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Residues in contact with ALA 344 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99H ARG* 3.6 17.6 + - - +
100H VAL* 3.7 30.3 - - + -
340H GLU 3.0 10.7 + - - +
341H ILE 3.0 9.7 + - - +
343H ARG* 1.3 77.0 - - - +
345H ILE* 1.3 60.7 + - + +
347H GLY 3.6 12.3 - - - +
349H ILE* 3.6 20.9 - - + +
352H SER* 5.7 0.4 - - - -
353H LEU* 3.9 14.1 - - + +
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Residues in contact with ILE 345 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262D ARG* 4.9 2.8 + - - -
34H PRO* 4.6 17.7 - - + -
36H VAL* 4.4 4.3 - - + -
51H LEU* 4.7 2.7 - - + -
54H LEU* 3.9 29.2 - - + -
55H ALA* 4.2 23.8 - - + -
77H VAL* 4.9 17.0 - - + -
99H ARG* 5.1 4.6 + - - +
100H VAL* 6.4 0.7 - - + -
341H ILE* 3.1 36.5 + - + +
342H ARG* 3.9 8.5 - - - +
344H ALA* 1.3 80.2 - - + +
346H THR* 1.3 63.4 + - - +
347H GLY 3.6 3.5 + - - +
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Residues in contact with THR 346 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235D GLN* 3.4 34.6 + - - +
262D ARG* 3.1 16.8 + - - -
54H LEU* 3.3 33.9 - - + -
342H ARG* 2.7 29.5 + - + +
343H ARG* 3.6 6.9 + - - -
345H ILE* 1.3 77.7 - - + +
347H GLY* 1.3 59.6 + - - +
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Residues in contact with GLY 347 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234D TYR 4.0 7.9 - - - -
235D GLN* 4.3 6.3 - - - -
262D ARG* 3.6 12.2 + - - -
99H ARG* 4.8 4.9 + - - -
343H ARG 2.8 17.2 + - - -
344H ALA 3.6 11.3 - - - +
345H ILE 3.9 2.8 - - - +
346H THR* 1.3 80.5 + - - +
348H ARG* 1.3 61.0 + - - -
349H ILE 4.2 0.3 + - - -
352H SER* 3.6 12.8 - - - -
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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