Contacts of the helix formed by residues 342 - 363 (chain A) in PDB entry 2O2C
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 342 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A GLU* 5.1 0.9 - - - -
185A ARG* 3.3 26.1 - - - +
338A MET* 2.7 25.8 + - - -
341A ILE* 1.3 75.5 - - - +
343A TYR* 1.3 60.4 + - - -
344A GLU 3.4 2.2 - - - -
345A ASN 3.4 1.5 + - - -
346A PHE* 3.0 28.1 + - - +
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Residues in contact with TYR 343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A ARG* 4.5 9.2 + - - -
174A LEU* 4.0 20.6 - - + +
175A ASP* 5.5 1.0 - - - -
178A ARG* 3.6 51.1 - - + -
181A SER* 4.8 3.1 + - - +
182A GLU* 4.5 13.9 + - - +
338A MET* 3.7 30.8 - - + +
342A GLY* 1.3 70.1 - - - -
344A GLU* 1.3 84.1 + - + +
346A PHE* 3.1 3.5 + - - +
347A VAL* 2.9 52.7 + - + +
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Residues in contact with GLU 344 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342A GLY 3.4 0.8 - - - -
343A TYR* 1.3 100.0 - - + +
345A ASN* 1.3 60.3 + - - +
347A VAL* 3.4 10.8 + - - +
348A GLU* 3.1 30.0 + - - +
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Residues in contact with ASN 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222A PHE* 3.5 29.7 + - - +
341A ILE* 3.0 41.4 + - + +
342A GLY 3.4 1.8 + - - +
343A TYR 3.2 0.4 - - - -
344A GLU* 1.3 77.2 - - - +
346A PHE* 1.3 60.1 + - - +
348A GLU* 3.2 10.3 + - - +
349A LEU* 3.1 21.7 + - - +
536A PRO* 3.3 28.5 - - + +
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Residues in contact with PHE 346 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A LEU* 4.0 12.6 - - + -
177A MET* 4.2 3.4 - - + -
329A MET 3.6 23.6 - - - -
330A TRP* 3.9 20.4 - - - -
331A SER 4.2 2.7 - - - -
334A GLY* 3.5 25.1 - - - -
337A ILE* 4.0 11.2 - - + -
338A MET* 3.6 44.4 - - + -
341A ILE* 4.0 4.7 - - + +
342A GLY 3.0 14.3 + - - +
343A TYR 3.1 7.6 + - - +
345A ASN* 1.3 75.1 - - - +
347A VAL* 1.3 60.3 + - + +
349A LEU* 3.2 23.1 + - + +
350A LEU* 3.0 43.9 + - + +
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Residues in contact with VAL 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A ARG* 3.6 32.3 - - - +
174A LEU* 6.4 0.2 - - + -
343A TYR* 2.9 56.5 + - + +
344A GLU* 3.6 12.6 - - - +
345A ASN 3.3 0.2 - - - -
346A PHE* 1.3 76.7 - - + +
348A GLU* 1.3 56.9 + - - +
350A LEU* 3.3 11.2 + - + +
351A THR* 2.7 43.2 + - - +
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Residues in contact with GLU 348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A SER* 4.9 3.3 - - - -
344A GLU 3.1 17.0 + - - +
345A ASN* 3.4 17.3 - - - +
346A PHE 3.2 0.2 - - - -
347A VAL* 1.3 79.2 - - + +
349A LEU* 1.3 55.2 + - - +
351A THR* 3.2 5.3 + - - -
352A GLY 3.0 24.8 + - - -
535A THR* 6.0 0.3 - - - -
536A PRO* 3.9 13.2 - - + -
537A ARG* 2.9 64.8 + - - +
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Residues in contact with LEU 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215A ALA* 5.0 0.9 - - + -
219A LEU* 4.4 6.3 - - + -
329A MET* 4.1 19.5 - - + +
330A TRP* 3.7 17.2 - - + -
337A ILE* 4.2 14.8 - - + -
341A ILE* 4.9 0.9 - - + -
345A ASN 3.1 12.2 + - - +
346A PHE* 3.3 38.1 - - + +
348A GLU* 1.3 75.4 - - - +
350A LEU* 1.3 61.2 + - + +
352A GLY 3.4 0.9 + - - -
353A ALA 3.4 6.4 + - - -
536A PRO* 3.4 25.5 + - + +
539A LEU* 4.0 20.9 - - + -
540A GLY* 3.4 41.2 - - - +
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Residues in contact with LEU 350 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A LEU 3.9 6.5 - - - +
152A ARG* 3.4 32.4 - - + +
154A ARG* 3.8 30.1 - - - +
174A LEU* 4.0 26.0 - - + -
330A TRP* 3.6 40.6 - - + +
346A PHE* 3.0 30.9 + - + +
347A VAL* 3.3 13.0 + - + +
349A LEU* 1.3 77.4 - - + +
351A THR* 1.3 56.2 + - - +
353A ALA* 3.2 2.4 + - - +
354A HIS* 2.9 24.4 + - - +
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Residues in contact with THR 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A ARG* 3.7 19.0 + - + +
347A VAL* 2.7 30.0 + - - +
348A GLU* 3.2 9.7 + - - -
350A LEU* 1.3 73.0 - - - +
352A GLY* 1.3 60.8 + - - +
354A HIS* 3.2 9.9 + - + +
355A VAL* 2.9 40.4 + - + +
537A ARG* 3.7 32.9 + - - +
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Residues in contact with GLY 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A LEU* 5.4 0.7 - - - -
348A GLU 3.0 11.1 + - - -
349A LEU 3.4 1.7 + - - -
350A LEU 3.3 0.2 - - - -
351A THR* 1.3 75.4 - - - +
353A ALA* 1.3 60.8 + - - +
355A VAL* 3.5 5.8 + - - +
356A ILE* 3.3 17.8 + - - +
537A ARG* 3.3 35.4 - - - +
541A ALA* 3.5 20.3 - - - +
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Residues in contact with ALA 353 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152A ARG* 3.7 21.3 - - - +
330A TRP* 3.7 24.9 - - + -
349A LEU 3.4 4.0 + - - -
350A LEU 3.2 9.1 + - - +
351A THR 3.2 0.4 - - - -
352A GLY* 1.3 77.4 - - - +
354A HIS* 1.3 56.4 + - - +
356A ILE* 3.2 5.2 + - - +
357A ASP* 2.9 34.4 + - - +
540A GLY 3.5 19.1 - - - +
544A ALA* 3.8 6.9 - - + +
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Residues in contact with HIS 354 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A ILE 5.2 0.4 + - - -
152A ARG* 3.2 26.2 + - - +
153A ASN* 3.4 28.3 - - - -
154A ARG* 3.6 19.0 + - + -
155A SER* 3.7 18.5 + - - -
157A ARG* 5.3 0.7 - - - -
350A LEU 2.9 8.7 + - - +
351A THR* 3.2 14.3 + - + +
353A ALA* 1.3 76.6 - - - +
355A VAL* 1.3 60.3 + - + +
357A ASP* 3.2 13.3 + - - +
358A GLU* 3.0 64.9 + - + +
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Residues in contact with VAL 355 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A VAL* 5.0 2.7 - - + -
90A SER 3.5 24.5 - - - +
91A LEU* 3.5 33.0 - - + +
92A GLY* 5.4 1.6 - - - -
351A THR* 2.9 32.2 + - + +
352A GLY* 3.8 7.6 - - - +
353A ALA 3.3 0.2 - - - -
354A HIS* 1.3 78.2 - - + +
356A ILE* 1.3 61.1 + - + +
358A GLU* 3.5 6.9 + - - +
359A HIS* 3.0 25.8 + - - +
537A ARG* 4.4 1.6 - - - +
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Residues in contact with ILE 356 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A VAL* 3.9 28.7 - - + -
91A LEU* 4.3 10.3 - - + -
99A LEU* 4.0 18.6 - - + -
352A GLY 3.3 12.9 + - - +
353A ALA 3.2 8.1 + - - +
355A VAL* 1.3 75.3 - - + +
357A ASP* 1.3 60.2 + - - +
359A HIS* 3.6 8.0 - - + +
360A PHE* 2.8 28.9 + - - +
369A VAL* 6.3 0.9 - - + -
370A PRO* 4.3 12.1 - - + -
541A ALA* 3.6 21.5 - - + +
544A ALA* 4.1 6.3 - - + -
545A MET* 3.8 32.8 - - + +
548A HIS* 4.5 2.2 - - + -
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Residues in contact with ASP 357 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A PHE* 3.5 26.4 - - + -
149A ILE* 3.8 14.9 - - + +
152A ARG* 2.8 46.9 + - - +
353A ALA 2.9 20.0 + - - +
354A HIS* 3.2 13.0 + - - +
356A ILE* 1.3 76.3 - - - +
358A GLU* 1.3 61.8 + - - +
360A PHE* 3.4 0.5 + - - +
361A ALA* 3.0 23.9 + - - +
544A ALA* 4.0 0.5 - - - +
548A HIS* 2.7 33.4 + - - -
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Residues in contact with GLU 358 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A PHE* 5.1 3.3 - - - -
155A SER* 5.7 0.7 - - - -
157A ARG* 3.1 31.8 + - - -
354A HIS* 3.0 45.9 + - + +
355A VAL* 3.7 7.2 - - - +
357A ASP* 1.3 77.3 - - - +
359A HIS* 1.3 62.7 + - - +
361A ALA* 4.8 1.3 - - - +
362A ASN* 2.7 46.9 + - - +
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Residues in contact with HIS 359 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A VAL* 4.9 0.9 - - + -
89A VAL* 3.5 44.1 - - + +
355A VAL 3.0 16.7 + - - +
356A ILE* 3.6 13.9 - - + +
358A GLU* 1.3 77.6 - - - +
360A PHE* 1.3 60.2 + - - +
362A ASN* 5.4 0.2 - - - -
363A ALA* 2.8 53.8 + - + +
367A GLN 3.3 23.1 - - - -
368A ASN* 3.8 1.5 + - - -
369A VAL* 3.0 24.6 + - + +
370A PRO* 3.9 17.7 - - + -
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Residues in contact with PHE 360 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A ILE* 5.4 0.7 - - + -
129A VAL* 3.5 43.5 - - + +
133A PHE* 4.2 6.3 - + - -
356A ILE 2.8 18.0 + - - +
357A ASP 3.7 3.4 - - - +
359A HIS* 1.3 79.1 - - - +
361A ALA* 1.3 59.1 + - - +
363A ALA 4.7 0.3 - - - +
368A ASN* 2.9 42.8 + - - +
370A PRO* 3.7 22.9 - - + -
371A LEU* 4.3 6.3 - - + -
548A HIS* 3.5 42.4 - + + -
551A LEU* 4.1 12.3 - - + -
552A VAL* 3.5 31.0 - - + -
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Residues in contact with ALA 361 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A ARG* 6.0 1.7 - - - +
129A VAL* 4.2 11.2 - - + +
130A GLN* 3.7 26.3 + - - +
133A PHE* 3.9 23.3 - - + -
357A ASP 3.0 17.5 + - - +
358A GLU* 4.8 1.3 - - - +
359A HIS 3.4 0.2 - - - -
360A PHE* 1.3 76.5 - - - +
362A ASN* 1.3 71.0 + - - +
363A ALA 5.3 0.2 - - - -
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Residues in contact with ASN 362 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A GLN* 5.5 1.4 + - - -
358A GLU* 2.7 47.6 + - - +
359A HIS* 5.4 0.2 - - - -
361A ALA* 1.3 88.7 - - - +
363A ALA* 1.3 64.6 + - - +
364A PRO* 3.7 4.2 - - - +
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Residues in contact with ALA 363 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359A HIS* 2.8 53.7 + - + +
360A PHE 4.7 0.3 - - - +
361A ALA 5.3 0.3 - - - -
362A ASN* 1.3 73.8 - - - +
364A PRO* 1.4 73.5 - - + +
365A PRO* 3.6 2.3 - - - +
367A GLN* 4.1 8.1 - - + +
368A ASN* 3.3 17.1 + - - +
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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
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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) + - + + + + + -
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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