Contacts of the helix formed by residues 368 - 383 (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 ASN 368 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359A HIS* 3.8 9.2 + - - -
360A PHE* 2.9 39.5 + - - -
363A ALA* 3.3 17.9 + - - +
364A PRO 3.5 10.8 - - - +
365A PRO* 3.3 12.7 + - + +
366A GLU 3.6 0.6 - - - -
367A GLN* 1.3 75.2 - - - +
369A VAL* 1.3 57.5 + - - +
370A PRO* 3.2 18.6 - - - +
371A LEU* 3.4 20.6 + - + +
372A LEU* 3.0 33.0 + - - +
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Residues in contact with VAL 369 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A VAL* 3.8 24.9 - - + +
89A VAL* 3.6 26.7 - - + -
99A LEU* 5.0 9.2 - - + +
101A LEU* 3.7 33.6 - - + +
356A ILE* 6.3 0.9 - - + -
359A HIS* 3.0 15.5 + - + +
368A ASN* 1.3 70.9 - - - +
370A PRO* 1.4 66.3 - - + +
372A LEU* 3.4 1.5 + - - -
373A LEU* 3.0 23.4 + - - +
529A LEU* 5.1 0.2 - - + -
545A MET* 3.6 31.2 - - + -
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Residues in contact with PRO 370 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A ILE* 4.3 7.9 - - + -
359A HIS* 3.9 11.2 - - + -
360A PHE* 3.7 20.0 - - + -
368A ASN* 3.2 16.8 - - - +
369A VAL* 1.4 87.0 - - + +
371A LEU* 1.3 55.0 - - - +
373A LEU* 3.6 6.1 + - + +
374A ALA* 3.0 28.9 + - - +
545A MET* 3.7 29.6 - - + +
548A HIS* 3.6 28.7 - - + -
549A LYS* 3.8 7.7 - - - +
552A VAL* 4.7 0.4 - - - +
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Residues in contact with LEU 371 (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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117A LEU* 4.1 9.4 - - + -
120A ALA* 4.0 19.1 - - + -
125A ILE* 3.9 19.3 - - + -
360A PHE* 4.3 4.6 - - + -
365A PRO* 3.6 42.2 - - + +
368A ASN* 3.4 22.9 + - + +
369A VAL 3.3 0.6 - - - -
370A PRO* 1.3 79.0 - - - +
372A LEU* 1.3 56.6 + - - +
374A ALA* 3.2 5.2 + - - +
375A LEU* 2.9 40.6 + - + +
552A VAL* 3.8 27.8 - - + -
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Residues in contact with LEU 372 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A VAL* 4.0 11.9 - - + -
101A LEU* 4.5 5.8 - - + -
103A TYR* 3.8 45.3 - - + +
113A LYS* 4.7 10.3 - - + -
117A LEU* 4.5 14.6 - - + -
365A PRO 4.0 12.8 - - - +
366A GLU 3.6 22.2 - - - +
368A ASN 3.0 29.9 + - - +
369A VAL* 3.9 4.5 - - - +
371A LEU* 1.3 74.5 - - - +
373A LEU* 1.3 58.3 + - - +
375A LEU* 3.3 7.3 + - + +
376A VAL* 3.0 37.1 + - + +
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Residues in contact with LEU 373 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A LEU* 3.8 25.5 - - + +
103A TYR* 6.1 0.4 - - + -
369A VAL 3.0 16.2 + - - +
370A PRO 3.8 4.3 - - - +
372A LEU* 1.3 76.4 - - - +
374A ALA* 1.3 61.8 + - - +
376A VAL* 3.6 5.7 + - - +
377A GLY* 3.2 16.3 + - - -
458A ASP* 4.3 10.1 - - - +
527A ASN* 3.5 29.4 + - + +
529A LEU* 4.9 2.0 - - + -
545A MET* 3.9 39.0 - - + -
546A TYR* 4.2 10.8 - - + -
549A LYS* 3.9 33.9 + - + +
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Residues in contact with ALA 374 (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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370A PRO 3.0 18.6 + - - +
371A LEU 3.2 4.9 + - - +
373A LEU* 1.3 77.8 - - - +
375A LEU* 1.3 57.1 + - - +
377A GLY 3.2 0.2 + - - -
378A VAL* 2.9 29.1 + - - +
549A LYS* 3.5 31.8 - - + +
552A VAL* 3.6 20.4 - - + -
553A GLN* 3.1 16.6 + - + +
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Residues in contact with LEU 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A LEU* 3.4 62.4 - - + +
117A LEU* 3.9 22.9 - - + -
119A LEU* 4.6 5.6 - - + -
120A ALA* 4.4 7.4 - - + -
371A LEU* 2.9 34.1 + - + +
372A LEU* 3.8 8.7 - - + +
374A ALA* 1.3 74.5 - - + +
376A VAL* 1.3 59.6 + - + +
377A GLY 3.1 0.2 - - - -
378A VAL* 3.3 3.4 + - + +
379A TRP* 3.0 29.1 + - - +
552A VAL* 5.3 0.2 - - + -
556A ILE* 3.7 26.0 - - + -
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Residues in contact with VAL 376 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A TYR* 4.1 27.6 - - + -
106A SER* 4.8 5.4 - - - -
108A ILE* 3.8 23.3 - - + -
116A LEU* 5.6 1.1 - - + -
372A LEU* 3.0 24.3 + - + +
373A LEU* 3.9 7.0 - - - +
375A LEU* 1.3 74.1 - - + +
377A GLY* 1.3 63.3 + - - +
379A TRP* 3.3 6.7 + - - +
380A TYR* 3.2 50.6 + - + -
527A ASN* 4.0 24.0 - - - +
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Residues in contact with GLY 377 (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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373A LEU 3.2 12.8 + - - -
375A LEU 3.1 0.6 - - - -
376A VAL* 1.3 75.9 - - - +
378A VAL* 1.3 57.7 + - - +
380A TYR* 3.2 6.7 + - - +
381A ILE* 2.9 38.5 + - - +
389A HIS* 5.9 5.6 - - - -
456A PRO* 6.5 1.3 - - - -
549A LYS* 5.1 4.0 - - - -
553A GLN* 3.5 19.5 - - - -
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Residues in contact with VAL 378 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A TRP* 4.2 20.0 - - + -
116A LEU* 4.9 2.9 - - + -
119A LEU* 4.3 15.3 - - + -
374A ALA 2.9 19.6 + - - +
375A LEU* 3.3 8.3 + - - +
377A GLY* 1.3 70.5 - - - +
379A TRP* 1.3 66.7 + - - +
381A ILE* 4.6 2.9 - - - -
382A ASN* 2.9 43.4 + - - +
383A PHE* 3.8 6.3 - - + -
553A GLN* 3.7 14.1 - - + +
556A ILE* 3.9 23.6 - - + -
557A TRP* 4.3 12.3 - - + +
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Residues in contact with TRP 379 (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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59A LEU* 3.5 40.8 - - + -
62A LEU* 4.5 0.2 - - + -
63A TYR* 3.6 32.8 - + + -
67A GLY* 5.4 2.7 - - - -
107A HIS 2.9 19.3 + - - -
108A ILE* 3.7 20.4 - - + +
112A ILE* 3.6 37.0 - - + -
116A LEU* 4.1 11.4 - - + +
375A LEU 3.0 13.9 + - - +
376A VAL* 3.4 9.4 - - - +
377A GLY 3.2 0.2 - - - -
378A VAL* 1.3 75.1 - - - +
380A TYR* 1.3 69.3 + + - +
383A PHE* 3.2 53.3 + + - +
384A PHE* 3.3 33.3 + + - -
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Residues in contact with TYR 380 (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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106A SER* 3.4 6.0 - - - -
107A HIS* 2.5 53.6 + + - -
376A VAL* 3.2 41.8 + - + +
377A GLY* 3.2 5.6 + - - +
379A TRP* 1.3 87.1 - + - +
381A ILE* 1.3 59.7 + - + +
384A PHE* 3.3 33.3 - + + +
385A GLY 3.0 10.7 + - - -
386A ALA* 2.9 24.5 + - + +
454A LEU* 4.2 9.2 - - + -
456A PRO* 3.8 31.2 - - + -
525A PRO* 3.3 29.7 - - + +
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Residues in contact with ILE 381 (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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377A GLY* 2.9 30.0 + - - +
378A VAL 4.2 1.8 - - - +
380A TYR* 1.3 73.1 - - + +
382A ASN* 1.3 66.6 + - - +
385A GLY* 3.2 23.2 - - - -
386A ALA 3.4 20.9 - - - +
387A VAL* 5.6 1.8 - - + -
427A LEU* 3.7 26.6 - - + +
428A THR 3.5 19.1 - - - +
430A PRO* 3.8 34.8 - - + -
553A GLN* 4.2 7.2 - - - +
557A TRP* 3.8 19.5 - - + -
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Residues in contact with ASN 382 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A TRP* 3.6 27.0 - - + -
60A GLN* 4.7 4.3 + - - -
378A VAL* 2.9 25.8 + - - +
381A ILE* 1.3 76.2 - - - +
383A PHE* 1.3 69.2 + - + +
385A GLY* 4.5 1.1 - - - -
426A THR* 3.6 7.2 - - - -
427A LEU* 2.8 46.2 + - - +
557A TRP* 2.7 27.3 + - - +
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Residues in contact with PHE 383 (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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56A TRP* 3.7 52.5 - + - -
59A LEU* 3.6 35.9 - - + -
60A GLN* 3.5 47.3 - - - +
63A TYR* 3.2 40.7 - - + -
116A LEU* 5.6 0.2 - - + -
378A VAL* 3.8 17.0 - - + -
379A TRP* 3.2 30.0 + + + +
382A ASN* 1.3 79.7 - - + +
384A PHE* 1.3 64.7 + - - +
385A GLY 3.3 1.5 + - - -
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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