Contacts of the helix formed by residues 368 - 383 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359B HIS* 3.7 7.7 + - - -
360B PHE* 2.9 44.0 + - - -
363B ALA* 3.3 17.9 + - - -
364B PRO 3.5 10.3 - - - +
365B PRO* 3.3 13.2 + - + +
366B GLU 3.7 0.4 - - - -
367B GLN* 1.3 75.4 - - - +
369B VAL* 1.3 57.6 + - - +
370B PRO* 3.2 18.6 - - - +
371B LEU* 3.4 18.8 + - + +
372B LEU* 3.0 33.7 + - - +
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Residues in contact with VAL 369 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B VAL* 3.9 23.6 - - + +
89B VAL* 3.6 28.7 - - + -
99B LEU* 5.2 7.4 - - + +
101B LEU* 3.8 32.9 - - + +
356B ILE* 6.0 1.8 - - + -
359B HIS* 3.0 14.9 + - + +
367B GLN 3.8 0.2 + - - -
368B ASN* 1.3 70.3 - - - +
370B PRO* 1.4 67.2 - - + +
371B LEU 3.3 0.2 + - - -
372B LEU* 3.3 2.4 + - - -
373B LEU* 3.0 22.9 + - + +
529B LEU* 5.0 0.2 - - + -
545B MET* 3.6 32.5 - - + -
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Residues in contact with PRO 370 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356B ILE* 4.4 7.4 - - + -
359B HIS* 3.8 11.2 - - + -
360B PHE* 3.7 19.5 - - + -
368B ASN* 3.2 17.3 - - - +
369B VAL* 1.4 87.7 - - + +
371B LEU* 1.3 59.0 + - - +
373B LEU* 3.5 5.2 + - + +
374B ALA* 3.1 25.3 + - - +
545B MET* 3.7 31.2 - - + +
548B HIS* 3.6 26.7 - - + -
549B LYS* 3.7 9.1 - - - +
552B VAL* 4.9 0.4 - - - -
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Residues in contact with LEU 371 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B LEU* 4.1 8.5 - - + -
120B ALA* 4.0 19.5 - - + -
125B ILE* 4.0 17.9 - - + -
360B PHE* 4.4 4.6 - - + -
365B PRO* 3.6 41.1 - - + +
368B ASN* 3.4 23.4 + - + +
369B VAL 3.3 0.6 - - - -
370B PRO* 1.3 76.3 - - - +
372B LEU* 1.3 57.6 + - - +
374B ALA* 3.3 3.3 + - - +
375B LEU* 2.9 41.6 + - + +
552B VAL* 3.7 31.4 - - + -
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Residues in contact with LEU 372 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B VAL* 3.9 15.0 - - + -
101B LEU* 4.5 6.3 - - + -
103B TYR* 3.7 45.3 - - + +
113B LYS* 4.7 11.2 - - + -
117B LEU* 4.4 14.8 - - + -
365B PRO 3.9 12.6 - - - +
366B GLU* 3.6 23.1 - - - +
368B ASN 3.0 25.1 + - - +
369B VAL* 3.8 4.5 - - - +
371B LEU* 1.3 74.2 - - - +
373B LEU* 1.3 58.1 + - - +
375B LEU* 3.3 6.8 + - + +
376B VAL* 3.0 37.7 + - + +
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Residues in contact with LEU 373 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B LEU* 3.9 25.9 - - + +
103B TYR* 6.0 0.2 - - + -
369B VAL 3.0 17.4 + - - +
370B PRO 3.8 4.7 - - - +
372B LEU* 1.3 74.5 - - - +
374B ALA* 1.3 61.6 - - - +
376B VAL* 3.6 6.1 + - - +
377B GLY* 3.2 18.4 + - - -
458B ASP* 4.2 9.9 - - - +
527B ASN* 3.5 29.5 + - + +
529B LEU* 4.9 2.2 - - + -
545B MET* 3.8 39.3 - - + -
546B TYR* 4.1 11.0 - - + +
549B LYS* 3.9 33.3 - - + +
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Residues in contact with ALA 374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370B PRO 3.1 18.1 + - - +
371B LEU 3.4 5.2 - - - +
372B LEU 3.2 0.2 - - - -
373B LEU* 1.3 77.4 - - - +
375B LEU* 1.3 59.0 + - - +
377B GLY 3.2 0.3 + - - -
378B VAL* 2.9 28.6 + - - +
549B LYS* 3.5 30.7 - - + +
552B VAL* 3.7 21.1 - - + -
553B GLN* 3.1 17.4 + - + +
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Residues in contact with LEU 375 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B LEU* 3.5 56.8 - - + +
117B LEU* 3.8 27.6 - - + -
119B LEU* 5.1 4.0 - - + -
120B ALA* 4.4 8.7 - - + +
371B LEU* 2.9 34.1 + - + +
372B LEU* 3.9 8.5 - - + +
374B ALA* 1.3 73.0 - - + +
376B VAL* 1.3 61.3 + - + +
378B VAL* 3.3 3.4 + - + +
379B TRP* 3.0 27.9 + - - +
552B VAL* 4.9 1.3 - - + -
556B ILE* 3.5 29.4 - - + -
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Residues in contact with VAL 376 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B TYR* 4.1 29.2 - - + -
106B SER* 4.8 4.9 - - - -
108B ILE* 3.8 24.2 - - + -
116B LEU* 5.5 1.1 - - + -
372B LEU* 3.0 22.6 + - + +
373B LEU* 3.9 6.7 - - - +
375B LEU* 1.3 75.0 - - + +
377B GLY* 1.3 62.0 + - - +
379B TRP* 3.4 8.0 + - - +
380B TYR* 3.2 43.8 + - + -
527B ASN* 4.0 24.0 - - - +
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Residues in contact with GLY 377 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373B LEU 3.2 12.8 + - - -
374B ALA 3.2 4.9 + - - -
375B LEU 3.2 0.2 - - - -
376B VAL* 1.3 76.0 - - - +
378B VAL* 1.3 58.4 + - - +
380B TYR* 3.2 6.5 + - - +
381B ILE* 2.9 37.9 + - - +
389B HIS* 6.0 5.8 - - - -
456B PRO* 6.5 1.1 - - - -
549B LYS* 5.2 4.3 - - - -
553B GLN* 3.6 15.3 - - - -
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Residues in contact with VAL 378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B TRP* 4.4 9.9 - - + -
116B LEU* 4.7 4.7 - - + -
119B LEU* 4.3 24.2 - - + -
374B ALA 2.9 18.5 + - - +
375B LEU* 3.3 8.5 + - + +
377B GLY* 1.3 71.7 - - - +
379B TRP* 1.3 62.5 + - - +
381B ILE* 4.6 2.7 - - - +
382B ASN* 2.9 47.0 + - - +
383B PHE* 3.9 5.5 - - + -
553B GLN* 4.2 8.1 - - + +
556B ILE* 4.0 23.6 - - + -
557B TRP* 4.1 20.2 - - + +
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Residues in contact with TRP 379 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B LEU* 3.5 39.9 - - + -
62B LEU* 4.2 0.4 - - + -
63B TYR* 3.6 31.4 - + + -
67B GLY* 5.0 2.7 - - - -
107B HIS 3.0 20.7 + - - -
108B ILE* 3.7 20.2 - - + +
112B ILE* 3.6 36.6 - - + -
116B LEU* 4.1 10.5 - - + +
375B LEU 3.0 14.1 + - - +
376B VAL* 3.4 9.2 - - - +
377B GLY 3.2 0.2 - - - -
378B VAL* 1.3 76.6 - - - +
380B TYR* 1.3 70.2 + + - +
383B PHE* 3.1 55.3 + + - +
384B PHE* 3.4 31.9 + + - -
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Residues in contact with TYR 380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B SER* 3.4 6.2 - - - -
107B HIS* 2.7 50.3 + - - -
376B VAL* 3.2 36.6 + - + +
377B GLY* 3.2 9.0 + - - +
379B TRP* 1.3 88.1 - + - +
381B ILE* 1.3 59.9 + - + +
384B PHE* 3.3 31.7 - + + +
385B GLY 3.0 11.3 + - - -
386B ALA* 2.9 24.1 + - + -
454B LEU* 3.8 18.2 - - + -
456B PRO* 3.8 28.0 - - + -
525B PRO* 3.4 29.2 - - + +
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Residues in contact with ILE 381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377B GLY* 2.9 27.1 + - - +
378B VAL 4.2 1.3 - - - +
380B TYR* 1.3 75.7 - - + +
382B ASN* 1.3 76.0 + - - +
385B GLY* 3.2 24.3 - - - -
386B ALA 3.4 19.1 - - - +
387B VAL* 5.6 2.0 - - + -
388B THR 6.0 0.2 - - - +
427B LEU* 3.9 19.9 - - + +
428B THR 3.5 19.1 - - - +
430B PRO* 3.8 34.8 - - + -
553B GLN* 4.2 7.0 - - - +
557B TRP* 3.8 19.1 - - + -
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Residues in contact with ASN 382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B TRP* 3.5 29.8 - - + -
60B GLN* 5.4 1.0 - - - +
378B VAL* 2.9 27.7 + - - +
381B ILE* 1.3 79.8 - - - +
383B PHE* 1.3 68.1 + - + +
385B GLY* 4.5 1.3 - - - -
426B THR* 3.6 8.5 - - - -
427B LEU* 2.9 43.7 + - - +
557B TRP* 2.9 26.7 + - - +
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Residues in contact with PHE 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B TRP* 3.8 53.6 - + - -
59B LEU* 3.6 30.3 - - + -
60B GLN* 3.5 50.4 - - + +
63B TYR* 3.2 38.7 + - + -
116B LEU* 5.6 0.2 - - + -
378B VAL* 3.9 11.9 - - + -
379B TRP* 3.1 38.6 + + + +
382B ASN* 1.3 80.2 - - + +
384B PHE* 1.3 61.9 + - - +
385B GLY 3.4 1.1 - - - -
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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
------------------------------------------------------------
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