Contacts of the helix formed by residues 351 - 366 (chain A) in PDB entry 2CSX
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 ILE 351 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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320A TYR* 4.5 7.6 - - + -
346A GLU 2.9 14.9 + - - +
347A LEU* 3.6 31.4 - - + +
350A GLU* 1.3 76.4 - - + +
352A GLY* 1.3 67.0 + - - +
354A LEU* 3.0 13.5 + - - +
355A TYR* 3.1 33.2 + - + -
405A ILE* 4.9 3.6 - - + -
406A LEU* 4.3 18.2 - - + -
409A THR* 4.5 13.0 - - + +
447A LEU* 4.0 10.3 - - + -
451A LEU* 3.8 35.9 - - + -
492A PHE* 4.8 7.9 - - + -
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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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347A LEU 2.7 19.7 + - - -
351A ILE* 1.3 73.6 - - - +
353A ASN* 1.3 63.3 + - - +
355A TYR* 3.1 12.3 + - - +
356A SER* 3.1 19.6 + - - -
489A LYS 5.4 0.7 - - - +
491A LEU* 4.9 4.6 + - - +
492A PHE* 4.4 8.6 - - - -
36C U 3.0 29.2 - - - -
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Residues in contact with ASN 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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348A ALA 2.8 13.3 + - - +
349A ASN* 2.7 22.1 + - - +
351A ILE 3.3 0.2 - - - -
352A GLY* 1.3 72.0 - - - +
354A LEU* 1.3 56.9 + - - +
356A SER* 4.5 0.4 - - - -
357A ARG* 2.8 38.3 + - - +
413A ASN* 4.6 0.6 + - - -
35C A 3.2 48.4 + - - +
36C U 3.6 16.9 - - + +
38C A 3.0 38.3 + - - +
39C G 3.9 6.3 + - - -
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Residues in contact with LEU 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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349A ASN 4.3 0.2 + - - -
350A GLU 3.1 19.2 + - - +
351A ILE 3.0 6.3 + - - +
353A ASN* 1.3 77.1 - - - +
355A TYR* 1.3 69.6 + - - +
357A ARG* 3.0 31.5 - - - +
358A VAL* 3.1 24.1 + - + +
409A THR* 3.6 21.1 - - - +
412A LEU* 3.4 39.7 - - + -
413A ASN* 3.8 12.8 + - - +
416A VAL* 4.2 9.9 - - + -
440A LEU* 5.3 0.9 - - + -
444A LEU* 4.0 13.5 - - + -
447A LEU* 4.5 4.5 - - + -
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Residues in contact with TYR 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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351A ILE* 3.1 45.4 + - + -
352A GLY* 3.1 6.5 + - - +
354A LEU* 1.3 77.2 - - - +
356A SER* 1.3 66.4 + - - +
358A VAL* 2.7 15.9 + - - +
359A VAL* 2.8 16.7 + - - -
444A LEU* 3.7 31.9 - - + -
447A LEU* 3.9 15.8 - - + +
448A THR* 3.2 33.9 + - - -
459A MET* 3.2 20.4 - - + -
462A ALA* 3.8 17.5 - - + -
465A MET* 3.1 26.2 - - + -
466A LEU* 4.6 5.2 - - + -
489A LYS 5.5 0.4 - - - +
491A LEU* 3.8 20.2 - - + -
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Residues in contact with SER 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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352A GLY 3.1 13.0 + - - -
353A ASN 3.9 1.1 - - - -
355A TYR* 1.3 77.3 - - - +
357A ARG* 1.3 64.3 + - - +
359A VAL* 4.6 5.2 - - - -
360A ASN* 3.0 28.2 + - - +
465A MET* 4.0 1.7 - - - +
488A ARG* 5.4 4.1 - - - +
489A LYS 4.3 15.2 + - - -
490A ILE* 5.6 2.3 - - - +
35C A 2.8 34.0 + - - -
36C U 4.0 14.9 + - - -
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Residues in contact with ARG 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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353A ASN* 2.8 22.3 + - - +
354A LEU* 3.0 31.0 - - - +
356A SER* 1.3 75.8 + - - +
358A VAL* 1.3 68.5 + - + +
361A MET* 3.1 13.4 + - - +
413A ASN* 2.8 24.8 + - - -
416A VAL* 3.8 17.1 - - + +
417A ASP* 5.1 3.6 - - - +
34C C 2.7 64.0 + - - +
35C A 3.0 48.1 + - - +
39C G 2.8 32.5 + - - -
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Residues in contact with VAL 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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354A LEU* 3.1 33.0 - - + +
355A TYR 2.7 12.2 + - - +
357A ARG* 1.3 78.4 - - + +
359A VAL* 1.3 68.4 + - - +
360A ASN 3.1 1.6 - - - -
361A MET* 2.6 21.4 + - - +
362A ALA* 3.1 9.2 + - + +
416A VAL* 4.1 5.8 - - + -
437A LEU* 4.9 7.0 - - + +
440A LEU* 3.9 33.7 - - + +
441A VAL* 4.0 26.2 - - + +
444A LEU* 4.1 14.4 - - + -
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Residues in contact with VAL 359 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355A TYR 2.8 17.4 + - - +
356A SER 4.0 2.5 - - - +
358A VAL* 1.3 74.1 - - - +
360A ASN* 1.3 60.8 + - - +
362A ALA* 3.2 4.3 + - - +
363A HIS* 3.1 31.0 + - + +
441A VAL* 5.6 0.2 - - - -
444A LEU* 4.1 14.6 - - + -
465A MET* 3.2 39.7 - - + +
466A LEU* 4.4 7.6 - - + -
485A LEU* 3.9 17.9 - - + +
486A GLY 4.3 4.3 - - - +
488A ARG* 3.3 33.2 - - + -
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Residues in contact with ASN 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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356A SER* 3.0 19.5 + - - +
357A ARG 4.2 0.4 - - - +
359A VAL* 1.3 74.9 - - - +
361A MET* 1.3 63.3 + - - +
363A HIS* 3.6 2.1 + - - +
364A LYS* 3.2 28.7 + - - +
488A ARG* 3.2 48.4 - - - +
34C C 3.4 24.3 + - - +
35C A 3.6 24.0 + - - -
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Residues in contact with MET 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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357A ARG 3.1 21.3 + - - +
358A VAL* 2.6 17.5 + - - +
360A ASN* 1.3 74.0 - - - +
362A ALA* 1.3 54.7 + - - +
364A LYS 3.1 1.0 + - - -
365A PHE* 2.7 57.1 + - + +
416A VAL* 4.2 9.2 - - - -
421A PRO* 3.1 36.8 - - + -
422A TRP* 3.4 23.3 - - + +
437A LEU* 3.8 17.9 - - + -
440A LEU* 5.5 0.9 - - - -
34C C 3.1 41.7 - - - +
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Residues in contact with ALA 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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358A VAL* 3.1 8.6 + - + +
359A VAL 3.6 1.8 - - - +
361A MET* 1.3 77.8 - - - +
363A HIS* 1.3 52.2 + - - +
366A LEU* 3.4 15.0 + - - +
367A GLY 3.4 0.2 + - - -
368A GLY* 2.7 26.8 + - - -
369A GLU 4.1 0.2 + - - -
370A VAL* 3.5 24.0 - - + -
437A LEU* 3.7 12.7 - - + +
441A VAL* 4.3 5.4 - - + -
485A LEU* 3.1 32.3 - - + -
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Residues in contact with HIS 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 VAL* 3.1 19.1 + - + +
360A ASN* 3.9 7.6 - - - +
361A MET 3.1 0.4 - - - -
362A ALA* 1.3 79.6 - - - +
364A LYS* 1.3 59.4 + - - +
367A GLY* 3.6 17.3 + - - -
368A GLY* 3.3 22.7 + - - +
485A LEU* 4.3 16.0 - - + +
486A GLY 3.0 29.2 + - - -
487A GLU* 4.6 1.8 + - - -
488A ARG* 4.0 28.7 - - + +
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Residues in contact with LYS 364 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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360A ASN* 3.2 22.3 + - - +
361A MET 3.1 1.6 + - - -
363A HIS* 1.3 81.4 - - - +
365A PHE* 1.3 92.1 + - + +
366A LEU 3.6 0.7 - - - -
367A GLY 4.7 0.8 + - - -
425A ASN* 4.6 1.9 - - - +
426A LYS* 4.4 18.2 - - - +
34C C 4.0 23.6 + - - +
35C A 6.2 0.4 - - - +
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Residues in contact with PHE 365 (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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361A MET* 2.7 44.4 + - + +
364A LYS* 1.3 123.1 - - + +
366A LEU* 1.3 73.3 + - + +
367A GLY 3.9 0.2 - - - -
421A PRO 4.0 7.4 - - - -
422A TRP* 3.2 31.6 - - + -
425A ASN* 2.8 38.6 - - + +
426A LYS* 5.5 2.9 - - - -
430A LYS* 3.7 16.2 + - - +
433A LEU* 3.8 12.2 - - + +
437A LEU* 4.4 2.9 - - + -
34C C 3.9 17.3 - - - -
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Residues in contact with LEU 366 (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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362A ALA 3.4 9.9 + - - +
365A PHE* 1.3 90.7 - - + +
367A GLY* 1.3 69.8 + - - +
368A GLY 3.3 1.3 - - - -
369A GLU* 3.1 24.1 + - - +
370A VAL* 3.3 33.7 - - + -
430A LYS* 5.1 3.4 - - + -
433A LEU* 4.1 18.6 - - + +
434A GLN* 3.5 33.9 - - + +
437A LEU* 3.5 27.8 - - + -
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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
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Atomic class I II III IV V VI VII VIII
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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