Contacts of the helix formed by residues 359 - 374 (chain A) in PDB entry 2ES0
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 359 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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354A LEU* 2.9 34.0 + - - +
357A GLU* 3.8 12.2 + - - +
358A PHE* 1.3 79.0 - - - +
360A SER* 1.3 64.7 + - - +
361A GLU* 3.1 13.9 + - - -
362A ASN* 3.2 33.4 + - - +
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Residues in contact with SER 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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351A LEU* 3.9 14.4 - - - -
354A LEU* 3.6 13.3 + - - -
355A GLU* 3.7 37.1 + - - +
358A PHE* 5.5 1.0 - - - -
359A SER* 1.3 75.1 - - - +
361A GLU* 1.3 68.0 + - - +
362A ASN 3.1 0.4 - - - -
363A LEU* 3.2 4.7 + - - +
364A ARG* 3.0 42.8 + - - +
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Residues in contact with GLU 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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358A PHE 3.7 9.4 - - - +
359A SER* 3.3 27.6 + - - -
360A SER* 1.3 82.6 + - - +
362A ASN* 1.3 64.5 + - - +
364A ARG* 3.5 22.3 + - - +
365A PHE* 2.9 32.1 + - - +
391A PHE* 3.7 3.1 - - - -
398A SER* 3.6 22.7 - - - +
399A ALA 3.6 22.8 - - - +
400A ILE* 3.9 10.7 - - + +
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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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354A LEU* 5.2 3.8 - - + -
359A SER* 3.2 26.9 + - - +
360A SER 3.1 0.2 - - - -
361A GLU* 1.3 90.7 + - - +
363A LEU* 1.3 62.1 + - - +
365A PHE* 3.7 6.0 - - - +
366A TRP* 3.1 23.4 + - - +
400A ILE* 4.2 13.4 - - - +
401A ASN 5.2 2.3 + - - +
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Residues in contact with LEU 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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337A PHE* 5.7 1.1 - - + -
341A LEU* 3.8 28.7 - - + -
347A ARG* 3.9 27.1 - - + +
350A PHE* 3.9 26.0 - - + -
351A LEU* 4.0 22.7 - - + -
354A LEU* 3.6 15.9 - - + -
359A SER 4.3 0.6 + - - -
360A SER 3.2 6.1 + - - +
362A ASN* 1.3 77.0 - - - +
364A ARG* 1.3 61.3 + - - +
366A TRP* 3.3 8.8 + - + +
367A LEU* 2.9 53.9 + - + +
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Residues in contact with ARG 364 (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 LEU* 4.3 19.1 - - + -
355A GLU* 5.7 2.5 + - - -
360A SER* 3.0 36.9 + - - +
361A GLU* 3.5 22.3 + - - +
363A LEU* 1.3 76.7 - - - +
365A PHE* 1.3 57.4 + - - +
367A LEU* 3.8 10.4 - - + +
368A ALA* 2.8 30.3 + - - +
390A GLU* 4.2 3.4 + - - -
391A PHE* 3.7 15.7 - - + -
398A SER* 3.3 30.5 + - - +
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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 GLU 2.9 18.4 + - - +
362A ASN* 3.7 5.4 - - - +
364A ARG* 1.3 74.7 - - - +
366A TRP* 1.3 70.3 + - + +
368A ALA* 3.0 2.6 + - - +
369A VAL* 2.9 44.9 + - + +
387A ILE* 3.6 23.3 - - + -
391A PHE* 3.6 36.9 - + + -
392A LEU* 4.2 16.6 - - + -
400A ILE* 3.8 31.6 - - + -
402A LEU* 5.3 6.5 - - + -
410A THR* 6.0 2.0 - - + -
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Residues in contact with TRP 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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337A PHE* 6.5 0.4 - + - -
341A LEU* 3.8 54.0 - - + +
347A ARG* 6.0 0.2 - - - -
362A ASN 3.1 15.0 + - - +
363A LEU* 3.6 9.2 - - + +
365A PHE* 1.3 86.0 - - + +
367A LEU* 1.3 85.2 + - + +
369A VAL* 3.3 6.4 + - - +
370A GLN* 3.0 58.5 + - + +
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Residues in contact with LEU 367 (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 ARG* 3.7 39.3 - - + +
351A LEU* 5.8 5.8 - - + -
363A LEU* 2.9 38.7 + - + +
364A ARG* 3.8 10.3 - - + +
366A TRP* 1.3 95.6 - - + +
368A ALA* 1.3 57.5 + - - +
370A GLN* 3.3 5.9 + - + +
371A ASP* 3.0 28.6 + - - +
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Residues in contact with ALA 368 (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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364A ARG 2.8 18.5 + - - +
365A PHE 3.0 4.7 + - - +
367A LEU* 1.3 76.4 - - - +
369A VAL* 1.3 59.0 + - - +
371A ASP* 3.3 8.8 + - - +
372A LEU 3.0 21.8 + - - -
383A ARG* 5.0 5.5 + - - +
387A ILE* 3.7 24.7 - - + +
391A PHE* 4.0 20.2 - - + -
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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
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365A PHE* 2.9 53.2 + - + +
366A TRP* 3.8 5.6 - - + +
368A ALA* 1.3 74.2 - - - +
370A GLN* 1.3 64.3 + - - +
372A LEU* 3.2 29.0 + - + +
373A LYS* 3.3 26.3 + - - +
387A ILE* 4.5 10.1 - - + -
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Residues in contact with GLN 370 (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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366A TRP* 3.0 56.6 + - + +
367A LEU* 3.6 11.2 - - + +
369A VAL* 1.3 76.9 - - - +
371A ASP* 1.3 62.2 + - - +
373A LYS* 2.7 49.3 + - - +
374A LYS* 3.1 39.0 + - - +
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Residues in contact with ASP 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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367A LEU 3.0 13.6 + - - +
368A ALA* 3.5 10.3 - - - +
370A GLN* 1.3 74.5 - - - +
372A LEU* 1.3 67.1 + - - +
374A LYS* 3.0 24.9 + - - +
375A GLN* 3.2 32.3 + - - +
383A ARG* 4.5 12.5 + - - +
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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
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368A ALA 3.0 13.1 + - - +
369A VAL* 3.2 20.6 + - + +
371A ASP* 1.3 77.8 + - - +
373A LYS* 1.3 64.1 + - + +
375A GLN* 3.1 26.4 + - + +
380A VAL* 4.0 21.2 - - + +
383A ARG* 3.9 28.9 - - + -
384A VAL* 3.9 29.6 - - + +
387A ILE* 4.0 14.6 - - + -
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Residues in contact with LYS 373 (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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369A VAL* 3.3 26.9 + - + +
370A GLN* 2.7 42.3 + - - +
371A ASP 3.2 0.6 - - - -
372A LEU* 1.3 78.2 - - + +
374A LYS* 1.3 62.6 + - + +
375A GLN 3.4 2.0 + - - +
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Residues in contact with LYS 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 GLN* 3.1 42.5 + - - +
371A ASP* 3.0 17.5 + - - +
373A LYS* 1.3 82.3 - - - +
375A GLN* 1.3 62.8 + - - +
376A PRO* 3.9 3.6 - - - +
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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