Contacts of the helix formed by residues 379 - 392 (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 ASP 379 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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375A GLN* 3.8 20.8 + - - +
376A PRO* 2.9 30.2 + - - +
378A GLN* 1.3 97.7 + - - +
380A VAL* 1.3 61.7 + - - +
381A ALA 3.5 1.3 - - - -
382A LYS* 3.7 9.2 + - - +
383A ARG* 3.2 23.0 + - - +
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Residues in contact with VAL 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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372A LEU* 4.1 17.9 - - + +
375A GLN* 4.1 17.3 - - + +
376A PRO 3.7 10.3 - - - +
377A LEU* 3.2 29.4 + - + +
379A ASP* 1.3 78.0 - - - +
381A ALA* 1.3 61.5 + - - +
383A ARG* 3.0 3.4 + - - +
384A VAL* 2.8 44.9 + - + +
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Residues in contact with ALA 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 LEU 4.7 1.4 + - - -
378A GLN 5.1 3.5 + - - +
379A ASP 3.5 0.6 - - - -
380A VAL* 1.3 79.4 - - - +
382A LYS* 1.3 62.7 + - - +
384A VAL* 3.5 7.1 + - - +
385A GLU* 3.2 21.8 + - - +
417A GLY 6.1 0.9 - - - +
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Residues in contact with LYS 382 (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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378A GLN 5.6 1.3 + - - +
379A ASP* 3.7 11.3 + - - +
380A VAL 3.2 0.6 - - - -
381A ALA* 1.3 76.4 - - - +
383A ARG* 1.3 60.0 + - - +
385A GLU* 3.3 8.4 + - + +
386A GLU* 3.0 55.3 + - + +
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Residues in contact with ARG 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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368A ALA* 5.0 6.7 + - - +
371A ASP* 4.5 12.4 + - - +
372A LEU* 3.9 22.0 - - + -
375A GLN* 4.5 18.8 - - + +
379A ASP 3.2 15.0 + - - +
380A VAL* 3.0 5.4 + - - +
382A LYS* 1.3 76.3 - - - +
384A VAL* 1.3 59.7 + - - +
386A GLU* 3.2 24.3 + - - +
387A ILE* 2.9 55.8 + - + +
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Residues in contact with VAL 384 (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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372A LEU* 3.9 27.3 - - + +
380A VAL* 2.8 30.0 + - + +
381A ALA* 3.7 7.6 - - - +
383A ARG* 1.3 75.7 - - - +
385A GLU* 1.3 57.0 + - - +
387A ILE* 3.2 7.5 + - - +
388A TRP* 2.9 28.2 + - - +
413A ASN 5.8 0.4 - - - +
414A VAL* 3.9 35.2 - - + +
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Residues in contact with GLU 385 (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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381A ALA 3.2 11.2 + - - +
382A LYS* 3.6 9.0 - - - +
384A VAL* 1.3 80.3 - - - +
386A GLU* 1.3 59.0 + - + +
388A TRP* 3.6 5.6 - - - +
389A GLN* 2.8 67.2 + - + +
414A VAL* 4.1 17.8 - - - +
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Residues in contact with GLU 386 (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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382A LYS* 3.0 47.6 + - + +
383A ARG* 3.2 34.4 + - - +
385A GLU* 1.3 75.5 - - + +
387A ILE* 1.3 60.0 + - - +
389A GLN* 3.5 5.3 + - - +
390A GLU* 2.9 31.2 + - - +
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Residues in contact with ILE 387 (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* 3.6 29.8 - - + -
368A ALA* 3.7 35.4 - - + +
369A VAL* 4.4 7.0 - - + +
372A LEU* 4.0 27.4 - - + -
383A ARG* 2.9 38.0 + - + +
384A VAL* 3.7 4.9 - - - +
386A GLU* 1.3 71.0 - - - +
388A TRP* 1.3 68.3 + - - +
390A GLU* 3.3 1.4 + - - -
391A PHE* 3.0 35.9 + - + +
392A LEU* 5.2 1.5 - - + +
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Residues in contact with TRP 388 (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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384A VAL 2.9 17.4 + - - +
385A GLU* 3.6 11.0 - - - +
387A ILE* 1.3 77.3 - - - +
389A GLN* 1.3 70.8 + - - +
392A LEU* 2.8 65.6 + - + -
393A ALA* 2.8 33.5 + - + +
394A PRO* 4.8 4.4 - - + +
407A TYR* 3.7 30.5 - + - -
410A THR* 3.9 12.8 - - + -
411A SER* 3.7 34.1 - - - -
414A VAL* 3.8 31.9 - - + -
415A LYS* 3.5 25.0 - - - +
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Residues in contact with GLN 389 (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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385A GLU* 2.8 52.6 + - + +
386A GLU* 3.9 5.2 - - - +
388A TRP* 1.3 87.1 - - - +
390A GLU* 1.3 61.2 + - - +
393A ALA* 3.6 18.0 - - - +
394A PRO 5.2 1.6 - - - +
396A ALA* 3.4 21.5 - - - +
397A PRO* 3.6 4.8 - - - +
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Residues in contact with GLU 390 (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* 4.2 4.2 + - - -
386A GLU 2.9 18.4 + - - +
387A ILE* 3.3 0.4 + - - -
389A GLN* 1.3 79.0 - - - +
391A PHE* 1.3 89.9 + - + +
396A ALA* 3.6 1.0 - - - +
397A PRO* 3.3 22.5 - - - +
398A SER* 2.4 53.4 + - - -
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Residues in contact with PHE 391 (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 3.7 5.8 - - - -
364A ARG* 3.7 33.2 - - + -
365A PHE* 3.6 58.8 - + + -
368A ALA* 4.0 21.3 - - + -
387A ILE* 3.0 28.7 + - + +
390A GLU* 1.3 95.7 - - + +
392A LEU* 1.3 62.3 + - + +
396A ALA* 3.8 6.3 - - - -
398A SER* 3.4 24.0 - - - -
399A ALA* 3.5 2.8 - - - -
400A ILE* 3.1 33.7 + - + +
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Residues in contact with LEU 392 (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* 4.2 25.1 - - + -
387A ILE* 5.5 1.3 - - + -
388A TRP* 2.8 51.3 + - + +
391A PHE* 1.3 77.0 - - + +
393A ALA* 1.3 66.3 + - - +
394A PRO* 4.5 0.2 - - - +
396A ALA* 3.7 1.0 - - - +
400A ILE* 3.7 23.8 - - + +
402A LEU* 3.6 28.0 - - + -
407A TYR* 4.0 32.5 + - + -
410A THR* 3.9 17.7 - - + -
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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