Contacts of the helix formed by residues 361 - 371 (chain A) in PDB entry 2AYO
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 GLU 361 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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251A GLU* 3.4 14.6 - - - +
359A THR* 3.1 20.7 - - + +
360A PRO* 1.3 76.0 - - + +
362A LEU* 1.3 56.5 - - - +
364A GLU* 2.7 45.3 + - - +
365A LYS* 3.7 3.0 + - - +
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Residues in contact with LEU 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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316A ILE* 2.8 29.2 - - + +
317A SER 2.9 23.1 - - - +
318A ARG* 3.6 15.5 - - + -
319A LEU* 4.4 6.3 - - + +
358A CYS* 3.6 20.2 - - + -
359A THR* 3.4 13.0 + - - +
361A GLU* 1.3 72.8 - - - +
363A GLN* 1.3 60.2 + - - +
364A GLU 2.6 16.5 + - - -
365A LYS* 2.8 30.5 + - + +
366A MET* 3.4 30.7 + - + -
413A ASN 6.1 0.7 - - - +
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Residues in contact with GLN 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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315A LYS* 5.5 2.6 - - - +
355A TYR* 3.1 61.0 + - + +
356A GLU* 4.7 5.9 - - - +
357A LEU 5.7 0.2 - - - -
358A CYS* 3.7 17.2 + - + +
359A THR 2.6 39.5 + - - +
360A PRO* 3.1 19.4 - - - +
361A GLU 3.2 0.2 + - - -
362A LEU* 1.3 77.6 - - + +
364A GLU* 1.3 57.1 + - - +
366A MET* 3.9 3.1 + - - -
367A VAL* 2.8 24.8 + - - +
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Residues in contact with GLU 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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360A PRO 3.7 10.8 - - - +
361A GLU* 2.7 22.6 + - - +
362A LEU 2.6 5.7 + - - -
363A GLN* 1.3 73.1 - - - +
365A LYS* 1.3 57.0 + - + +
366A MET 3.1 1.1 - - - -
367A VAL* 2.6 38.8 + - + +
368A SER* 3.5 4.9 + - - -
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Residues in contact with LYS 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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318A ARG* 3.8 35.5 - - + +
361A GLU 4.9 1.8 - - - +
362A LEU* 2.8 25.5 + - + +
364A GLU* 1.3 76.3 - - + +
366A MET* 1.3 60.8 + - + +
367A VAL 3.1 3.3 + - - -
368A SER* 3.2 20.0 + - - -
369A PHE* 3.6 11.9 - - + -
407A ASP* 4.9 16.7 - - + +
414A CYS* 4.7 17.5 - - - -
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Residues in contact with MET 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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319A LEU* 5.1 12.1 - - + -
354A MET 5.4 1.8 - - - +
355A TYR* 4.4 23.1 - - + -
358A CYS* 5.3 1.3 - - - -
362A LEU* 3.4 29.1 + - + +
363A GLN 4.0 9.6 - - - +
364A GLU 3.1 0.6 - - - -
365A LYS* 1.3 77.6 - - + +
367A VAL* 1.3 56.9 + - - +
369A PHE* 4.5 4.7 - - - +
370A ARG* 2.4 54.6 + - + +
413A ASN* 3.8 14.4 - - - +
414A CYS* 3.7 13.5 - - + -
415A GLY* 2.6 51.6 - - - +
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Residues in contact with VAL 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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355A TYR* 4.1 9.4 - - + +
363A GLN 2.8 24.9 + - - +
364A GLU* 2.6 31.8 + - + +
366A MET* 1.3 70.0 - - - +
368A SER* 1.3 66.2 + - - +
371A SER* 2.6 46.7 + - - +
372A LYS* 3.3 1.6 + - - +
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Residues in contact with SER 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 GLU 4.3 3.3 + - - -
365A LYS* 3.2 12.3 + - - -
367A VAL* 1.3 81.7 - - - +
369A PHE* 1.3 68.1 + - - +
372A LYS* 2.5 39.6 - - - +
373A PHE* 4.1 4.8 - - - -
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Residues in contact with PHE 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 LYS* 3.6 14.3 + - + -
366A MET* 3.5 3.2 + - - +
368A SER* 1.3 86.9 - - - +
370A ARG* 1.3 65.8 + - - +
371A SER 2.9 1.3 - - - -
373A PHE* 2.7 60.2 + + + +
374A LYS 3.5 0.9 + - - -
402A PRO 6.4 0.2 - - - -
403A PHE* 5.7 8.7 - - - -
404A SER 4.9 9.4 - - - -
406A ALA* 5.4 15.0 - - + -
414A CYS* 4.3 33.2 - - + -
415A GLY* 4.7 6.3 - - - +
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Residues in contact with ARG 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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353A ASP* 2.4 45.1 + - - -
355A TYR* 3.1 45.0 - - + +
366A MET* 2.4 41.3 + - + +
367A VAL* 4.9 0.2 - - - -
369A PHE* 1.3 76.4 - - - +
371A SER* 1.3 52.9 + - - +
374A LYS* 2.7 37.0 - - + +
415A GLY* 3.8 18.1 + - - -
416A TYR* 2.9 50.0 + - + +
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Residues in contact with SER 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 VAL* 2.6 41.7 + - - +
369A PHE 2.9 0.6 + - - -
370A ARG* 1.3 83.0 - - - +
372A LYS* 1.3 57.8 + - - +
373A PHE 3.6 0.2 - - - -
374A LYS* 4.3 5.3 + - - +
375A ASP* 3.2 19.9 - - - +
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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