Contacts of the helix formed by residues 357 - 369 (chain A) in PDB entry 2R5N
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 357 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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355A ILE 3.6 2.4 + - - -
356A ALA* 1.3 71.7 - - - +
358A ARG* 1.3 55.9 + - - +
360A ALA* 3.6 8.5 - - - +
361A SER* 2.9 28.6 + - - -
493A PRO* 4.3 5.6 + - - -
495A ASP 4.9 2.0 - - - -
499A SER* 3.4 20.2 - - - -
517A ILE 4.3 1.9 + - - -
518A LEU* 3.2 18.9 - - - +
519A SER* 2.7 39.2 + - - -
523A LEU* 3.7 18.8 - - - +
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Residues in contact with ARG 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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356A ALA* 3.8 7.8 - - + +
357A SER* 1.3 77.3 + - - +
359A LYS* 1.3 59.4 + - + +
361A SER* 3.3 7.6 - - - -
362A GLN* 3.1 24.6 + - - +
384A PRO 4.6 2.6 + - - -
385A SER* 3.0 28.5 + - - +
386A ASN 4.3 2.6 - - - +
387A LEU* 3.8 22.4 - - + +
460A THR* 3.8 20.9 - - + -
461A HIS* 3.4 14.4 + - - -
518A LEU* 3.9 8.6 - - - +
519A SER 3.1 21.6 + - - +
520A ARG* 3.7 35.1 + - - +
670A R5P 2.9 29.7 + - - -
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Residues in contact with LYS 359 (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 ILE* 4.2 20.6 - - + -
356A ALA* 2.9 21.0 + - + +
358A ARG* 1.3 79.1 - - - +
360A ALA* 1.3 59.7 + - - +
362A GLN* 2.8 31.6 + - - +
363A ASN* 2.8 55.3 + - - +
387A LEU* 3.8 14.1 - - + -
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Residues in contact with ALA 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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344A PHE* 5.5 0.9 - - - -
355A ILE* 3.9 9.9 - - + +
356A ALA 2.9 6.9 + - - +
357A SER* 3.3 12.3 + - - +
359A LYS* 1.3 76.4 - - - +
361A SER* 1.3 56.5 + - - +
363A ASN* 3.4 6.6 + - - +
364A ALA* 3.0 27.0 + - - +
496A GLN* 3.6 27.8 - - + +
499A SER* 3.5 30.4 - - - +
500A ALA* 5.3 1.0 + - - +
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Residues in contact with SER 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 SER 2.9 14.1 + - - -
358A ARG* 3.3 10.8 - - - -
360A ALA* 1.3 74.5 - - - +
362A GLN* 1.3 64.1 + - - +
364A ALA* 3.0 4.2 + - - +
365A ILE* 2.9 28.2 + - - +
386A ASN 5.5 0.9 - - - -
387A LEU 5.2 0.9 + - - -
458A VAL* 3.8 12.2 - - - +
499A SER* 4.7 1.7 - - - -
503A TRP* 2.8 32.8 + - - +
518A LEU* 3.5 26.1 - - - +
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Residues in contact with GLN 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 ARG 3.1 7.6 + - - +
359A LYS* 2.8 42.6 + - - +
361A SER* 1.3 75.8 + - - +
363A ASN* 1.3 58.2 + - - +
365A ILE* 3.2 7.4 + - + +
366A GLU* 2.8 29.1 + - + +
387A LEU* 3.3 54.5 + - + +
389A LEU* 2.9 30.0 + - - +
390A TRP* 5.0 2.5 - - + +
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Residues in contact with ASN 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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344A PHE* 3.7 14.1 - - + -
348A LEU* 6.1 3.9 - - + +
355A ILE* 3.5 30.1 - - - +
359A LYS* 2.8 41.2 + - - +
360A ALA* 3.6 7.3 - - - +
361A SER 3.2 0.2 - - - -
362A GLN* 1.3 76.5 - - - +
364A ALA* 1.3 56.3 + - - +
366A GLU* 3.3 8.8 + - - +
367A ALA* 2.9 27.9 + - - +
496A GLN* 4.7 4.6 + - - +
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Residues in contact with ALA 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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344A PHE* 3.9 20.4 - - + -
360A ALA 3.0 13.3 + - - +
361A SER 3.0 7.8 + - - +
363A ASN* 1.3 72.5 - - - +
365A ILE* 1.3 61.4 + - - +
367A ALA 3.2 0.2 + - - -
368A PHE* 2.8 42.4 + - + -
500A ALA* 4.6 7.9 - - - -
503A TRP* 3.6 33.0 - - + -
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Residues in contact with ILE 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 SER* 2.9 23.6 + - - +
362A GLN* 3.5 7.4 - - + +
364A ALA* 1.3 76.7 - - - +
366A GLU* 1.3 53.3 + - - +
368A PHE* 4.1 0.8 - - - +
369A GLY* 2.7 33.1 + - - -
375A PHE* 4.3 10.5 - - + -
387A LEU 4.0 19.3 - - - +
388A THR* 4.0 10.5 - - + +
389A LEU 5.2 0.2 - - - -
390A TRP* 3.5 31.0 - - + +
430A TYR* 3.6 32.8 - - + +
458A VAL* 5.2 1.6 - - + -
503A TRP* 3.4 33.0 - - + -
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Residues in contact with GLU 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 GLN* 2.8 14.7 + - + +
363A ASN* 3.5 12.8 - - - +
364A ALA 3.2 0.2 - - - -
365A ILE* 1.3 75.7 - - - +
367A ALA* 1.3 63.3 + - - +
370A PRO* 3.1 22.0 - - - +
390A TRP* 3.3 17.8 - - + +
391A SER* 2.6 50.0 + - - -
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Residues in contact with ALA 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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344A PHE* 3.6 40.6 - - + -
363A ASN 2.9 16.5 + - - +
364A ALA 3.2 3.8 + - - +
366A GLU* 1.3 78.5 - - - +
368A PHE* 1.3 63.8 + - + +
370A PRO* 3.6 8.7 - - - +
371A LEU* 3.8 15.2 - - - +
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Residues in contact with PHE 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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337A PHE* 3.7 33.0 - + + -
341A ALA* 4.1 15.0 - - + -
344A PHE* 4.3 20.9 - + + -
345A ILE* 6.0 0.7 - - + -
364A ALA* 2.8 25.9 + - + +
367A ALA* 1.3 79.0 - - + +
369A GLY* 1.3 57.0 + - - +
370A PRO 3.3 0.2 - - - -
371A LEU* 2.8 32.5 + - + +
372A LEU* 2.9 17.4 + - + +
375A PHE* 3.9 15.9 - + + -
500A ALA 4.3 6.5 - - - -
503A TRP* 3.8 30.3 - + + -
504A LYS* 3.8 35.0 - - + -
507A VAL* 4.1 7.9 - - + -
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Residues in contact with GLY 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 ILE 2.7 21.5 + - - -
368A PHE* 1.3 73.0 - - - +
370A PRO* 1.3 68.0 - - - +
371A LEU 3.1 1.0 + - - -
372A LEU 3.3 16.6 + - - +
373A PRO* 4.1 2.9 - - - +
375A PHE* 4.0 12.5 - - - -
390A TRP* 3.3 30.4 - - - -
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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