Contacts of the helix formed by residues 355 - 367 (chain A) in PDB entry 5W6V
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 THR 355 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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194A ARG* 5.9 0.2 - - - +
255A ARG* 5.5 9.0 - - - +
353A LYS 5.5 1.3 - - - +
354A LEU* 1.3 78.4 - - - +
356A ASP* 1.3 66.0 + - - +
357A ASN* 3.5 10.6 + - - +
358A GLN* 2.9 38.7 + - - +
359A THR* 3.0 21.2 + - - +
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Residues in contact with ASP 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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353A LYS* 5.9 2.3 - - - -
354A LEU 5.1 1.0 - - - +
355A THR* 1.3 76.8 - - - +
357A ASN* 1.3 66.8 + - - +
359A THR* 3.2 7.6 + - - -
360A SER* 3.1 25.5 + - - -
523A LYS* 3.9 31.5 + - - +
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Residues in contact with ASN 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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355A THR* 3.3 8.9 + - - +
356A ASP* 1.3 79.4 - - - +
358A GLN* 1.3 59.2 + - + +
360A SER* 3.5 4.2 + - - -
361A THR* 2.9 32.8 + - - +
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Residues in contact with GLN 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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190A LEU* 3.2 23.5 + - + +
191A GLY 2.9 30.1 + - - -
192A GLY* 4.2 4.8 - - - -
194A ARG* 3.5 27.3 + - - +
354A LEU* 3.4 27.7 - - + +
355A THR* 2.9 38.6 + - - +
357A ASN* 1.3 76.6 - - + +
359A THR* 1.3 60.1 + - - +
361A THR* 3.2 10.0 - - - +
362A MET* 3.1 27.2 + - - +
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Residues in contact with THR 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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353A LYS* 6.2 0.4 - - + -
354A LEU* 3.6 29.2 - - + +
355A THR 3.0 13.9 + - - +
356A ASP* 3.2 13.3 + - - -
358A GLN* 1.3 74.6 - - - +
360A SER* 1.3 61.5 + - - +
362A MET* 3.8 4.8 - - - +
363A ILE* 2.9 37.8 + - - +
7R A 4.3 25.5 - - + +
8R A 6.0 0.9 - - + +
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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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356A ASP 3.1 16.4 + - - -
357A ASN* 3.9 5.4 - - - -
359A THR* 1.3 84.1 + - - +
361A THR* 1.3 60.4 + - - +
363A ILE* 3.6 10.5 + - - +
364A LYS* 3.4 20.3 + - - +
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Residues in contact with THR 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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189A PRO 4.5 7.3 + - - +
190A LEU* 3.6 29.2 - - + +
357A ASN 2.9 19.1 + - - +
358A GLN* 3.2 21.5 - - - +
360A SER* 1.3 74.8 - - - +
362A MET* 1.3 61.4 + - - +
364A LYS* 3.7 6.1 + - - +
365A ALA* 3.4 20.4 + - - +
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Residues in contact with MET 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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190A LEU* 4.2 13.0 - - + -
196A VAL* 4.0 24.9 - - + -
219A ALA* 3.9 8.3 - - + +
220A THR* 3.5 45.5 - - - +
221A ALA* 3.7 3.6 - - - +
354A LEU* 4.3 18.4 - - - -
358A GLN 3.1 18.4 + - - +
359A THR* 3.9 5.2 - - - +
360A SER 3.3 0.2 - - - -
361A THR* 1.3 76.9 - - - +
363A ILE* 1.3 64.1 + - - +
364A LYS 3.2 0.2 - - - -
365A ALA* 3.2 11.1 + - - +
366A THR* 2.9 25.7 + - + +
7R A 4.1 24.2 - - - +
8R A 5.1 5.8 - - - +
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Residues in contact with ILE 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 THR* 2.9 25.2 + - - +
360A SER* 3.8 9.2 - - - +
361A THR 3.5 0.2 - - - -
362A MET* 1.3 77.6 - - - +
364A LYS* 1.3 63.1 + - - +
366A THR* 3.3 6.2 + - - -
367A ALA* 3.1 27.6 + - + +
755A GLN* 5.7 1.6 - - - +
6R U 3.6 42.8 - - + +
7R A 3.7 45.5 - - + +
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Residues in contact with LYS 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 SER 3.4 12.9 + - - +
361A THR* 4.0 7.2 - - - +
362A MET 3.2 0.6 - - - -
363A ILE* 1.3 82.6 - - + +
365A ALA* 1.3 60.6 + - - +
366A THR 3.4 1.0 + - - -
367A ALA* 4.0 11.3 + - - +
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Residues in contact with ALA 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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188A HIS* 3.3 41.2 - - + +
190A LEU* 6.1 0.2 - - + -
196A VAL* 5.2 3.6 - - + -
198A PHE* 3.3 19.8 - - + -
361A THR 3.4 13.3 + - - +
362A MET* 3.2 9.0 + - - +
364A LYS* 1.3 77.6 - - - +
366A THR* 1.3 62.5 + - + +
367A ALA 5.4 0.2 - - - -
368A ARG* 5.6 1.7 + - - -
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Residues in contact with THR 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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196A VAL* 4.5 3.1 - - + -
198A PHE* 3.8 13.5 - - + -
217A VAL* 6.0 0.5 - - - +
219A ALA* 3.6 29.6 - - + -
362A MET* 2.9 26.5 + - + +
363A ILE 3.4 3.8 + - - -
365A ALA* 1.3 85.4 - - + +
367A ALA* 1.3 62.0 + - - +
368A ARG* 3.5 15.9 + - - +
373A ARG* 4.8 7.6 + - - -
7R A 3.0 42.6 + - - +
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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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363A ILE* 3.1 20.2 + - + +
364A LYS* 4.0 10.3 + - - +
365A ALA 5.4 0.3 - - - -
366A THR* 1.3 75.6 - - - +
368A ARG* 1.3 63.6 + - - +
755A GLN* 5.4 4.3 - - + -
756A GLY* 4.3 13.0 - - - +
6R U 3.5 23.6 - - - +
7R A 5.4 2.5 - - - -
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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