Contacts of the helix formed by residues 389 - 398 (chain A) in PDB entry 4WCX
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 389 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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165A ARG* 5.5 2.9 - - - +
229A ASP* 3.0 26.6 + - - +
230A ASP* 3.8 17.5 - - - +
383A CYS 4.5 7.6 - - - +
384A TYR* 4.9 15.5 - - + +
386A MET 5.4 0.2 - - - +
387A GLY 3.0 12.5 + - - +
388A ARG* 1.3 78.6 - - - +
390A GLY* 1.3 69.9 + - - +
391A ASP* 3.3 1.4 + - - +
392A ARG* 3.1 22.2 + - - +
393A PHE* 3.6 3.1 - - - -
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Residues in contact with GLY 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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229A ASP* 3.5 34.2 - - - -
230A ASP* 2.9 15.4 + - - -
262A VAL* 3.5 18.0 - - - +
389A THR* 1.3 71.2 - - - +
391A ASP* 1.3 57.8 + - - -
393A PHE* 3.0 18.3 + - - +
394A MET* 3.1 10.4 + - - +
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Residues in contact with ASP 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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229A ASP* 5.4 1.7 - - - +
261A GLY 4.3 7.2 - - - +
262A VAL* 3.3 27.1 - - + +
389A THR 4.6 0.9 - - - +
390A GLY* 1.3 69.5 - - - -
392A ARG* 1.3 72.6 + - - +
394A MET* 3.8 5.1 - - - +
395A SER* 2.9 30.7 + - - -
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Residues in contact with ARG 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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229A ASP* 5.9 0.6 + - - -
387A GLY* 3.8 29.8 + - - +
388A ARG* 4.2 5.5 - - - +
389A THR* 3.1 16.7 + - - +
391A ASP* 1.3 90.1 - - - +
393A PHE* 1.3 62.8 + - - +
395A SER* 2.9 19.1 + - - +
396A PHE* 3.1 14.4 + - - +
254C ASN* 4.9 9.5 - - - +
258C GLU* 2.1 46.9 + - - -
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Residues in contact with PHE 393 (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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74A TYR* 6.3 1.1 - + - -
265A HIS* 3.4 32.5 - + + -
305A TYR 4.0 13.7 - - - -
383A CYS* 3.9 18.4 - - + -
388A ARG* 3.5 22.4 - - - +
389A THR* 3.2 8.3 + - - +
390A GLY 3.0 11.6 + - - +
392A ARG* 1.3 80.5 - - - +
394A MET* 1.3 82.3 + - + +
396A PHE* 3.2 10.7 + + - +
397A ALA* 2.9 39.5 + - + +
502A SF4 3.7 25.4 - - - -
505A ALA 3.6 17.9 - - - -
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Residues in contact with MET 394 (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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257A GLU* 4.8 9.6 - - - +
261A GLY 6.1 0.4 - - - +
262A VAL* 3.7 24.9 - - + -
263A GLY* 4.7 15.0 - - - +
264A PRO 4.4 15.7 - - - +
265A HIS* 5.9 1.1 - - - -
305A TYR* 3.9 35.7 - - + +
306A THR* 4.5 4.0 - - - +
390A GLY 3.1 3.3 + - - +
391A ASP* 3.3 8.9 + - - +
393A PHE* 1.3 103.7 - - + +
395A SER* 1.3 62.0 + - - +
397A ALA* 3.3 1.7 + - - +
398A LYS* 3.1 49.0 + - - +
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Residues in contact with SER 395 (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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391A ASP* 2.9 14.5 + - - -
392A ARG* 2.9 22.0 + - - +
394A MET* 1.3 76.3 - - - +
396A PHE* 1.3 58.7 + - - +
398A LYS* 3.6 5.9 + - - +
399A SER* 3.4 21.5 + - - -
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Residues in contact with PHE 396 (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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383A CYS* 4.0 14.4 - - - -
388A ARG* 3.5 43.7 - - + -
392A ARG 3.1 14.7 + - - +
393A PHE* 3.5 14.8 - + - +
395A SER* 1.3 79.8 + - - +
397A ALA* 1.3 67.7 + - - +
399A SER* 2.7 31.0 + - - -
402A ILE* 4.5 17.5 + - + +
405A PHE* 3.6 49.8 - + + -
406A CYS* 4.6 1.8 - - - -
502A SF4 4.2 15.9 - - - -
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Residues in contact with ALA 397 (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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73A ILE* 5.6 0.4 - - + -
305A TYR* 3.6 30.1 + - + -
393A PHE* 2.9 38.3 + - + +
394A MET* 3.3 4.9 + - - +
396A PHE* 1.3 83.0 - - - +
398A LYS* 1.3 58.3 + - - +
399A SER 3.1 3.7 + - - -
400A GLY 4.5 1.4 + - - -
402A ILE* 3.8 35.1 - - + +
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Residues in contact with LYS 398 (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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257A GLU* 4.9 9.5 + - - -
305A TYR* 3.6 51.6 + - + +
394A MET* 3.1 43.6 + - - +
395A SER* 3.6 6.3 + - - +
396A PHE 3.2 0.4 - - - -
397A ALA* 1.3 76.2 - - - +
399A SER* 1.3 60.2 + - - +
400A GLY 3.5 2.0 + - - -
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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