Contacts of the helix formed by residues 390 - 398 (chain C) 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 GLY 390 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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229C ASP* 3.3 32.2 + - - -
230C ASP* 2.7 16.4 + - - -
262C VAL* 3.5 16.8 - - - +
389C THR* 1.3 70.6 - - - +
391C ASP* 1.3 63.4 + - - -
393C PHE* 3.1 5.9 + - - +
394C MET* 3.1 18.5 + - - +
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Residues in contact with ASP 391 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229C ASP* 4.4 3.0 + - - -
261C GLY 4.2 11.1 - - - +
262C VAL* 3.6 23.6 - - + +
389C THR 3.3 1.8 + - - -
390C GLY* 1.3 71.3 - - - -
392C ARG* 1.3 64.1 + - - +
394C MET* 3.2 6.0 + - - +
395C SER* 3.1 29.8 + - - -
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Residues in contact with ARG 392 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386C MET 3.4 17.1 + - - -
387C GLY* 3.1 26.0 + - - +
388C ARG* 3.8 17.4 - - + +
389C THR 3.3 13.2 + - - +
391C ASP* 1.3 79.5 + - - +
393C PHE* 1.3 62.6 + - - +
395C SER* 3.2 17.2 + - - +
396C PHE* 3.2 13.9 + - - +
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Residues in contact with PHE 393 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230C ASP* 5.4 0.2 - - - -
265C HIS* 3.6 39.0 - + + -
305C TYR 4.5 9.2 - - - -
383C CYS* 3.7 21.3 - - + -
388C ARG* 3.6 23.1 - - - +
389C THR* 3.6 8.8 + - - +
390C GLY 3.1 9.2 + - - +
392C ARG* 1.3 80.2 - - - +
394C MET* 1.3 82.5 + - + +
396C PHE* 3.4 6.3 + + - +
397C ALA* 3.0 35.1 + - + +
502C SF4 3.7 28.5 - - - -
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Residues in contact with MET 394 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262C VAL* 4.1 17.0 - - + -
263C GLY 5.5 2.9 - - - +
264C PRO 5.8 3.4 - - - +
265C HIS* 6.1 1.6 - - - -
305C TYR* 3.3 52.0 - - + +
390C GLY 3.1 14.4 + - - +
391C ASP* 3.2 11.2 + - - +
393C PHE* 1.3 91.5 - - + +
395C SER* 1.3 65.3 + - - +
397C ALA* 3.0 13.3 + - + +
398C LYS* 3.1 42.8 + - + +
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Residues in contact with SER 395 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391C ASP* 3.1 22.9 + - - -
392C ARG* 3.2 13.2 + - - +
394C MET* 1.3 76.0 - - - +
396C PHE* 1.3 60.8 + - - +
398C LYS* 3.5 9.2 + - - +
399C SER* 3.2 21.5 + - - -
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Residues in contact with PHE 396 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383C CYS* 4.0 16.4 - - - -
388C ARG* 3.5 40.2 - - - -
392C ARG 3.2 15.0 + - - +
393C PHE* 3.5 10.3 - + - +
394C MET 3.2 0.4 - - - -
395C SER* 1.3 77.9 + - - +
397C ALA* 1.3 60.7 + - - +
399C SER* 2.7 34.2 + - - -
402C ILE* 3.7 13.2 - - + +
405C PHE* 3.6 53.2 - + + -
406C CYS* 4.2 6.1 - - - -
502C SF4 4.1 19.7 - - - -
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Residues in contact with ALA 397 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73C ILE* 5.7 2.9 - - + +
305C TYR* 4.0 18.9 + - + -
393C PHE* 3.0 31.1 + - + +
394C MET* 3.0 23.5 + - + +
396C PHE* 1.3 79.0 - - - +
398C LYS* 1.3 58.5 + - - +
399C SER 3.3 0.9 + - - -
400C GLY 4.5 1.9 + - - -
402C ILE* 3.6 31.1 - - + +
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Residues in contact with LYS 398 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C LEU 5.8 0.4 - - - -
40C LYS* 6.0 8.5 - - - +
257C GLU* 5.6 3.8 + - - -
305C TYR* 4.2 35.1 - - + +
394C MET* 3.1 45.2 + - + +
395C SER* 3.5 8.0 + - - +
396C PHE 3.3 0.2 - - - -
397C ALA* 1.3 75.5 - - - +
399C SER* 1.3 59.7 + - - +
400C GLY 3.0 8.0 + - - -
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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