Contacts of the helix formed by residues 40 - 47 (chain 4) in PDB entry 2WSC
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 PHE 40 (chain 4).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384 ARG* 4.8 10.3 - - - -
394 TRP* 1.3 120.0 - + + +
414 VAL* 1.3 62.4 + - - +
424 GLN 3.1 0.4 - - - -
434 ALA* 3.2 34.6 + - + +
444 GLU* 3.4 11.4 + - - +
12074 CLA 4.5 26.0 - + + -
138F VAL* 5.8 10.8 - - + -
142F ARG* 4.0 30.5 - - + -
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Residues in contact with VAL 41 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374 LEU 4.9 2.7 - - - +
384 ARG 3.8 7.9 - - - +
394 TRP* 3.3 28.9 - - + +
404 PHE* 1.3 77.7 - - - +
424 GLN* 1.3 68.4 + - - +
444 GLU* 3.5 13.8 + - - +
454 LEU* 3.6 20.2 + - + +
1194 PRO 5.6 1.1 - - - +
1204 ILE 5.7 4.0 - - - +
1214 PHE* 6.4 1.3 - - - -
1224 LYS* 5.0 7.6 - - + +
1414 LEU* 4.9 17.7 - - + -
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Residues in contact with GLN 42 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384 ARG 4.3 4.7 + - - +
394 TRP 3.8 14.4 - - - +
414 VAL* 1.3 79.7 - - - +
434 ALA* 1.3 65.3 + - - +
454 LEU* 2.8 23.3 + - - +
464 VAL* 3.0 24.7 + - + +
1054 ARG* 3.8 26.2 - - - +
1094 ILE* 4.1 17.6 - - + +
1194 PRO* 2.9 42.4 - - - +
1204 ILE* 3.2 30.8 - - - +
12074 CLA 5.2 4.9 - - + -
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Residues in contact with ALA 43 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394 TRP 4.5 0.2 + - - -
404 PHE* 3.2 44.6 + - + +
424 GLN* 1.3 77.6 - - - +
444 GLU* 1.3 50.6 + - - +
464 VAL 3.2 1.2 + - - -
474 ASN* 2.8 47.0 + - - +
12074 CLA 3.2 26.2 + - + +
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Residues in contact with GLU 44 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404 PHE 3.4 7.5 + - - +
414 VAL* 3.6 12.0 - - - +
424 GLN 3.1 0.6 - - - -
434 ALA* 1.3 77.3 - - - +
454 LEU* 1.3 57.3 + - - +
474 ASN* 2.9 10.3 + - - +
484 GLY* 2.8 28.1 + - - -
1614 LEU* 3.8 11.6 - - + +
12024 CLA 3.0 71.1 + - + +
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Residues in contact with LEU 45 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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414 VAL* 3.6 19.9 + - + +
424 GLN* 2.8 24.9 + - - +
444 GLU* 1.3 75.7 - - - +
464 VAL* 1.3 60.8 + - + +
484 GLY* 4.3 2.9 - - - +
494 ARG* 3.3 51.7 + - - +
1184 ASP 5.0 0.2 - - - +
1194 PRO* 3.6 47.8 - - + +
1224 LYS* 3.9 21.5 - - - +
12004 CLA 6.2 0.9 - - + -
12064 CLA 5.0 5.9 - - + +
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Residues in contact with VAL 46 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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424 GLN* 3.0 32.3 + - + +
434 ALA 3.5 0.4 - - - +
454 LEU* 1.3 85.2 - - + +
474 ASN* 1.3 61.5 + - - +
494 ARG* 4.2 1.9 - - - +
504 TRP* 3.2 41.8 + - + +
1054 ARG* 4.1 22.4 - - - +
12064 CLA 5.4 12.6 - - + -
12074 CLA 3.1 45.3 - - + +
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Residues in contact with ASN 47 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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434 ALA* 2.8 29.4 + - - +
444 GLU* 2.9 5.5 + - - +
464 VAL* 1.3 77.4 - - - +
484 GLY* 1.3 51.1 + - - +
504 TRP* 3.2 4.3 - - - +
514 ALA* 2.7 34.5 + - - +
1614 LEU* 3.2 22.8 - - + +
12074 CLA 3.5 21.3 - - - +
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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