Contacts of the helix formed by residues 383 - 388 (chain B) in PDB entry 4WQ6
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 383 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193B PHE* 3.6 8.6 - - - +
194B GLY* 3.4 26.1 - - - -
353B GLY 5.8 0.6 + - - -
356B VAL 4.8 0.6 + - - -
382B SER* 1.3 74.9 + - - +
384B GLY* 1.3 66.6 + - - +
385B GLY 3.1 1.4 - - - +
386B LEU* 3.0 14.4 + - - +
387B LEU* 3.1 16.0 + - - +
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Residues in contact with GLY 384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391A THR* 5.6 6.7 - - - -
194B GLY* 4.5 0.6 - - - -
197B GLY* 4.7 12.7 - - - -
383B GLY* 1.3 71.8 - - - +
385B GLY* 1.3 58.1 + - - +
388B GLN* 2.9 23.6 + - - -
389B LYS* 2.8 31.1 + - - -
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Residues in contact with GLY 385 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B ASN* 4.0 13.7 + - - -
168B GLN* 5.3 0.8 + - - -
356B VAL 4.0 16.2 + - - -
357B ASP* 4.2 18.1 - - - +
358B ILE 5.5 0.2 + - - -
382B SER* 3.8 4.8 + - - -
383B GLY 3.1 2.4 - - - +
384B GLY* 1.3 76.7 - - - +
386B LEU* 1.3 58.6 + - - +
389B LYS* 4.3 23.1 - - - +
390B LEU* 4.7 3.3 - - - +
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Residues in contact with LEU 386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B VAL* 3.8 8.1 - - + +
164B ASN* 4.6 5.3 + - - +
165B SER* 4.3 10.5 - - - +
168B GLN* 3.8 23.6 - - - +
190B LEU* 4.2 7.9 - - + -
191B HIS 4.6 1.8 - - - +
192B ASP* 3.8 24.2 - - + +
211B HIS* 3.6 44.2 - - + +
382B SER* 3.3 30.2 + - - +
383B GLY 3.0 8.3 + - - +
385B GLY* 1.3 79.7 - - - +
387B LEU* 1.3 68.7 + - + +
390B LEU* 3.5 18.6 - - - +
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Residues in contact with LEU 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B TYR* 2.6 33.6 + - - +
161B VAL* 3.7 10.3 - - + -
192B ASP* 3.4 34.8 - - - +
194B GLY* 4.0 10.3 - - - +
198B VAL* 3.4 27.7 - - + +
204B ALA* 4.7 5.6 - - - +
207B GLY* 3.4 29.6 - - - +
208B ALA* 4.2 9.2 - - - +
211B HIS* 4.8 0.9 - - + -
220B THR* 4.3 3.6 - - + +
383B GLY 3.1 10.5 + - - +
386B LEU* 1.3 97.5 - - + +
388B GLN* 1.3 60.3 + - - +
390B LEU* 4.4 4.7 - - - -
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Residues in contact with GLN 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156A TRP* 3.8 17.6 - - + -
157A TYR* 4.9 4.6 - - - -
199A SER* 5.0 0.3 + - - -
388A GLN* 3.6 29.6 + - - +
390A LEU 3.1 27.2 + - - +
391A THR* 4.1 6.7 - - + -
197B GLY 3.4 22.7 - - - +
198B VAL* 3.4 5.9 - - + +
199B SER* 3.3 32.5 + - - -
203B THR* 4.7 2.1 - - - +
384B GLY* 2.9 18.9 + - - +
386B LEU 3.9 0.2 - - - -
387B LEU* 1.3 76.6 - - - +
389B LYS* 1.3 59.6 + - - +
390B LEU* 2.8 20.5 + - - +
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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