Contacts of the helix formed by residues 191 - 200 (chain B) in PDB entry 4WMJ
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 ASP 191 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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345A ASP* 3.5 10.2 - - - +
346A GLN* 2.7 31.7 + - + +
387A GLY 5.0 0.2 - - - +
415A THR* 4.3 8.5 + - - -
424A HIS* 4.8 1.2 - - - -
425A HIS* 5.0 2.3 + - - -
428A LEU* 3.8 28.3 - - + +
189B ASN* 3.0 25.2 + - + +
190B ILE* 1.4 79.8 - - - +
192B GLY* 1.3 61.6 + - - +
193B THR* 3.1 24.4 + - - -
194B HIS* 3.0 28.2 + - - +
195B LEU 4.3 1.0 + - - -
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Residues in contact with GLY 192 (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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415A THR* 5.4 0.6 + - - -
417A ASN* 4.0 13.4 + - - -
419A ILE* 3.8 28.6 - - - +
424A HIS* 3.7 11.2 - - - +
425A HIS* 5.2 1.8 + - - +
190B ILE 2.9 8.4 + - - -
191B ASP* 1.3 71.2 + - - +
193B THR* 1.3 63.8 + - - +
194B HIS 3.2 0.6 + - - -
195B LEU 3.5 1.8 + - - -
196B ALA* 3.0 27.0 + - - +
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Residues in contact with THR 193 (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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345A ASP* 5.3 1.4 + - - -
346A GLN* 4.2 13.7 - - + -
347A TYR* 3.4 50.8 - - + -
415A THR* 4.3 3.8 + - - -
416A HIS 5.4 0.5 + - - -
417A ASN* 2.9 29.0 + - - +
191B ASP* 3.1 23.2 + - - -
192B GLY* 1.3 75.6 - - - +
194B HIS* 1.3 63.6 + - - +
197B GLU* 3.0 27.4 + - + +
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Residues in contact with HIS 194 (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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346A GLN* 3.5 34.0 + - + +
389A ASN* 4.6 1.6 + - - -
165B ASP* 5.5 0.4 + - - -
186B PHE 3.6 18.0 + - - -
187B VAL* 3.9 6.1 - - + -
188B SER* 3.0 41.3 + - - -
189B ASN* 3.0 29.8 - - + +
191B ASP 3.0 14.0 + - - +
193B THR* 1.3 83.8 - - - +
195B LEU* 1.3 62.2 + - - +
197B GLU* 4.2 2.7 - - - +
198B VAL* 3.4 25.6 + - + +
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Residues in contact with LEU 195 (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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419A ILE* 4.2 10.3 - - + -
424A HIS* 4.9 0.2 - - - +
159B ILE* 4.7 4.7 - - + -
187B VAL* 4.0 26.8 - - + +
191B ASP 4.3 0.8 + - - -
192B GLY 3.5 7.1 + - - +
194B HIS* 1.3 76.5 - - - +
196B ALA* 1.3 60.5 + - - +
198B VAL* 3.1 4.6 + - + -
199B LEU* 2.8 58.6 + - + +
209B PHE* 4.9 2.7 - - + -
224B ASN* 3.6 43.5 - - - +
227B SER* 3.6 22.0 - - - -
228B ALA* 4.0 15.0 - - + +
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Residues in contact with ALA 196 (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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417A ASN* 3.9 21.8 - - - +
419A ILE* 4.0 21.3 - - + +
192B GLY 3.0 19.8 + - - +
193B THR 3.9 1.8 - - - +
195B LEU* 1.3 77.2 - - - +
197B GLU* 1.3 62.7 + - + +
199B LEU* 3.3 8.8 + - - +
200B LYS* 3.2 31.8 + - + +
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Residues in contact with GLU 197 (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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176A LYS* 3.3 31.1 + - - +
177A PRO* 5.7 0.7 - - - +
347A TYR* 2.6 41.1 + - + +
417A ASN* 4.8 2.7 + - - +
193B THR* 3.0 21.9 + - + +
194B HIS* 4.2 3.6 - - - +
196B ALA* 1.3 78.4 - - + +
198B VAL* 1.3 64.2 + - + +
200B LYS* 3.8 23.3 + - - +
201B ARG* 2.6 50.6 + - - +
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Residues in contact with VAL 198 (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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157B ILE* 4.0 24.9 - - + -
185B HIS* 3.9 37.7 - - + -
186B PHE 4.8 6.1 - - - +
187B VAL* 3.8 16.4 - - + -
194B HIS* 3.4 14.4 + - + +
195B LEU* 3.1 7.9 + - + +
197B GLU* 1.3 77.7 - - + +
199B LEU* 1.3 68.4 + - + +
200B LYS 3.1 0.2 - - - -
201B ARG* 3.0 21.7 + - - +
202B LEU* 3.4 15.3 - - + +
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Residues in contact with LEU 199 (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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419A ILE* 6.1 3.4 - - + -
195B LEU* 2.8 57.8 + - + +
196B ALA* 3.3 7.6 + - - +
198B VAL* 1.3 72.3 - - + +
200B LYS* 1.3 62.1 + - - +
202B LEU* 3.0 25.5 + - + +
209B PHE* 4.0 16.8 - - + -
227B SER* 4.8 1.3 - - - +
228B ALA* 4.7 3.8 - - - -
231B TRP* 3.8 67.3 + - + +
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Residues in contact with LYS 200 (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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347A TYR* 5.7 0.4 + - - -
417A ASN* 4.7 11.1 + - - -
196B ALA* 3.2 18.6 + - - +
197B GLU* 3.8 31.6 + - - +
198B VAL 3.1 0.2 - - - -
199B LEU* 1.3 77.0 - - - +
201B ARG* 1.3 65.0 + - + +
202B LEU 3.3 2.3 + - - +
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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