Contacts of the helix formed by residues 232 - 236 (chain B) in PDB entry 4CQM
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 232 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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249A THR* 3.5 19.1 - - - +
199B PRO* 3.3 27.7 - - - +
230B ASP* 3.1 10.9 + - - -
231B GLY* 1.3 79.5 - - - +
233B LEU* 1.3 61.7 + - - +
234B GLN 3.2 3.4 - - - -
235B LEU* 3.3 24.2 + - - +
236B ILE* 4.0 2.4 - - - +
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Residues in contact with LEU 233 (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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136B ILE* 4.3 12.6 - - + -
179B GLY* 4.2 17.3 - - - -
180B PHE* 3.6 44.2 - - + +
195B LYS* 6.2 0.2 - - + -
198B ILE* 3.7 27.8 - - + +
199B PRO* 4.1 3.8 - - - +
230B ASP* 2.8 21.3 + - + +
231B GLY 3.4 1.6 - - - -
232B GLY* 1.3 76.8 - - - +
234B GLN* 1.3 64.5 + - - +
236B ILE* 3.1 17.4 + - + +
237B LEU* 3.2 39.2 + - + +
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Residues in contact with GLN 234 (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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181A GLN* 5.5 6.5 - - - +
250A GLY 3.8 17.6 - - - +
251A THR* 4.7 2.4 + - - -
252A SER 5.7 0.5 + - - -
136B ILE* 4.3 18.7 - - + +
139B LEU* 6.3 1.6 - - - +
140B LYS* 3.1 54.3 + - - +
228B VAL* 4.0 25.0 - - - +
230B ASP* 2.6 21.1 + - - +
233B LEU* 1.3 74.3 - - - +
235B LEU* 1.3 64.6 - - + +
236B ILE 3.1 3.5 + - - -
237B LEU* 3.9 2.0 + - - -
161D VAL* 4.3 5.0 - - + +
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Residues in contact with LEU 235 (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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181A GLN* 3.4 49.8 - - + +
184A ALA* 4.4 5.6 - - + -
185A ARG* 4.4 18.0 + - + +
250A GLY* 4.1 26.2 - - - +
199B PRO* 5.1 0.2 - - + -
232B GLY* 3.7 19.3 - - - +
233B LEU 3.1 1.0 - - - -
234B GLN* 1.3 86.7 - - + +
236B ILE* 1.3 69.3 + - + +
161D VAL* 3.3 35.8 - - + +
162D GLY 4.9 2.5 - - - +
260D PHE* 3.5 18.2 - - - -
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Residues in contact with ILE 236 (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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185A ARG* 3.4 45.3 - - + +
197B ASN* 3.9 35.0 - - + +
198B ILE* 5.4 0.2 - - - -
199B PRO* 4.5 3.4 - - + -
232B GLY 4.0 13.0 - - - +
233B LEU* 3.1 10.7 + - + +
235B LEU* 1.3 88.7 - - - +
237B LEU* 1.3 71.7 + - + +
221D MET* 4.2 21.0 - - + +
259D LEU* 5.6 0.3 - - - +
260D PHE* 3.1 23.5 - - + -
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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