Contacts of the helix formed by residues 188 - 193 (chain C) in PDB entry 4IGM
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 TRP 188 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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239B GLY* 3.6 20.9 - - - -
242B MET* 4.7 4.0 - - + -
243B ARG* 3.4 43.6 - - + +
246B LEU* 4.1 25.3 + - + +
247B CYS* 3.8 10.1 - - - -
47C ARG* 5.2 7.9 - - - -
186C LYS 2.8 5.5 + - - -
187C TYR* 1.3 75.9 - - - +
189C LEU* 1.3 64.8 + - - +
190C PRO* 3.3 8.5 - - + -
191C TRP* 3.1 52.5 + + + -
192C LEU* 3.0 36.0 + - + +
295C PRO* 5.3 6.1 - - + -
296C LEU* 3.6 44.0 - - + -
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Residues in contact with LEU 189 (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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151B ASP* 4.4 2.5 - - - +
201B ILE* 4.2 23.6 - - + -
204B CYS* 4.2 25.6 - - + -
205B SER* 4.8 3.6 - - - +
208B MET* 4.6 1.8 - - + -
183C ARG 3.9 20.6 - - - +
184C MET* 3.8 19.3 - - + +
186C LYS* 2.9 30.1 + - + +
187C TYR* 3.0 14.6 - - + +
188C TRP* 1.3 77.4 - - - +
190C PRO* 1.3 67.8 - - + +
192C LEU* 4.3 4.7 - - + +
193C VAL* 2.8 39.1 + - + +
194C GLY 2.9 5.9 + - - -
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Residues in contact with PRO 190 (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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178C MET* 3.4 28.0 - - + +
179C GLN 3.6 23.3 - - - +
180C MET* 4.2 18.8 - - + +
184C MET* 3.1 26.4 - - + +
185C ALA* 5.3 0.7 - - - -
186C LYS 5.3 0.2 - - - +
188C TRP* 3.4 7.0 - - + -
189C LEU* 1.3 89.5 - - + +
191C TRP* 1.3 67.3 + - + +
194C GLY* 3.1 9.0 - - - +
195C MET 3.0 24.8 + - - -
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Residues in contact with TRP 191 (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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235B ARG* 2.6 30.5 + - - +
46C PHE* 4.0 26.9 - + - -
47C ARG* 4.0 25.9 - - - +
176C TRP* 4.0 23.2 - + - -
178C MET* 4.2 3.8 - - + -
180C MET* 3.8 32.8 - - + -
188C TRP* 3.1 50.9 + + + +
190C PRO* 1.3 89.3 - - + +
192C LEU* 1.3 63.6 + - - +
195C MET* 3.5 26.1 - - - +
196C PRO* 3.9 5.2 - - - +
296C LEU* 4.0 19.1 - - + -
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Residues in contact with LEU 192 (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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204B CYS* 5.9 0.2 - - - -
208B MET* 4.9 8.1 - - + -
232B THR* 5.2 2.1 + - - -
235B ARG* 3.7 20.9 - - - +
236B ILE* 4.1 41.8 - - + +
239B GLY* 3.7 18.4 - - - -
247B CYS* 4.3 10.1 - - - -
187C TYR 3.4 22.9 - - - +
188C TRP* 3.0 44.4 + - + +
189C LEU* 4.5 4.0 - - + +
191C TRP* 1.3 81.9 - - - +
193C VAL* 1.3 63.3 + - + +
196C PRO* 3.4 15.2 - - - +
296C LEU* 4.4 7.2 - - + -
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Residues in contact with VAL 193 (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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197B ALA* 4.3 16.8 - - + +
200B THR* 3.7 30.3 - - + -
201B ILE* 3.9 28.9 - - + -
204B CYS* 4.1 18.8 - - - -
236B ILE* 4.5 2.2 - - + -
184C MET* 4.9 2.9 - - + -
189C LEU* 2.8 23.7 + - + +
192C LEU* 1.3 78.8 - - + +
194C GLY* 1.3 68.2 + - - +
195C MET 3.5 0.9 - - - -
196C PRO* 3.4 5.7 - - - +
197C ALA* 3.3 19.9 + - + +
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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