Contacts of the helix formed by residues 188 - 193 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47A ARG* 5.4 8.7 - - - -
186A LYS 2.7 9.3 + - - -
187A TYR* 1.3 75.7 - - - +
189A LEU* 1.3 57.4 + - - +
190A PRO* 3.3 8.1 - - + -
191A TRP* 3.1 59.3 + + + -
192A LEU* 3.0 36.8 + - + +
295A PRO* 5.1 7.4 - - + -
296A LEU* 3.9 28.9 - - + -
239F GLY* 3.7 27.6 - - - -
242F MET* 4.7 3.6 - - + -
243F ARG* 3.4 44.7 - - + +
246F LEU* 3.6 34.3 + - + +
247F CYS* 3.8 9.6 - - - -
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Residues in contact with LEU 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A ARG 4.2 11.4 - - - +
184A MET* 4.1 19.1 - - + +
186A LYS* 3.0 38.3 + - + +
187A TYR* 4.2 15.0 - - + +
188A TRP* 1.3 73.8 - - - +
190A PRO* 1.4 66.7 - - + +
192A LEU* 4.3 3.6 - - + +
193A VAL* 2.8 46.0 + - + +
194A GLY 2.9 7.4 + - - -
201F ILE* 4.2 24.7 - - + -
204F CYS* 4.0 26.9 - - + -
205F SER* 4.8 2.5 - - - +
208F MET* 4.7 1.8 - - + -
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Residues in contact with PRO 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178A MET* 3.4 20.8 - - + +
179A GLN 3.9 18.8 - - - +
180A MET* 4.3 10.1 - - + +
184A MET* 3.2 30.9 - - + +
186A LYS 4.5 0.4 - - - +
188A TRP* 3.3 7.9 - - - -
189A LEU* 1.4 93.5 - - + +
191A TRP* 1.3 76.1 + - + +
194A GLY* 3.5 8.4 - - - +
195A MET* 2.9 30.3 + - - +
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Residues in contact with TRP 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A PHE* 6.3 4.3 - + - -
47A ARG* 4.9 21.6 - - - +
178A MET* 4.7 6.1 - - + -
180A MET* 4.4 20.4 - - + -
188A TRP* 3.1 53.2 + + + +
189A LEU 3.0 0.6 - - - -
190A PRO* 1.3 108.3 - - + +
192A LEU* 1.3 66.0 + - - +
193A VAL 3.4 0.2 - - - -
195A MET* 3.6 33.3 - - + +
296A LEU* 4.3 15.3 - - + -
235F ARG* 2.6 31.4 + - - -
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Residues in contact with LEU 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187A TYR 3.7 18.4 - - - +
188A TRP* 3.0 27.1 + - + +
189A LEU* 4.4 2.5 - - + +
191A TRP* 1.3 80.6 - - + +
193A VAL* 1.3 68.4 + - + +
196A PRO* 3.3 17.7 - - - +
296A LEU* 4.5 8.7 - - + -
208F MET* 4.0 20.4 - - + -
232F THR* 4.9 2.3 - - - -
235F ARG* 3.4 31.1 + - + +
236F ILE* 3.9 35.0 - - + +
239F GLY* 4.1 13.2 - - - -
240F PHE 4.8 0.7 - - - +
247F CYS* 4.2 11.4 - - - -
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Residues in contact with VAL 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184A MET* 4.7 2.7 - - + -
189A LEU* 2.8 30.9 + - + +
192A LEU* 1.3 83.5 - - + +
194A GLY* 1.3 67.1 + - - +
195A MET 3.2 2.2 - - - -
196A PRO* 3.0 14.1 - - - +
197A ALA* 3.2 13.8 + - + +
197F ALA* 4.4 13.5 - - + +
200F THR* 3.7 32.3 - - + -
201F ILE* 3.7 30.3 - - + +
204F CYS* 4.2 10.8 - - - -
232F THR* 5.8 0.2 - - - +
236F ILE* 4.6 2.0 - - + -
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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