Contacts of the helix formed by residues 188 - 193 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47B ARG* 5.0 10.1 - - - -
185B ALA 5.0 1.4 + - - -
186B LYS 2.9 2.6 + - - -
187B TYR* 1.3 79.3 - - - +
189B LEU* 1.3 59.0 + - - +
190B PRO* 3.2 7.4 - - + -
191B TRP* 3.0 57.7 + + + -
192B LEU* 2.9 40.9 + - + +
295B PRO* 5.1 6.5 - - + -
296B LEU* 3.5 40.2 - - + -
239C GLY* 3.8 20.4 - - - -
242C MET* 4.9 2.0 - - + -
243C ARG* 3.7 37.9 - - + +
246C LEU* 3.2 33.7 + - + +
247C CYS* 3.8 10.3 - - - -
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Residues in contact with LEU 189 (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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183B ARG 4.5 7.6 - - - +
184B MET* 4.0 17.0 - - + +
186B LYS* 3.0 38.6 + - + +
187B TYR* 3.1 11.4 - - + +
188B TRP* 1.3 76.7 - - - +
190B PRO* 1.4 62.8 - - + +
192B LEU* 4.2 4.7 - - + +
193B VAL* 2.7 51.2 + - + +
194B GLY 2.8 7.5 + - - -
201C ILE* 3.9 28.7 - - + -
204C CYS* 4.0 22.7 - - + -
205C SER* 4.8 2.9 - - - +
208C MET* 4.4 5.2 - - + -
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Residues in contact with PRO 190 (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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178B MET* 3.5 28.8 - - + +
179B GLN 3.5 22.4 - - - +
180B MET* 4.2 13.0 - - - +
184B MET* 3.2 30.7 - - + +
185B ALA* 5.3 1.8 - - - -
188B TRP* 3.2 9.2 - - + -
189B LEU* 1.4 91.2 - - - +
191B TRP* 1.3 68.7 + - + +
194B GLY* 3.5 5.9 - - - +
195B MET* 2.9 23.4 + - - +
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Residues in contact with TRP 191 (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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46B PHE* 5.8 11.0 - + - -
47B ARG* 4.2 23.2 - - - +
176B TRP* 3.8 28.7 - + - -
178B MET* 4.4 4.3 - - + -
180B MET* 3.7 32.8 - - + -
188B TRP* 3.0 56.9 + + + +
190B PRO* 1.3 92.0 - - + +
192B LEU* 1.3 62.3 + - - +
193B VAL 3.3 0.8 + - - -
195B MET* 3.4 30.0 - - + +
196B PRO* 3.8 5.0 - - - +
296B LEU* 4.5 11.4 - - + -
235C ARG* 2.9 27.9 + - - -
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Residues in contact with LEU 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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187B TYR 3.5 21.8 - - - +
188B TRP* 2.9 43.2 + - + +
189B LEU* 4.4 3.4 - - + +
191B TRP* 1.3 79.5 - - - +
193B VAL* 1.3 66.4 + - + +
196B PRO* 3.5 15.1 - - - +
296B LEU* 4.5 7.0 - - + -
208C MET* 4.5 9.6 - - + -
232C THR* 5.0 2.4 - - - -
235C ARG* 3.8 20.0 - - + +
236C ILE* 4.0 42.8 - - + +
239C GLY* 3.8 17.3 - - - -
247C CYS* 4.3 11.7 - - - -
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Residues in contact with VAL 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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184B MET* 4.9 0.9 - - + -
189B LEU* 2.7 37.8 + - + +
191B TRP 3.3 0.2 - - - -
192B LEU* 1.3 82.5 - - + +
194B GLY* 1.3 66.6 + - - +
195B MET 3.3 1.3 - - - -
196B PRO* 3.1 14.1 - - - +
197B ALA* 3.1 13.7 + - + +
197C ALA* 4.5 9.9 - - + +
200C THR* 4.2 24.0 - - + -
201C ILE* 3.8 31.2 - - + -
204C CYS* 4.1 17.5 - - - -
236C ILE* 4.7 1.6 - - + -
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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