Contacts of the helix formed by residues 188 - 193 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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239D GLY* 3.9 22.7 - - - -
242D MET* 4.9 2.5 - - + -
243D ARG* 3.3 40.0 - - + +
246D LEU* 3.4 33.0 - - + +
247D CYS* 3.8 9.6 - - - -
47E ARG* 4.3 19.7 - - - -
185E ALA 4.7 2.3 + - - -
186E LYS 2.8 7.9 + - - -
187E TYR* 1.3 76.6 - - - +
189E LEU* 1.3 62.9 + - - +
190E PRO* 3.3 7.2 - - + -
191E TRP* 3.3 53.5 + + + -
192E LEU* 3.1 35.8 + - + +
295E PRO* 5.0 2.2 - - + -
296E LEU* 4.0 30.3 - - + -
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Residues in contact with LEU 189 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201D ILE* 4.8 17.7 - - + +
204D CYS* 4.1 27.1 - - + -
205D SER* 4.8 1.8 - - - +
208D MET* 5.1 2.2 - - + -
183E ARG 3.9 11.7 - - - +
184E MET* 3.8 22.4 - - + +
186E LYS* 3.0 42.7 + - + +
187E TYR* 4.3 15.3 - - + +
188E TRP* 1.3 77.0 - - - +
190E PRO* 1.4 64.2 - - + +
192E LEU* 4.5 3.4 - - + +
193E VAL* 2.8 43.0 + - + +
194E GLY 3.0 6.2 + - - -
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Residues in contact with PRO 190 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178E MET* 3.3 29.8 - - + +
179E GLN 3.7 22.2 - - - +
180E MET* 4.0 13.5 - - + +
184E MET* 2.9 27.1 - - + +
185E ALA* 5.3 1.1 - - - +
188E TRP* 3.4 7.9 - - - -
189E LEU 1.4 88.6 - - - +
191E TRP* 1.3 68.6 + - + +
194E GLY* 3.3 7.8 - - - +
195E MET 2.8 30.1 + - - -
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Residues in contact with TRP 191 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235D ARG* 3.0 26.1 + - - -
46E PHE* 4.7 14.8 - + - -
47E ARG* 4.7 17.6 - - - +
176E TRP* 4.0 24.7 - + - -
178E MET* 4.5 4.7 - - + -
180E MET* 3.5 32.1 - - + -
188E TRP* 3.3 54.6 + + + +
189E LEU 3.2 0.4 - - - -
190E PRO* 1.3 92.9 - - + +
192E LEU* 1.3 64.3 + - + +
193E VAL 3.4 0.4 + - - -
195E MET* 3.6 29.5 - - + +
196E PRO* 3.7 8.3 - - - +
296E LEU* 4.5 14.6 - - + -
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Residues in contact with LEU 192 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204D CYS* 5.9 0.2 - - - -
208D MET* 4.1 17.3 - - + -
232D THR* 5.0 2.6 - - - -
235D ARG* 3.6 30.4 - - + +
236D ILE* 4.1 30.1 - - + +
239D GLY* 3.7 26.5 - - - -
240D PHE 4.9 0.2 - - - +
247D CYS* 3.9 15.7 - - - -
187E TYR 3.5 22.4 - - - +
188E TRP* 3.1 27.9 + - + +
189E LEU* 4.4 3.1 - - + +
191E TRP* 1.3 82.8 - - - +
193E VAL* 1.3 66.5 + - + +
196E PRO* 3.6 6.1 - - - +
296E LEU* 4.6 8.3 - - + -
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Residues in contact with VAL 193 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197D ALA* 4.3 13.2 - - + +
200D THR* 3.9 31.2 - - + -
201D ILE* 3.9 28.3 - - + -
204D CYS* 4.1 18.4 - - - -
236D ILE* 4.4 2.9 - - + -
184E MET* 4.8 2.7 - - + -
189E LEU* 2.8 29.0 + - + +
192E LEU* 1.3 80.3 - - + +
194E GLY* 1.3 59.2 + - - +
196E PRO* 3.1 9.7 - - - +
197E ALA* 3.0 26.5 + - + +
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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