Contacts of the helix formed by residues 203 - 212 (chain M) in PDB entry 4G7Z
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 ASP 203 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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198M ARG* 3.5 20.6 + - - +
201M GLY 3.9 1.9 + - - +
202M TYR* 1.3 75.5 - - - +
204M GLN* 1.3 68.1 + - - +
205M GLU* 3.0 16.7 + - - +
206M THR* 2.7 39.5 + - - +
207M LEU* 3.0 14.3 + - - +
228M ALA* 5.0 1.6 - - - +
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Residues in contact with GLN 204 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198M ARG* 5.1 1.0 - - - +
203M ASP* 1.3 80.0 + - - +
205M GLU* 1.3 59.1 + - - +
207M LEU* 4.2 5.6 - - - +
208M ALA* 3.5 21.7 + - - +
222M MET* 3.5 41.0 + - + +
225M SER* 3.9 22.4 + - - -
228M ALA* 3.9 23.3 - - + +
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Residues in contact with GLU 205 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203M ASP* 2.8 15.0 + - - +
204M GLN* 1.3 76.4 - - - +
206M THR* 1.3 65.7 + - - +
207M LEU 3.2 1.8 - - - -
208M ALA* 3.2 12.4 + - - +
209M ARG* 2.7 62.9 + - + +
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Residues in contact with THR 206 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201M GLY 5.0 4.2 + - - +
202M TYR* 4.0 24.4 - - + -
203M ASP* 2.7 35.2 + - - +
205M GLU* 1.3 75.9 - - - +
207M LEU* 1.3 57.6 + - - +
209M ARG* 4.0 5.8 + - - +
210M GLU* 3.2 27.2 - - - +
304M LEU* 5.5 3.4 - - + +
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Residues in contact with LEU 207 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194M VAL* 5.2 2.2 - - + -
197M LEU* 3.8 26.0 - - + -
202M TYR* 3.7 38.4 - - + +
203M ASP 3.0 13.8 + - - +
204M GLN* 4.4 2.2 - - - +
206M THR* 1.3 76.6 - - - +
208M ALA* 1.3 62.3 + - - +
209M ARG 3.3 0.7 - - - -
211M LEU* 3.1 40.4 + - + +
212M GLY 3.8 0.5 + - - -
221M LEU* 3.7 28.7 - - + -
222M MET* 3.8 16.8 - - + +
304M LEU* 4.0 22.0 - - + -
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Residues in contact with ALA 208 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204M GLN 3.5 16.1 + - - +
205M GLU* 3.2 10.3 + - - +
207M LEU* 1.3 76.7 - - - +
209M ARG* 1.3 69.6 + - - +
212M GLY* 3.1 23.6 + - - +
218M VAL* 4.7 1.6 - - + -
222M MET* 3.5 18.4 - - + +
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Residues in contact with ARG 209 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205M GLU* 2.7 57.8 + - + +
206M THR* 4.3 4.7 - - - +
207M LEU 3.3 0.6 - - - -
208M ALA* 1.3 83.5 - - - +
210M GLU* 1.3 79.6 + - - +
212M GLY* 4.1 2.1 + - - -
213M ALA* 4.8 2.9 + - - +
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Residues in contact with GLU 210 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206M THR* 3.2 23.2 - - - +
207M LEU 4.1 0.4 + - - -
209M ARG* 1.3 86.7 - - - +
211M LEU* 1.3 62.7 + - + +
212M GLY 3.6 0.2 + - - -
213M ALA* 4.2 11.8 + - - +
214M TYR* 5.0 4.7 - - - -
304M LEU* 5.4 14.4 - - + +
308M ARG* 5.3 7.7 - - + +
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Residues in contact with LEU 211 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207M LEU* 3.1 23.5 + - + +
210M GLU* 1.3 76.4 - - + +
212M GLY* 1.3 61.8 + - - +
213M ALA 3.3 3.2 + - - -
214M TYR* 3.8 17.2 - - + -
218M VAL* 3.1 30.9 - - + +
221M LEU* 4.7 7.9 - - + -
304M LEU* 3.9 22.2 - - + -
307M LEU* 3.7 40.2 - - + +
308M ARG* 4.8 9.6 - - + +
311M PHE* 3.6 29.8 - - + -
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Residues in contact with GLY 212 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207M LEU 3.8 0.8 + - - -
208M ALA* 3.1 24.3 + - - -
210M GLU 3.4 0.8 - - - -
211M LEU* 1.3 75.5 - - - +
213M ALA* 1.3 63.8 + - - +
214M TYR 2.9 14.1 + - - +
215M GLY* 4.3 1.9 + - - -
218M VAL* 3.4 19.3 - - - +
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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