Contacts of the helix formed by residues 204 - 217 (chain A) in PDB entry 3MTG
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 SER 204 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179A ILE* 4.0 4.2 - - - +
202A GLY 4.2 0.2 + - - -
203A GLU* 1.3 75.1 - - - +
205A GLU* 1.3 64.5 + - - +
206A ASP* 3.7 8.5 + - - +
207A ASP* 3.1 33.0 + - - -
208A PHE* 3.1 23.2 + - - +
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Residues in contact with GLU 205 (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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179A ILE* 5.1 12.1 - - + +
204A SER* 1.3 73.4 - - - +
206A ASP* 1.3 65.6 + - - +
208A PHE* 3.5 13.5 - - + +
209A TRP* 3.0 32.9 - - + +
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Residues in contact with ASP 206 (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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204A SER* 3.2 7.4 + - - +
205A GLU* 1.3 82.2 + - - +
207A ASP* 1.4 64.5 + - - +
209A TRP* 3.5 6.7 + - - +
210A TRP* 3.4 19.9 + - - +
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Residues in contact with ASP 207 (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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200A TRP* 3.9 22.4 + - + -
202A GLY 4.9 1.6 - - - +
203A GLU* 3.8 14.8 - - + -
204A SER* 3.1 34.6 + - - +
206A ASP* 1.4 75.9 - - - +
208A PHE* 1.3 62.5 + - - +
210A TRP* 3.2 18.6 + - - +
211A CYS* 3.3 21.0 + - - -
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Residues in contact with PHE 208 (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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151A CYS* 5.2 0.7 - - - -
175A SER* 4.7 0.6 + - - -
176A ALA 3.2 26.9 - - - -
177A CYS* 3.8 22.0 - - - -
178A ASN* 4.9 1.6 - - - -
179A ILE* 3.8 21.3 - - + -
203A GLU* 3.6 16.8 + - - -
204A SER 3.1 13.3 + - - +
205A GLU* 3.5 12.6 - - + +
207A ASP* 1.3 76.7 - - - +
209A TRP* 1.3 100.0 + + - +
211A CYS* 3.9 2.8 + - - +
212A ILE* 3.5 39.8 + - + +
232A ASP* 4.2 17.5 - - + -
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Residues in contact with TRP 209 (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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205A GLU* 3.0 28.9 + - + +
206A ASP* 3.5 6.9 + - - +
207A ASP 3.3 0.4 - - - -
208A PHE* 1.3 95.7 - + - +
210A TRP* 1.3 59.5 + - - +
211A CYS 3.5 0.2 - - - -
212A ILE* 3.8 22.6 - - + +
213A ASP* 3.2 26.2 + - - +
232A ASP* 3.5 47.6 - - + -
235A HIS* 6.3 2.5 - + + -
236A TRP* 3.7 44.0 - + + -
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Residues in contact with TRP 210 (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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106A CYS* 4.1 33.4 - - + -
198A PHE* 4.8 2.2 - + - -
200A TRP* 4.4 6.5 - + - -
206A ASP 3.4 12.8 + - - +
207A ASP* 3.2 14.1 + - - +
209A TRP* 1.3 76.5 - - - +
211A CYS* 1.4 85.5 + - - +
213A ASP* 3.5 5.3 + - - +
214A ARG* 2.9 77.0 + - + +
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Residues in contact with CYS 211 (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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175A SER* 4.0 10.5 - - - +
176A ALA 5.6 0.4 - - - +
198A PHE* 3.3 30.0 - - + +
200A TRP* 3.7 22.0 - - - -
203A GLU* 4.4 11.7 - - - +
207A ASP 3.3 17.9 + - - +
208A PHE 4.2 3.8 - - - +
210A TRP* 1.4 91.7 - - - +
212A ILE* 1.4 65.0 + - - +
214A ARG* 3.1 15.0 + - - +
215A CYS* 3.2 19.1 + - - -
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Residues in contact with ILE 212 (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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151A CYS* 4.2 14.4 - - - -
175A SER* 3.4 24.0 - - - +
208A PHE* 3.5 47.6 + - + +
209A TRP* 3.8 24.5 - - + +
210A TRP 3.5 0.2 - - - -
211A CYS* 1.4 77.6 - - - +
213A ASP* 1.3 62.5 + - - +
215A CYS* 3.2 12.8 + - - +
216A VAL* 3.2 13.9 - - - +
232A ASP* 4.7 0.4 - - + -
233A LEU* 3.8 24.6 - - + +
236A TRP* 3.6 34.8 - - + +
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Residues in contact with ASP 213 (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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209A TRP 3.2 20.9 + - - +
210A TRP* 3.7 6.1 - - - +
212A ILE* 1.3 74.9 - - - +
214A ARG* 1.4 63.4 + - - +
216A VAL* 3.2 2.9 + - - -
217A ASN* 3.0 49.0 + - - +
236A TRP* 3.0 40.0 + - + +
240A LYS* 4.5 1.7 - - - +
241A TYR* 2.6 21.8 + - - -
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Residues in contact with ARG 214 (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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103A SER 5.6 1.0 + - - -
104A ASN* 3.8 13.7 + - - +
105A PHE 5.2 1.2 + - - +
106A CYS* 5.3 1.8 - - - +
173A ARG* 2.6 30.0 + - - +
198A PHE* 3.3 43.0 - - + -
210A TRP* 2.9 61.2 + - + +
211A CYS* 3.1 12.5 + - - +
213A ASP* 1.4 74.8 - - - +
215A CYS* 1.4 51.6 + - - +
217A ASN* 3.1 24.8 + - - +
218A MET* 5.5 3.8 - - - +
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Residues in contact with CYS 215 (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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149A VAL* 3.2 30.0 - - + +
150A GLY 4.1 1.8 - - - -
173A ARG* 3.2 41.3 + - - +
174A TRP 3.3 28.7 - - - -
175A SER* 3.7 9.6 - - - -
198A PHE* 4.4 4.3 - - - -
211A CYS 3.2 15.7 + - - -
212A ILE 3.3 9.6 - - - +
214A ARG* 1.4 77.7 - - - +
216A VAL* 1.3 61.3 + - - +
217A ASN 4.8 0.2 - - - +
221A TRP* 3.6 11.6 + - - -
233A LEU* 4.7 2.5 - - + -
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Residues in contact with VAL 216 (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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149A VAL* 4.4 8.6 - - + +
212A ILE 3.2 16.8 - - - +
213A ASP 3.2 4.4 + - - +
215A CYS* 1.3 76.6 - - - +
217A ASN* 1.4 57.9 + - - +
221A TRP* 4.0 17.5 - - - +
222A GLN* 5.5 0.2 - - - -
223A ALA* 5.3 5.9 + - + +
233A LEU* 4.4 7.6 - - + -
236A TRP* 3.7 25.4 - - + +
237A VAL* 3.9 28.9 - - + -
241A TYR* 3.4 34.5 - - + -
244A VAL* 4.8 12.9 - - + +
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Residues in contact with ASN 217 (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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213A ASP* 3.0 41.0 + - - +
214A ARG* 3.1 25.3 + - - +
215A CYS 4.9 0.2 - - - -
216A VAL* 1.4 76.5 - - - +
218A MET* 1.3 61.9 + - - +
221A TRP 5.2 1.1 - - - -
241A TYR* 3.3 29.6 + - + +
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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