Contacts of the helix formed by residues 197 - 206 (chain A) in PDB entry 1PG2
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 PHE 197 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118A PHE* 3.6 47.3 - + - -
192A PHE* 3.6 19.3 - + - -
193A ASP 3.5 19.7 - - - -
194A LEU 2.9 11.3 + - - +
196A SER* 1.3 81.4 - - - +
198A SER* 1.3 64.8 + - - +
199A GLU 3.4 2.2 - - - -
200A MET* 3.3 28.3 + - + +
201A LEU* 2.9 29.3 + - + +
307A ALA* 3.5 43.5 - - + -
310A GLU* 4.0 8.1 - - + -
311A GLY* 3.6 15.7 - - - -
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Residues in contact with SER 198 (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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194A LEU 3.9 1.8 + - - -
195A PRO* 3.2 19.3 + - - +
196A SER 3.5 0.8 - - - -
197A PHE* 1.3 75.8 - - - +
199A GLU* 1.3 57.9 + - - +
201A LEU* 3.3 4.0 + - - +
202A GLN* 2.9 36.0 + - - +
222A PHE* 4.0 5.5 - - - -
226A LEU* 3.3 32.2 - - - +
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Residues in contact with GLU 199 (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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196A SER 5.4 0.6 + - - -
197A PHE 3.4 0.8 - - - -
198A SER* 1.3 78.8 - - - +
200A MET* 1.3 63.7 + - - +
202A GLN* 3.2 9.2 + - + +
203A ALA* 3.0 23.2 + - + +
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Residues in contact with MET 200 (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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197A PHE* 3.3 22.9 + - + +
199A GLU* 1.3 79.0 + - - +
201A LEU* 1.3 84.4 + - + +
203A ALA* 3.3 7.0 + - - +
204A TRP* 2.9 26.6 + - - +
306A PRO 4.3 2.2 - - - +
307A ALA* 4.5 0.2 - - - -
310A GLU* 3.6 47.6 - - + +
316A LYS* 3.6 32.3 - - + +
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Residues in contact with LEU 201 (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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194A LEU* 3.9 27.6 - - + -
197A PHE* 2.9 24.9 + - + +
198A SER 3.7 3.4 - - - +
200A MET* 1.3 93.3 - - + +
202A GLN* 1.3 54.5 + - - +
204A TRP* 3.7 7.5 - - + +
205A THR* 2.7 43.4 + - - +
222A PHE* 3.7 11.9 - - + -
226A LEU* 4.0 11.7 - - + -
302A SER 4.0 10.5 - - - +
303A LEU* 3.9 23.6 - - + +
306A PRO* 3.9 24.9 - - + -
307A ALA 4.4 1.3 - - - +
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Residues in contact with GLN 202 (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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198A SER* 2.9 20.1 + - - +
199A GLU* 3.4 12.6 - - + +
201A LEU* 1.3 77.1 - - - +
203A ALA* 1.3 62.7 + - - +
205A THR* 3.4 1.9 + - - -
206A ARG* 2.9 77.3 + - - +
219A GLN* 3.1 16.9 - - - +
222A PHE* 3.3 40.7 - - + +
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Residues in contact with ALA 203 (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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199A GLU* 3.0 13.6 + - + +
200A MET* 3.6 10.3 - - + +
202A GLN* 1.3 76.6 - - - +
204A TRP* 1.3 59.6 + - - +
206A ARG* 3.2 15.1 + - - +
207A SER* 2.8 20.6 + - - -
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Residues in contact with TRP 204 (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 MET* 2.9 19.0 + - - +
201A LEU* 3.7 9.4 - - + +
203A ALA* 1.3 75.8 - - - +
205A THR* 1.3 78.3 + - - +
207A SER* 3.2 22.7 + - - -
209A ALA* 5.5 4.3 - - - +
210A LEU* 4.5 21.5 - - + +
218A MET* 4.6 1.1 - - + -
301A HIS 4.6 0.2 - - - -
302A SER* 3.6 27.1 - - - -
306A PRO* 3.7 22.7 - - + -
316A LYS* 3.6 34.4 - - + +
317A PRO* 3.3 42.1 + - + -
318A SER 5.1 5.8 + - - -
319A ASN 5.3 0.4 - - - -
320A LEU* 4.6 19.3 - - + -
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Residues in contact with THR 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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201A LEU 2.7 26.2 + - - -
202A GLN* 3.5 6.3 - - - +
204A TRP* 1.3 77.7 - - - +
206A ARG* 1.3 59.1 + - + +
207A SER 3.2 3.7 + - - -
208A GLY 4.5 2.9 + - - -
209A ALA 5.1 0.2 + - - -
210A LEU* 4.2 24.3 + - + +
215A ALA* 4.3 28.9 - - + +
218A MET* 3.1 44.1 - - + +
219A GLN* 4.5 9.0 - - - +
222A PHE* 3.6 10.8 - - + -
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Residues in contact with ARG 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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202A GLN* 2.9 56.1 + - - +
203A ALA* 3.2 8.7 + - - +
205A THR* 1.3 76.2 - - + +
207A SER* 1.3 55.4 + - - +
208A GLY 3.2 9.9 + - - -
219A GLN* 3.4 27.6 + - - +
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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