Contacts of the helix formed by residues 198 - 213 (chain A) in PDB entry 2IQ6
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 198 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A MET* 5.0 1.7 - - - +
197A THR* 1.3 72.1 - - - +
199A SER* 1.3 61.7 + - - +
200A ASN* 3.1 16.6 + - - +
201A PHE* 2.7 34.3 + - + +
202A THR* 2.8 34.1 + - - -
234A HIS* 5.7 1.6 - - + +
239A PRO* 3.9 16.6 - - + +
240A ALA 2.7 27.8 + - - +
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Residues in contact with SER 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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197A THR* 3.9 2.8 + - - -
198A ASP* 1.3 72.1 + - - +
200A ASN* 1.3 67.7 + - - +
202A THR* 3.8 6.2 - - - -
203A GLN* 2.8 38.7 + - - +
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Residues in contact with ASN 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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1A MET* 3.8 17.8 - - + +
198A ASP* 3.1 14.3 + - - +
199A SER* 1.3 85.9 + - - +
201A PHE* 1.3 64.1 + - - +
203A GLN* 3.9 3.9 - - - +
204A TYR* 3.0 23.4 + - - +
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Residues in contact with PHE 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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1A MET* 3.9 18.1 - - - +
174A SER* 3.7 17.9 - - - -
175A ALA 3.5 23.8 - - - -
176A LEU* 4.1 5.6 - - + -
198A ASP* 2.7 25.6 + - + +
200A ASN* 1.3 73.4 - - - +
202A THR* 1.3 63.0 + - - +
204A TYR* 3.2 14.0 + + - +
205A LEU* 3.0 41.2 + - + +
239A PRO* 3.9 13.9 - - + -
240A ALA 3.6 10.3 - - - -
241A ALA* 3.5 22.4 - - + -
282A TYR* 3.5 37.7 - + - -
286A MET* 5.5 0.2 - - + -
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Residues in contact with THR 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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192A PHE* 3.6 36.3 - - + -
193A ILE 4.7 4.0 + - - +
194A THR* 5.4 4.0 - - + -
197A THR* 3.9 11.8 + - - -
198A ASP 2.8 26.2 + - - -
199A SER* 3.8 7.6 - - - -
201A PHE* 1.3 77.4 - - - +
203A GLN* 1.3 62.5 + - - +
205A LEU* 3.1 15.8 + - - +
206A THR* 3.2 12.1 + - - +
220A PHE* 4.1 15.7 - - + -
241A ALA* 3.9 18.5 - - + +
242A MET 5.3 0.4 + - - +
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Residues in contact with GLN 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 SER* 2.8 28.3 + - - +
200A ASN* 3.9 4.5 - - - +
202A THR* 1.3 73.7 - - - +
204A TYR* 1.3 62.1 + - - +
206A THR* 2.4 37.5 + - - +
207A GLN* 3.2 21.7 + - - +
220A PHE* 3.7 26.4 - - - -
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Residues in contact with TYR 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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1A MET* 3.6 28.7 - - + -
2A PRO* 3.2 25.6 + - + +
3A PRO 5.3 0.7 + - - -
4A ILE* 5.0 7.6 - - + +
200A ASN 3.0 13.9 + - - +
201A PHE* 3.2 24.0 - + - +
203A GLN* 1.3 76.9 - - - +
205A LEU* 1.3 69.4 + - + +
207A GLN* 3.0 32.2 + - + +
208A LEU* 3.1 37.5 + - + +
282A TYR* 4.6 0.7 - + - -
285A GLU* 3.3 30.8 + - - +
286A MET* 3.7 32.3 + - + +
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Residues in contact with LEU 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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176A LEU* 3.5 29.6 - - + -
192A PHE* 3.7 26.9 - - + -
201A PHE* 3.0 34.5 + - + +
202A THR* 3.1 7.6 + - - +
204A TYR* 1.3 79.1 - - + +
206A THR* 1.3 61.2 - - - +
208A LEU* 3.2 28.7 + - + +
209A MET* 3.0 24.6 + - - +
241A ALA* 3.7 22.0 - - + -
243A PRO* 4.3 2.7 - - + -
278A LEU* 3.9 9.8 - - + +
282A TYR* 4.2 14.4 - - + -
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Residues in contact with THR 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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192A PHE* 3.7 23.1 - - + -
202A THR 3.4 13.9 - - - +
203A GLN* 2.4 40.3 + - - +
205A LEU* 1.3 77.6 - - - +
207A GLN* 1.3 60.1 + - - +
209A MET* 3.3 7.0 + - - +
210A ASP* 2.9 34.0 + - - +
218A TYR* 3.6 28.8 + - + -
220A PHE* 3.8 18.2 - - + -
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Residues in contact with GLN 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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4A ILE* 3.7 16.7 - - + +
203A GLN* 3.4 29.0 + - - +
204A TYR* 3.0 23.4 + - + +
206A THR* 1.3 79.5 + - - +
208A LEU* 1.3 64.5 + - - +
210A ASP* 3.1 13.0 + - - +
211A GLU* 2.9 26.3 + - - +
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Residues in contact with LEU 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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4A ILE* 4.1 13.0 - - + -
204A TYR* 3.1 44.6 + - + +
205A LEU* 3.2 33.6 + - + +
207A GLN* 1.3 76.4 - - - +
209A MET* 1.3 54.4 + - - +
212A TYR* 2.7 54.8 + - + +
213A LEU* 5.8 0.4 - - - -
278A LEU* 4.1 11.4 - - + +
281A ALA* 4.4 3.1 - - + +
282A TYR* 3.8 25.8 - - + +
285A GLU* 3.9 21.1 - - + -
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Residues in contact with MET 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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190A VAL* 3.7 30.5 - - + -
192A PHE* 3.8 23.6 - - - -
205A LEU 3.0 13.9 + - - +
206A THR 3.5 8.7 - - - +
207A GLN 3.1 0.2 - - - -
208A LEU* 1.3 75.5 - - - +
210A ASP* 1.3 61.3 + - - +
213A LEU* 2.8 49.9 + - + +
214A PRO* 3.9 0.2 - - - +
216A LEU* 3.7 35.7 - - + +
217A THR 4.3 1.6 - - - +
218A TYR* 3.7 33.2 - - + -
278A LEU* 3.9 17.3 - - + -
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Residues in contact with ASP 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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206A THR* 2.9 19.6 + - - +
207A GLN* 3.1 16.9 + - - +
209A MET* 1.3 77.1 - - - +
211A GLU* 1.3 61.2 + - - +
214A PRO* 3.8 19.3 - - - +
218A TYR* 2.9 30.1 + - - -
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Residues in contact with GLU 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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4A ILE* 3.6 23.4 - - + +
7A GLN* 3.8 22.0 - - - +
207A GLN 2.9 15.9 + - - +
208A LEU 3.8 1.8 - - - +
210A ASP* 1.3 81.4 - - - +
212A TYR* 1.3 87.5 + - + +
214A PRO* 4.0 7.2 - - - +
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Residues in contact with TYR 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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4A ILE* 3.1 25.9 - - + +
7A GLN* 3.3 25.2 + - + -
10A VAL* 3.4 37.1 - - + +
11A THR* 4.1 16.2 - - + -
14A LEU* 3.7 21.7 - - + +
208A LEU* 2.7 40.2 + - + +
211A GLU* 1.3 84.9 - - + +
213A LEU* 1.3 68.2 + - + +
214A PRO* 3.2 11.0 - - - +
281A ALA* 3.8 15.0 - - + -
285A GLU* 2.6 28.0 + - + -
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Residues in contact with LEU 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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14A LEU* 4.0 12.3 - - + -
190A VAL* 6.3 0.4 - - + -
209A MET* 2.8 37.8 + - + +
212A TYR* 1.3 87.7 - - + +
214A PRO* 1.3 63.7 - - - +
215A SER* 3.3 2.9 - - - -
216A LEU* 3.1 45.7 + - + +
274A LYS 3.8 22.0 - - - +
277A GLN* 3.8 26.0 - - + +
278A LEU* 4.0 23.1 - - + +
281A ALA* 6.4 0.2 - - + -
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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