Contacts of the helix formed by residues 199 - 214 (chain A) in PDB entry 1QGI
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 GLU 199 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160A GLY 5.0 0.7 - - - +
161A PHE* 3.4 42.8 - - + +
162A THR 4.3 1.9 + - - -
163A SER* 2.8 31.9 + - - -
166A THR* 2.7 30.9 + - - +
197A SER 3.6 5.3 + - - -
198A ASN* 1.3 71.5 - - - +
200A LYS* 1.3 58.0 + - - +
202A PHE* 3.8 0.9 - - - +
203A MET* 3.0 35.4 + - + +
241A MET* 3.8 11.9 - - + -
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Residues in contact with LYS 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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198A ASN* 3.3 12.3 - - - +
199A GLU* 1.3 77.7 - - - +
201A THR* 1.3 59.7 + - - +
203A MET* 3.4 2.3 + - - +
204A LYS* 2.9 41.3 + - + +
236A VAL* 3.6 38.2 + - + +
237A ASP* 4.5 17.7 + - - +
239A GLY* 6.2 0.6 - - - -
241A MET* 4.6 9.8 - - + +
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Residues in contact with THR 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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196A SER* 3.4 22.9 - - - +
198A ASN* 2.8 26.4 + - - +
200A LYS* 1.3 72.8 - - - +
202A PHE* 1.3 66.2 + - - +
204A LYS* 3.2 8.5 + - - +
205A ASN* 3.0 42.2 + - - +
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Residues in contact with PHE 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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159A ARG* 3.9 19.5 - - - -
161A PHE* 3.6 25.1 - + + -
170A PHE* 4.0 13.2 - + - -
190A LEU* 3.8 33.4 - - + -
193A SER* 3.8 23.5 - - - +
194A GLY 3.6 22.7 - - - -
195A SER* 5.0 1.1 - - - -
196A SER* 3.9 22.4 + - - +
198A ASN 2.9 18.1 + - - +
199A GLU 3.8 3.6 - - - +
201A THR* 1.3 75.4 - - - +
203A MET* 1.3 68.5 + - - +
205A ASN* 3.1 10.9 + - - +
206A PHE* 2.8 34.0 + - + -
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Residues in contact with MET 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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161A PHE* 5.7 0.2 - - + -
165A VAL* 4.6 1.6 - - + +
166A THR* 3.5 36.8 - - - +
169A SER* 3.6 35.2 - - - +
170A PHE* 3.7 22.9 - - + -
199A GLU* 3.0 23.9 + - + +
200A LYS* 3.9 4.3 - - - +
202A PHE* 1.3 83.8 - - + +
204A LYS* 1.3 59.0 + - - +
206A PHE* 3.6 11.5 - - + +
207A HIS* 2.9 48.5 + - + +
236A VAL* 4.3 17.9 - - + -
241A MET* 4.9 4.0 - - + -
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Residues in contact with LYS 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 LYS* 2.9 32.4 + - + +
201A THR* 3.6 7.6 - - - +
203A MET* 1.3 75.9 - - - +
205A ASN* 1.3 65.0 + - - +
207A HIS* 3.5 2.1 + - - +
208A ALA* 3.1 23.4 + - - +
233A ASP* 2.8 37.2 + - - +
236A VAL* 4.0 13.7 - - + -
237A ASP* 2.7 33.5 + - - +
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Residues in contact with ASN 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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193A SER* 3.7 22.1 + - - +
194A GLY* 5.8 0.8 - - - -
196A SER* 4.8 5.5 - - - -
201A THR* 3.0 37.4 + - - +
202A PHE* 3.4 8.9 - - - +
204A LYS* 1.3 76.4 - - - +
206A PHE* 1.3 65.6 + - - +
208A ALA* 3.1 8.7 + - - +
209A LYS* 3.0 30.6 + - + +
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Residues in contact with PHE 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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169A SER* 3.8 13.9 - - - -
170A PHE* 4.0 12.3 - + - -
173A THR* 3.5 30.7 - - + -
186A LEU* 3.9 24.9 - - + -
189A LEU* 3.8 24.9 - - + -
190A LEU* 4.0 15.5 - - + -
193A SER* 3.4 25.3 + - - +
202A PHE* 2.8 26.1 + - + +
203A MET* 3.6 17.0 - - + +
205A ASN* 1.3 73.3 - - - +
207A HIS* 1.3 71.5 + + - +
209A LYS* 3.2 4.2 + - - +
210A ARG* 2.9 32.8 + - - +
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Residues in contact with HIS 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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165A VAL* 5.2 0.4 - - + -
169A SER* 2.9 28.2 + - - -
203A MET* 2.9 28.5 + - + +
204A LYS 3.8 2.0 - - - +
206A PHE* 1.3 86.3 - + - +
208A ALA* 1.3 56.2 + - - +
210A ARG* 3.7 8.0 - - + +
211A THR* 2.9 34.3 + - - -
229A VAL* 3.8 16.3 - - + +
232A TRP* 3.5 17.3 - - + +
233A ASP* 2.8 57.8 + - + +
236A VAL* 3.8 14.1 - - + -
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Residues in contact with ALA 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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204A LYS 3.1 14.5 + - - +
205A ASN* 3.1 11.6 + - - +
207A HIS* 1.3 76.2 - - - +
209A LYS* 1.3 66.0 + - + +
211A THR* 3.3 14.7 + - - -
212A LEU* 3.6 17.4 + - - +
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Residues in contact with LYS 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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189A LEU* 3.8 21.7 - - + +
192A ARG* 3.7 40.3 + - + +
193A SER* 4.4 10.8 - - - +
205A ASN* 3.0 19.6 + - - +
206A PHE 3.7 6.1 - - - +
208A ALA* 1.3 75.7 - - - +
210A ARG* 1.3 67.2 + - - +
212A LEU* 3.2 35.7 + - + +
213A VAL* 4.0 3.3 + - - +
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Residues in contact with ARG 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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169A SER* 4.4 3.2 + - - -
172A ASP* 2.9 36.1 + - - +
173A THR* 3.4 31.6 + - - +
176A ASN* 3.1 36.8 - - - +
177A GLN* 2.8 20.6 + - - +
189A LEU* 4.0 21.9 - - + +
206A PHE* 2.9 24.3 + - + +
207A HIS* 3.7 9.8 - - - +
209A LYS* 1.3 78.5 - - - +
211A THR* 1.3 57.6 + - - +
212A LEU 3.1 0.7 + - - -
213A VAL* 3.1 3.1 + - - +
214A VAL* 2.9 34.2 + - + +
228A ARG* 3.7 6.0 - - - +
229A VAL* 4.1 26.8 - - + +
232A TRP* 4.8 4.8 - - - -
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Residues in contact with THR 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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207A HIS 2.9 21.7 + - - -
208A ALA* 3.6 9.3 - - - -
209A LYS 3.2 0.6 - - - -
210A ARG* 1.3 76.9 - - - +
212A LEU* 1.3 63.8 + - + +
213A VAL 3.4 0.5 + - - -
214A VAL* 3.6 18.6 + - + +
215A ASP* 4.6 4.7 + - - +
226A LYS* 4.8 25.2 + - + -
229A VAL* 3.2 19.1 - - - +
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Residues in contact with LEU 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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208A ALA 3.6 15.7 - - - +
209A LYS* 3.5 30.3 - - + +
210A ARG 3.1 0.8 - - - -
211A THR* 1.3 83.0 - - + +
213A VAL* 1.3 64.9 + - + +
215A ASP 5.3 0.6 + - - -
216A THR* 5.1 0.9 + - - -
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Residues in contact with VAL 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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177A GLN* 3.8 20.4 - - - +
184A ASP* 3.5 35.0 - - + +
189A LEU* 4.2 17.3 - - + -
192A ARG* 4.6 9.9 - - - +
209A LYS 4.3 0.9 - - - +
210A ARG 3.7 7.6 - - - +
212A LEU* 1.3 83.2 - - + +
214A VAL* 1.3 68.4 + - - +
215A ASP 3.3 3.4 - - - -
216A THR* 3.0 28.5 + - - +
219A TYR* 3.4 7.4 - - + -
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Residues in contact with VAL 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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177A GLN* 3.5 24.2 - - - +
210A ARG* 2.9 24.2 + - - +
211A THR* 3.6 22.0 - - - +
213A VAL* 1.3 78.1 - - - +
215A ASP* 1.3 62.3 + - - +
216A THR 3.2 3.5 + - - -
219A TYR* 3.6 9.6 - - - +
220A ASN* 3.1 35.7 - - - +
225A GLY* 3.4 33.2 - - - +
226A LYS* 3.6 5.4 - - - +
228A ARG* 4.4 1.1 - - - -
229A VAL* 3.8 14.4 - - + -
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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