Contacts of the helix formed by residues 189 - 199 (chain A) in PDB entry 3QI5
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 GLY 189 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115A THR* 5.1 3.1 - - - -
116A GLU 4.2 5.2 - - - -
117A LEU* 3.4 16.4 - - - +
188A GLU* 1.3 80.5 - - - +
190A LEU* 1.3 64.4 + - - +
191A GLU 3.3 3.1 - - - -
192A THR* 3.3 8.1 + - - -
193A MET* 3.1 24.4 + - - +
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Residues in contact with LEU 190 (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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186A PRO* 3.8 35.7 - - + +
187A LEU 3.7 8.5 - - - +
188A GLU* 3.6 28.7 - - - +
189A GLY* 1.3 78.1 - - - +
191A GLU* 1.3 57.9 + - + +
193A MET* 3.4 9.6 + - - +
194A ARG* 3.0 36.7 + - - +
211A ASP* 3.8 30.1 - - - +
214A LEU* 4.1 9.9 - - + +
284A TRP* 6.2 0.7 - - + -
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Residues in contact with GLU 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A GLY 3.3 0.8 - - - -
190A LEU* 1.3 75.2 - - + +
192A THR* 1.3 64.2 + - - +
194A ARG* 2.9 40.5 + - - +
195A GLN* 3.2 35.1 + - - +
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Residues in contact with THR 192 (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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111A LEU* 3.6 30.5 - - + -
113A ASN* 5.6 3.1 - - - +
115A THR* 3.8 15.8 + - + +
117A LEU* 3.9 8.7 - - + -
189A GLY* 3.3 11.5 + - - -
191A GLU* 1.3 75.4 - - - +
193A MET* 1.3 61.1 + - - +
195A GLN* 3.2 15.9 + - + +
196A LEU* 2.9 39.7 + - + +
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Residues in contact with MET 193 (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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117A LEU* 4.2 12.8 - - + -
118A ARG 3.5 26.5 - - - +
119A GLY* 5.1 0.2 - - - -
186A PRO* 3.8 26.7 - - + -
188A GLU 3.6 15.3 - - - +
189A GLY 3.1 14.9 + - - +
190A LEU* 3.4 13.2 - - - +
192A THR* 1.3 77.6 - - - +
194A ARG* 1.3 55.7 + - - +
196A LEU* 3.3 2.3 + - - +
197A ARG* 2.9 34.3 + - - +
214A LEU* 4.2 11.0 - - + -
215A CYS* 4.0 15.9 - - - -
224A ALA* 3.5 28.9 - - + +
225A LEU* 4.0 19.5 - - + -
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Residues in contact with ARG 194 (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 LEU* 3.0 29.6 + - - +
191A GLU* 2.9 42.1 + - - +
192A THR 3.3 0.2 - - - -
193A MET* 1.3 72.7 - - - +
195A GLN* 1.3 56.7 + - + +
197A ARG* 4.0 2.0 - - - +
198A SER* 2.7 40.2 + - - +
208A VAL* 4.6 10.9 - - - +
209A LEU* 2.7 52.0 + - + +
210A LYS 4.1 0.6 - - - -
211A ASP* 3.1 29.3 + - - +
214A LEU* 3.8 18.4 - - + +
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Residues in contact with GLN 195 (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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191A GLU* 3.2 22.6 + - - +
192A THR* 3.2 17.0 + - + +
194A ARG* 1.3 75.4 - - + +
196A LEU* 1.3 62.6 + - + +
198A SER* 4.2 0.2 - - - -
199A THR* 2.5 59.3 + - + +
200A LEU* 3.4 1.1 + - - -
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Residues in contact with LEU 196 (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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111A LEU* 4.7 4.5 - - + -
117A LEU* 4.3 5.4 - - + -
192A THR* 2.9 37.4 + - + +
193A MET 3.7 4.0 - - - +
195A GLN* 1.3 76.3 - - + +
197A ARG* 1.3 60.2 + - - +
200A LEU* 3.7 43.8 - - + +
201A ARG* 4.7 1.9 + - - +
223A GLN* 3.3 31.1 - - - +
224A ALA* 3.4 22.0 - - - +
226A ALA* 4.3 23.8 - - + -
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Residues in contact with ARG 197 (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 MET 2.9 20.7 + - - +
194A ARG* 4.1 2.5 - - - +
196A LEU* 1.3 78.5 - - - +
198A SER* 1.3 57.3 + - - +
201A ARG 3.3 13.8 + - - +
209A LEU* 3.7 23.8 - - + +
213A GLU* 2.8 28.5 + - - +
214A LEU* 3.2 26.4 + - + +
220A LYS* 3.2 36.7 - - - +
223A GLN* 2.9 29.6 + - - +
224A ALA* 3.8 10.8 - - + -
9C T 4.4 0.8 + - - -
10C G 2.7 44.2 + - - -
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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 ARG* 2.7 24.2 + - - +
195A GLN* 3.2 0.4 + - - -
197A ARG* 1.3 79.6 - - - +
199A THR* 1.3 78.4 + - - +
200A LEU 3.3 2.0 - - - -
201A ARG 3.1 18.2 + - - +
202A LYS 3.8 10.4 - - - -
209A LEU* 3.8 19.3 - - - -
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Residues in contact with THR 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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195A GLN* 2.5 53.4 + - + +
198A SER* 1.3 85.1 + - - +
200A LEU* 1.3 70.9 + - - +
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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