Contacts of the helix formed by residues 191 - 205 (chain A) in PDB entry 3QKL
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 191 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A SMR 3.8 17.3 - - + +
161A PHE* 3.4 36.1 - - + -
186A ILE* 2.7 30.6 + - + +
189A LYS* 4.0 13.0 - - + +
190A ASP* 1.3 72.4 - - - +
192A VAL* 1.3 64.0 + - - +
193A ALA 3.4 2.5 - - - -
194A HIS* 2.7 47.0 + - - +
195A THR* 3.0 22.5 + - - -
8C PHE* 5.7 1.4 - - - -
9C ALA* 5.2 6.2 + - - +
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Residues in contact with VAL 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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186A ILE* 3.8 20.2 - - + +
187A VAL* 4.0 25.1 - - + +
190A ASP* 3.4 6.2 - - - +
191A GLU* 1.3 77.8 - - - +
193A ALA* 1.3 63.2 + - - +
195A THR* 3.3 4.3 + - - -
196A LEU* 3.1 34.3 + - + +
467A PRO* 5.7 2.0 - - + -
469A PHE* 3.8 27.5 - - + -
470A PRO* 6.2 1.8 - - + -
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Residues in contact with ALA 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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190A ASP 5.0 2.2 + - - +
191A GLU 3.4 0.2 - - - -
192A VAL* 1.3 79.8 - - - +
194A HIS* 1.3 62.8 + - + +
196A LEU* 3.4 8.6 + - - +
197A THR* 2.9 35.0 + - - +
200A ARG* 4.7 1.0 + - - -
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Residues in contact with HIS 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A SMR 4.7 4.7 - - + -
190A ASP 4.9 7.4 + - - -
191A GLU* 2.7 45.3 + - - +
193A ALA* 1.3 78.9 - - + +
195A THR* 1.3 54.3 + - - +
197A THR* 3.2 3.4 + - - -
198A GLU* 2.7 32.9 + - - +
294A GLY* 3.3 37.8 - - - +
295A LEU* 4.0 12.5 - - + +
308A TPO 5.8 4.4 + - - +
9C ALA* 3.6 32.0 - - + +
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Residues in contact with THR 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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1A SMR 3.6 19.0 - - - +
181A LEU* 4.3 4.3 - - + -
186A ILE* 3.8 12.8 - - - +
191A GLU 3.0 14.2 + - - -
192A VAL 3.7 7.2 - - - -
194A HIS* 1.3 74.6 - - - +
196A LEU* 1.3 58.7 + - - +
198A GLU* 3.4 6.9 + - - +
199A ASN* 3.0 27.3 + - - +
223A LEU* 3.6 26.9 - - + -
225A PHE* 3.7 25.5 - - + -
469A PHE* 4.4 8.3 - - + -
472A PHE* 3.9 6.3 - - + -
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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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192A VAL* 3.1 32.7 + - + +
193A ALA* 3.9 7.2 - - - +
194A HIS 3.3 0.2 - - - -
195A THR* 1.3 72.6 - - - +
197A THR* 1.3 60.2 + - - +
199A ASN* 3.4 5.8 + - - +
200A ARG* 3.1 49.1 + - - +
469A PHE* 3.8 26.5 - - + -
470A PRO* 4.1 33.7 - - + +
471A GLN 5.6 0.4 - - - -
472A PHE* 4.0 18.8 - - + -
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Residues in contact with THR 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 ALA* 2.9 21.9 + - - +
194A HIS* 3.5 8.0 - - - -
196A LEU* 1.3 74.1 - - - +
198A GLU* 1.3 69.0 + - - +
200A ARG* 3.2 22.6 + - - +
201A VAL* 2.9 24.5 + - + +
293A PHE 3.8 12.8 - - - +
294A GLY 4.3 3.4 - - - +
296A CYS* 3.6 30.3 - - + +
298A GLU* 4.0 14.8 + - + +
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Residues in contact with GLU 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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1A SMR 5.5 5.6 - - + +
179A LYS* 2.7 33.0 + - - -
181A LEU* 5.6 0.3 - - - +
194A HIS 2.7 18.2 + - - +
195A THR* 3.7 7.1 - - - +
197A THR* 1.3 72.1 - - - +
199A ASN* 1.3 58.0 + - - +
201A VAL* 3.8 1.0 - - - +
202A LEU* 2.9 49.5 + - + +
225A PHE* 4.2 11.6 - - + -
227A MET* 5.2 2.6 - - - +
292A ASP* 3.2 14.1 + - - -
293A PHE* 2.9 41.2 + - + +
294A GLY* 3.7 13.1 + - - +
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Residues in contact with ASN 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 THR 3.0 17.7 + - - +
196A LEU* 3.6 8.3 + - - +
198A GLU* 1.3 76.5 - - - +
200A ARG* 1.3 58.3 + - - +
202A LEU* 3.8 2.9 - - - +
203A GLN* 3.0 51.2 + - - +
213A LEU* 3.8 4.3 - - - +
216A SER* 2.7 25.8 + - - -
225A PHE* 3.8 13.4 - - + -
471A GLN 4.1 3.4 + - - -
472A PHE* 2.8 50.6 + - + +
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Residues in contact with ARG 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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193A ALA 4.7 1.4 + - - -
196A LEU* 3.1 36.8 + - - +
197A THR* 3.2 30.8 + - - +
199A ASN* 1.3 74.1 - - - +
201A VAL* 1.3 61.9 + - - +
203A GLN* 3.3 10.2 + - - +
204A ASN* 2.9 46.8 + - - +
298A GLU* 2.7 31.4 + - - +
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Residues in contact with VAL 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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197A THR* 2.9 19.8 + - + +
198A GLU 4.0 2.7 - - - +
200A ARG* 1.3 77.4 - - - +
202A LEU* 1.3 60.1 + - - +
204A ASN* 3.9 3.8 - - - +
205A SER* 2.8 31.1 + - - +
264A LEU* 4.3 17.9 - - + -
268A LYS* 5.8 0.8 - - + +
270A VAL* 4.4 11.0 - - + -
293A PHE* 3.9 32.8 - - + +
296A CYS* 4.1 26.0 - - + -
298A GLU* 4.0 25.6 - - + +
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Residues in contact with LEU 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 GLU* 2.9 40.8 + - + +
199A ASN 3.8 0.4 - - - +
201A VAL* 1.3 79.3 - - - +
203A GLN* 1.3 60.5 + - - +
205A SER* 3.4 20.4 + - - +
206A ARG* 3.9 2.9 + - - -
211A THR* 3.3 34.8 - - + +
212A ALA* 5.7 1.2 - - - -
213A LEU* 3.8 35.7 + - + +
225A PHE* 3.9 23.1 - - + -
227A MET* 4.4 10.5 - - - -
293A PHE* 3.6 28.0 - - + -
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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 ASN* 3.0 55.5 + - - +
200A ARG* 3.7 8.9 - - - +
202A LEU* 1.3 75.2 - - - +
204A ASN* 1.3 65.9 + - - +
206A ARG* 3.0 29.9 + - - +
213A LEU* 3.8 8.7 - - + -
471A GLN 4.8 4.0 + - - -
472A PHE 3.7 1.8 + - - -
473A ASP 4.8 0.6 + - - -
474A TYR* 3.4 58.0 + - + +
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Residues in contact with ASN 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 ARG* 2.9 37.1 + - - +
201A VAL* 4.2 4.5 - - - +
203A GLN* 1.3 84.0 - - - +
205A SER* 1.3 57.6 + - - +
206A ARG* 4.0 1.9 + - - +
263A TYR* 3.8 0.2 + - - -
268A LYS* 2.6 43.6 + - + +
298A GLU* 4.5 8.9 + - - -
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Residues in contact with SER 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 VAL* 2.8 23.2 + - - +
202A LEU* 3.4 11.1 + - - +
203A GLN 3.3 0.6 - - - -
204A ASN* 1.3 79.2 - - - +
206A ARG* 1.3 83.5 + - - +
207A HIS 4.2 0.4 - - - -
210A LEU* 3.7 32.3 - - - +
211A THR 5.1 3.3 + - - -
212A ALA* 5.9 2.9 - - - +
263A TYR* 3.4 11.2 - - - -
264A LEU* 4.8 4.5 - - - -
268A LYS* 4.3 6.7 - - - +
293A PHE* 5.7 1.6 - - - -
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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