Contacts of the helix formed by residues 208 - 224 (chain A) in PDB entry 1QL6
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 LYS 208 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141A HIS* 3.0 81.1 + - + +
144A ASN* 3.1 28.1 + - - +
145A ILE 4.2 5.8 - - - +
146A VAL* 4.1 14.4 - - + -
174A LEU* 4.4 13.1 - - + +
207A GLY* 1.3 70.5 - - - -
209A GLU* 1.3 68.2 + - + +
211A ASP* 3.1 14.4 + - - +
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Residues in contact with GLU 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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179A LYS* 5.2 6.2 + - - -
193A GLU* 4.0 1.4 - - - +
207A GLY* 3.5 21.8 + - - -
208A LYS* 1.3 81.5 + - + +
210A VAL* 1.3 62.5 + - - +
212A MET* 2.8 25.1 + - + +
213A TRP 3.3 2.6 + - - -
272A PRO* 3.7 36.8 - - + +
273A GLN* 5.8 0.7 - - - -
275A ARG* 3.1 31.4 + - + +
276A TYR 6.0 1.1 - - - +
277A THR* 6.1 5.4 - - + -
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Residues in contact with VAL 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A VAL* 3.8 17.5 - - + -
148A ARG* 4.3 9.9 - - + -
191A ALA* 3.8 18.3 + - + +
193A GLU* 3.5 15.9 - - - +
194A ILE* 3.7 22.4 - - + -
206A TYR* 3.4 39.0 - - + -
207A GLY 3.1 15.2 + - - +
209A GLU* 1.3 74.0 - - - +
211A ASP* 1.3 64.4 + - - +
213A TRP* 3.4 5.5 + - - +
214A SER* 3.4 22.3 + - - -
275A ARG* 4.0 0.2 - - - +
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Residues in contact with ASP 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A ILE* 4.6 2.8 - - + +
140A LEU* 5.5 0.9 - - - +
141A HIS* 3.0 26.6 + - + +
146A VAL* 3.1 14.0 - - - +
147A HIS* 2.8 25.1 + - - +
148A ARG* 2.9 27.7 + - - -
150A LEU* 3.6 24.3 - - + +
208A LYS 3.1 9.6 + - - +
210A VAL* 1.3 77.4 - - - +
212A MET* 1.3 56.7 + - - +
214A SER* 3.3 5.9 + - - -
215A THR* 2.9 33.6 + - - -
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Residues in contact with MET 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A LEU* 3.7 19.1 - - + -
137A ILE* 3.8 27.1 - - - -
141A HIS* 4.0 12.8 - - + +
208A LYS 4.5 1.1 - - - +
209A GLU* 2.8 22.5 + - + +
211A ASP* 1.3 72.0 - - - +
213A TRP* 1.3 57.5 + - - +
215A THR* 3.8 6.0 - - + -
216A GLY 3.2 15.1 + - - -
267A PHE* 3.4 30.6 - - + +
275A ARG* 3.9 9.9 - - - -
276A TYR 3.2 21.8 - - - +
277A THR* 3.5 12.3 - - + -
278A ALA* 3.2 33.7 - - - +
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Residues in contact with TRP 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A SER 4.9 1.4 + - - -
189A TYR 3.4 21.2 + - - -
190A LEU 3.3 11.3 + - - -
191A ALA* 3.5 20.9 - - + -
192A PRO* 3.5 20.9 - - + -
209A GLU 3.3 4.6 + - - -
210A VAL 3.6 8.3 - - - +
211A ASP 3.2 0.8 - - - -
212A MET* 1.3 74.5 - - - +
214A SER* 1.3 59.2 + - - +
216A GLY* 3.0 4.5 + - - -
217A VAL* 3.0 35.6 + - + +
229A PHE* 3.4 39.6 - + - -
241A ILE* 3.8 28.8 - - + +
244A GLY* 4.7 0.7 - - - -
267A PHE 3.8 18.2 - - - -
268A LEU* 3.7 33.6 - - + +
269A VAL 3.8 21.3 - - - -
270A VAL* 4.1 5.4 - - + -
275A ARG* 3.8 8.8 - - - +
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Residues in contact with SER 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A ARG 5.8 1.7 - - - -
150A LEU* 3.7 35.2 + - - +
189A TYR* 3.1 27.3 + - - +
210A VAL 3.4 9.8 + - - -
211A ASP* 3.3 10.0 + - - -
213A TRP* 1.3 76.5 - - - +
215A THR* 1.3 67.1 + - - +
217A VAL* 3.3 6.5 + - - +
218A ILE* 3.0 28.2 + - - +
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Residues in contact with THR 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A MET* 3.6 24.2 - - + +
133A LEU* 4.3 4.6 - - + +
134A LEU* 3.9 24.5 - - + -
137A ILE* 2.9 29.1 - - + +
150A LEU* 3.5 4.3 - - - +
211A ASP 2.9 16.9 + - - -
212A MET* 3.8 10.7 - - + -
213A TRP 3.2 0.2 - - - -
214A SER* 1.3 76.0 - - - +
216A GLY* 1.3 54.6 + - - +
218A ILE* 3.1 10.6 + - - +
219A MET* 3.0 30.6 + - - +
267A PHE* 4.3 9.0 - - + -
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Residues in contact with GLY 216 (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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212A MET 3.2 6.5 + - - -
213A TRP 3.0 9.4 + - - -
215A THR* 1.3 73.7 - - - +
217A VAL* 1.3 61.1 + - - +
219A MET* 3.3 1.4 + - - +
220A TYR* 3.1 26.9 + - - +
264A VAL* 4.5 2.6 - - - +
267A PHE* 3.4 32.0 - - - +
268A LEU* 3.9 12.8 - - - +
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Residues in contact with VAL 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A SER 3.7 19.3 - - - +
189A TYR* 3.6 29.8 - - + -
213A TRP* 3.0 35.1 + - + +
214A SER 3.3 6.0 + - - +
216A GLY* 1.3 75.1 - - - +
218A ILE* 1.3 54.6 + - - +
220A TYR* 4.0 0.7 - - - +
221A THR* 2.5 38.0 + - - +
227A PRO* 4.8 5.2 - - + -
228A PRO* 3.9 28.9 - - + -
229A PHE* 4.7 2.9 - - + -
268A LEU* 4.1 8.3 - - + -
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Residues in contact with ILE 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A LEU* 4.9 3.1 - - + -
129A ILE* 6.0 0.4 - - + -
130A MET* 4.1 17.5 - - - -
133A LEU* 4.1 15.3 - - + -
150A LEU* 4.0 10.1 - - + -
151A LYS* 3.8 27.1 - - - +
152A PRO* 4.1 8.1 - - + -
155A ILE* 3.9 22.9 - - + -
189A TYR* 4.0 18.4 - - + -
214A SER 3.0 19.4 + - - +
215A THR* 3.5 6.3 - - - +
217A VAL* 1.3 74.0 - - - +
219A MET* 1.3 61.5 + - - +
221A THR* 3.6 4.2 + - - -
222A LEU* 3.0 44.5 + - + +
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Residues in contact with MET 219 (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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126A THR* 4.6 2.4 - - + +
130A MET* 3.7 34.3 - - + -
215A THR 3.0 15.7 + - - +
216A GLY* 3.3 6.9 + - - +
218A ILE* 1.3 77.1 - - - +
220A TYR* 1.3 65.7 + - - +
222A LEU* 3.3 10.1 + - - +
223A LEU* 3.3 21.7 + - + +
260A VAL* 3.6 24.2 - - + +
263A LEU* 3.6 31.4 - - + -
264A VAL* 3.3 29.6 - - + -
267A PHE* 3.4 24.2 - - - -
286A PHE* 4.9 4.0 - - + -
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Residues in contact with TYR 220 (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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216A GLY 3.1 15.5 + - - +
219A MET* 1.3 79.1 - - - +
221A THR* 1.3 54.5 + - - +
223A LEU* 3.1 5.7 + - - +
224A ALA* 2.9 36.8 + - + +
226A SER* 3.4 14.8 - - - -
227A PRO 3.7 2.3 + - - -
228A PRO* 3.3 56.7 - - + +
246A TYR* 3.8 11.9 - + - -
247A GLN 2.9 27.6 + - - -
248A PHE* 3.9 13.5 - + - -
249A GLY 5.0 0.2 + - - -
253A TRP* 3.5 37.5 + + - -
264A VAL* 4.1 10.7 - - + +
268A LEU* 4.4 1.3 - - + -
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Residues in contact with THR 221 (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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115A LEU* 3.8 20.1 - - + +
152A PRO* 5.4 5.2 - - + -
189A TYR* 4.9 12.4 + - - +
217A VAL* 2.5 27.8 + - - +
218A ILE* 3.9 5.8 - - - -
220A TYR* 1.3 72.2 - - - +
222A LEU* 1.3 61.6 + - + +
225A GLY* 2.9 26.4 + - - -
226A SER* 3.4 25.6 - - - +
227A PRO* 3.5 21.6 - - + +
228A PRO* 3.8 0.5 - - - +
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Residues in contact with LEU 222 (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* 3.9 27.8 - - + -
115A LEU* 3.9 21.5 - - + +
120A THR* 3.7 4.5 - - - -
121A LEU* 2.8 48.8 + - + +
126A THR* 4.1 20.2 - - + +
129A ILE* 4.2 24.2 - - + -
130A MET* 4.2 15.7 - - - -
152A PRO* 5.0 5.8 - - + -
218A ILE* 3.0 33.5 + - + +
219A MET 3.3 3.8 + - - +
221A THR* 1.3 77.3 - - - +
223A LEU* 1.3 58.6 + - - +
225A GLY 4.3 0.2 - - - -
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Residues in contact with LEU 223 (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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120A THR* 3.7 8.0 - - - +
121A LEU 3.9 4.0 - - - +
122A SER 4.2 3.1 - - - +
123A GLU* 4.2 6.7 - - + -
126A THR* 3.4 32.8 - - + +
219A MET* 3.3 26.0 + - + +
220A TYR 3.1 6.0 + - - +
222A LEU* 1.3 75.6 - - - +
224A ALA* 1.3 61.0 - - - +
252A GLU 4.6 1.0 - - - +
253A TRP* 3.8 23.6 - - + -
256A TYR* 2.5 64.4 + - + -
260A VAL* 4.1 22.2 - - + -
264A VAL* 4.4 1.6 - - + -
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Residues in contact with ALA 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A THR* 3.8 10.5 - - - +
220A TYR* 2.9 26.3 + - + +
223A LEU* 1.3 77.4 - - - +
225A GLY* 1.3 61.5 - - - +
226A SER* 3.3 26.8 + - - +
252A GLU* 4.1 26.3 - - + +
253A TRP* 3.9 16.2 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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