Contacts of the helix formed by residues 208 - 225 (chain A) in PDB entry 6QVC
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 THR 208 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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204A LYS 4.4 0.7 + - - -
205A GLU* 2.5 30.7 + - - -
206A TYR 3.3 3.6 + - - -
207A LEU* 1.3 77.9 - - - +
209A MET* 1.3 65.8 + - - +
210A LYS* 3.4 24.9 - - + +
211A ALA* 3.4 20.9 + - - +
212A PHE* 3.6 8.3 + - - +
241A ILE* 4.4 7.3 - - - +
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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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207A LEU 3.6 3.8 + - - -
208A THR* 1.3 73.8 - - - +
210A LYS* 1.3 70.5 + - - +
212A PHE* 2.8 40.5 + - + +
213A VAL* 3.7 25.8 + - + +
241A ILE* 4.7 5.4 - - + -
245A VAL* 4.5 24.8 - - + +
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Residues in contact with LYS 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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182A ILE* 4.6 15.4 - - + +
208A THR* 3.2 16.3 - - + +
209A MET* 1.3 90.1 - - - +
211A ALA* 1.3 60.1 + - - +
212A PHE 3.4 0.3 + - - -
213A VAL* 4.0 3.7 + - + +
214A ALA* 3.4 18.7 + - - +
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Residues in contact with ALA 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A ILE* 5.7 1.6 - - - -
183A SER* 5.2 9.7 - - - +
184A PRO* 5.4 5.8 - - + -
186A ALA* 4.6 20.5 - - + +
206A TYR 5.7 3.1 - - - +
208A THR* 3.4 20.9 + - - +
209A MET 3.2 0.4 - - - -
210A LYS* 1.3 76.2 - - - +
212A PHE* 1.3 54.9 + - - +
214A ALA* 3.0 10.5 + - + +
215A LYS* 2.6 38.4 + - - +
237A HIS* 6.3 0.9 - - - +
241A ILE* 5.6 3.4 - - + -
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Residues in contact with PHE 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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127A LEU* 5.9 1.3 - - + -
131A VAL* 5.3 14.4 - - + -
208A THR 3.6 1.8 + - - +
209A MET* 2.8 31.6 + - + +
211A ALA* 1.3 76.2 - - - +
213A VAL* 1.3 82.2 + - + -
215A LYS* 3.0 20.4 + - - +
216A VAL* 3.1 25.6 + - + +
238A ILE* 3.6 40.1 - - + +
241A ILE* 4.0 31.6 - - + +
242A CYS* 3.6 27.8 - - - -
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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
----------------------------------------------------------
209A MET* 3.7 21.8 + - + +
210A LYS* 4.7 3.8 - - + +
212A PHE* 1.3 96.5 - - + +
214A ALA* 1.3 59.9 + - - +
215A LYS 3.3 0.3 + - - -
216A VAL* 3.7 13.8 + - + +
217A VAL* 3.4 24.6 - - + +
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Residues in contact with ALA 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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178A PHE* 4.0 28.5 - - - +
182A ILE* 3.7 33.4 - - + -
183A SER* 4.8 9.8 - - - +
210A LYS 3.4 15.1 + - - +
211A ALA* 3.0 15.6 + - - +
213A VAL* 1.3 79.4 - - - +
215A LYS* 1.3 59.4 + - - +
217A VAL* 4.9 2.0 - - - -
218A ALA* 4.1 2.8 + - - +
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Residues in contact with LYS 215 (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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183A SER* 5.8 0.6 - - - -
186A ALA* 2.7 45.6 + - + +
189A SER* 3.3 21.1 - - - +
211A ALA* 2.6 17.6 + - - +
212A PHE* 3.0 5.3 + - - +
214A ALA* 1.3 74.8 - - - +
216A VAL* 1.3 58.7 + - - +
217A VAL 3.3 0.9 - - - -
218A ALA* 3.0 10.8 + - - +
219A LEU* 2.8 32.6 + - + -
234A PRO* 4.0 23.3 - - + -
237A HIS* 4.0 10.5 - - + -
238A ILE* 4.0 18.6 - - + -
241A ILE* 5.9 0.7 - - - -
480A PRO* 4.1 20.8 - - + +
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Residues in contact with VAL 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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131A VAL* 4.8 9.4 - - + -
135A MET* 3.7 30.5 - - + -
212A PHE* 3.1 26.6 + - + +
213A VAL* 3.8 17.5 - - + +
215A LYS* 1.3 79.3 - - - +
217A VAL* 1.3 55.7 + - + +
219A LEU* 3.0 13.3 + - + +
220A THR* 2.6 39.2 + - - +
238A ILE* 4.9 15.5 - - + -
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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
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174A PHE* 5.3 6.2 - - + -
178A PHE* 4.0 27.4 - - + -
213A VAL* 3.4 23.1 - - + +
214A ALA* 4.8 1.8 - - - +
216A VAL* 1.3 81.0 - - + +
218A ALA* 1.3 55.6 + - - +
220A THR* 3.0 16.6 + - + -
221A ALA* 2.7 31.7 + - - +
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Residues in contact with ALA 218 (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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175A SER* 3.3 24.3 + - - +
178A PHE* 3.7 33.0 - - + -
179A CYS* 5.0 5.4 - - - +
214A ALA 4.1 4.0 - - - +
215A LYS* 3.0 10.4 + - - +
217A VAL* 1.3 83.2 - - - +
219A LEU* 1.3 49.3 + - - +
221A ALA* 3.0 12.8 + - - +
222A GLY* 2.5 31.0 + - - -
480A PRO* 5.3 4.3 - - + -
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Residues in contact with LEU 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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135A MET* 4.2 24.0 - - + -
215A LYS* 2.8 16.2 + - + +
216A VAL* 3.0 14.8 + - + +
218A ALA* 1.3 72.3 - - - +
220A THR* 1.3 54.4 + - - +
222A GLY* 3.0 6.0 + - - +
223A LEU* 2.4 47.3 + - + +
229A VAL* 5.6 1.8 - - + -
230A GLY 4.5 14.8 - - - +
231A LYS* 4.6 19.3 - - + +
234A PRO* 4.5 20.9 - - + -
235A PHE* 5.5 5.4 - - + +
480A PRO* 3.9 31.1 - - + +
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Residues in contact with THR 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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135A MET* 3.8 40.1 - - - +
138A VAL* 4.6 18.6 - - + -
139A SER* 4.7 5.4 - - - +
216A VAL* 2.6 22.9 + - - +
217A VAL* 3.0 20.8 + - + -
219A LEU* 1.3 71.4 - - - +
221A ALA* 1.3 53.4 + - - +
223A LEU* 3.0 6.1 + - - +
224A GLY* 2.5 35.3 + - - -
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Residues in contact with ALA 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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171A LEU* 3.2 42.3 - - + +
172A ILE* 4.6 1.4 - - - +
174A PHE* 4.6 12.8 - - + -
175A SER* 3.8 21.3 - - - +
217A VAL 2.7 15.4 + - - +
218A ALA* 3.1 13.2 - - - +
220A THR* 1.3 73.4 - - - +
222A GLY* 1.3 59.2 + - - +
225A SER* 3.3 8.5 + - - -
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Residues in contact with GLY 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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172A ILE* 5.0 5.8 - - - -
175A SER* 4.3 5.7 + - - -
218A ALA 2.5 18.5 + - - -
219A LEU* 3.2 8.5 - - - -
221A ALA* 1.3 74.0 - - - +
223A LEU* 1.3 59.9 + - - +
225A SER* 3.5 16.1 + - - +
227A ILE 4.5 0.2 - - - +
229A VAL* 3.3 31.0 - - - +
479A ILE* 5.7 6.3 - - - -
480A PRO 6.1 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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135A MET* 4.5 10.3 - - + +
136A ASP* 4.2 22.4 - - + +
139A SER* 3.3 26.5 + - - +
219A LEU* 2.4 25.8 + - + +
220A THR* 3.6 6.5 - - - +
222A GLY* 1.3 73.2 - - - +
224A GLY* 1.3 63.3 + - - +
225A SER 3.2 8.8 + - - +
229A VAL* 4.3 14.9 - - + +
230A GLY 5.1 1.1 - - - +
231A LYS* 4.6 35.0 - - + -
421A ARG* 5.9 11.7 - - - +
485A MET* 6.4 1.6 - - + -
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Residues in contact with GLY 224 (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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139A SER* 3.3 16.5 + - - -
142A SER* 4.1 18.5 + - - -
143A LEU* 4.4 15.6 - - - +
167A PHE* 5.2 4.0 - - - -
171A LEU* 3.9 13.7 - - - +
220A THR 2.5 21.0 + - - -
221A ALA 4.1 0.9 - - - -
223A LEU* 1.3 70.5 - - - +
225A SER* 1.3 63.2 + - - +
226A GLY 3.8 0.3 + - - -
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Residues in contact with SER 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A LEU* 5.3 2.1 - - - +
168A PRO* 4.6 2.8 - - - +
171A LEU* 3.8 16.2 - - - +
172A ILE* 3.8 20.3 - - - +
221A ALA 3.3 16.5 + - - -
222A GLY 3.6 8.9 - - - +
223A LEU 3.1 10.8 - - - +
224A GLY* 1.3 80.6 - - - +
226A GLY* 1.3 60.6 + - - +
227A ILE* 2.9 38.0 + - - +
229A VAL* 5.7 0.6 - - - +
420A PRO* 5.5 3.3 - - - +
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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