Contacts of the helix formed by residues 203 - 218 (chain F) in PDB entry 2WQT
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 HIS 203 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123F PHE* 3.9 13.0 - + - -
127F TYR* 4.6 5.6 + - - -
178F LEU* 3.6 22.6 - - + +
179F LYS* 3.6 28.6 + - + +
197F GLY 3.8 2.4 + - - -
200F CYS 3.0 12.3 + - - +
201F LEU 3.1 2.4 + - - -
202F GLY* 1.3 79.0 - - - +
204F PRO* 1.3 68.1 - - + +
205F LEU* 3.1 46.9 + - + +
206F ASN* 2.8 31.5 + - - +
207F ALA 3.7 0.5 + - - -
90G ASP* 3.6 42.5 + - + +
168G GLY* 5.6 4.8 + - - -
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Residues in contact with PRO 204 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108F ILE* 3.8 26.7 - - + -
110F LEU* 6.0 0.2 - - + -
178F LEU* 3.4 28.5 - - + +
197F GLY* 3.3 20.2 - - - +
200F CYS* 4.1 17.0 - - + +
203F HIS* 1.3 89.8 - - + +
205F LEU* 1.3 65.4 + - + +
207F ALA* 3.2 14.6 + - - +
208F ALA 3.2 9.0 + - - -
230F THR* 3.7 28.0 - - + +
233F LEU* 4.9 1.1 - - + -
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Residues in contact with LEU 205 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110F LEU* 3.7 21.8 - - + -
123F PHE* 3.5 24.0 - - + +
126F LEU* 3.8 12.1 - - + -
127F TYR* 3.6 50.3 - - + +
130F ILE* 3.5 24.7 - - + -
178F LEU* 4.2 11.7 - - + -
203F HIS* 3.0 16.6 + - + +
204F PRO* 1.3 76.3 - - + +
206F ASN* 1.3 60.9 + - - +
208F ALA* 3.7 4.2 - - - +
209F VAL* 2.8 32.2 + - - +
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Residues in contact with ASN 206 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123F PHE* 3.3 21.2 - - - -
201F LEU* 3.0 35.2 + - + +
202F GLY* 4.1 0.6 - - - -
203F HIS* 2.8 16.8 + - - +
205F LEU* 1.3 76.7 - - - +
207F ALA* 1.3 58.9 + - - +
209F VAL* 3.3 5.8 + - - +
210F TRP* 2.9 30.0 + - - +
89G GLY* 3.4 6.6 - - - -
90G ASP 2.9 25.0 + - - -
92G GLU* 3.4 32.0 + - - +
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Residues in contact with ALA 207 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61F VAL* 3.9 20.1 - - + +
64F THR* 4.6 3.6 - - + -
200F CYS* 4.6 4.5 - - - -
201F LEU* 3.9 17.8 - - + +
203F HIS 3.7 1.4 + - - -
204F PRO 3.2 10.1 + - - +
206F ASN* 1.3 79.6 - - - +
208F ALA* 1.3 56.1 + - - +
210F TRP* 3.4 3.7 + - - +
211F LEU* 3.0 30.0 + - - +
230F THR* 3.1 31.4 - - - +
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Residues in contact with ALA 208 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110F LEU* 3.7 23.1 - - + -
126F LEU* 3.4 31.2 - - + +
204F PRO 3.2 7.2 + - - +
205F LEU 3.7 2.7 - - - +
206F ASN 3.3 0.2 - - - -
207F ALA* 1.3 80.5 - - - +
209F VAL* 1.3 56.3 + - - +
211F LEU* 3.4 5.3 + - - +
212F ALA* 2.9 31.0 + - - +
228F ILE* 4.5 16.7 - - + +
230F THR* 4.5 3.2 - - + +
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Residues in contact with VAL 209 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121F ILE* 3.6 13.0 - - + +
122F THR 4.3 1.1 - - - -
123F PHE* 3.8 33.0 - - + +
126F LEU* 4.0 20.6 - - + -
205F LEU 2.8 23.3 + - - +
206F ASN* 3.7 6.3 - - - +
207F ALA 3.3 0.2 - - - -
208F ALA* 1.3 75.3 - - - +
210F TRP* 1.3 63.0 - - - +
212F ALA* 3.2 4.3 + - - +
213F ARG* 3.1 58.8 + - - +
92G GLU* 6.2 0.4 - - - +
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Residues in contact with TRP 210 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39F TYR* 4.4 6.1 - - - -
61F VAL* 4.2 5.4 - - + -
76F GLN* 3.7 32.5 + - - +
77F PRO* 3.5 39.0 - - + +
78F ASP* 3.7 37.9 - - - -
79F PHE* 4.3 13.5 - + + -
201F LEU* 4.5 6.7 - - + -
206F ASN 2.9 17.6 + - - +
207F ALA* 3.6 7.9 - - - +
209F VAL* 1.3 77.8 - - - +
211F LEU* 1.3 86.7 + - + +
213F ARG* 3.5 9.2 + - - +
214F LYS* 3.1 50.9 + - + +
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Residues in contact with LEU 211 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59F ARG* 3.8 24.9 - - + +
61F VAL* 3.9 13.5 - - + -
79F PHE* 3.8 30.1 - - + -
207F ALA 3.0 17.4 + - - +
208F ALA* 3.7 4.0 - - - +
210F TRP* 1.3 83.3 - - + +
212F ALA* 1.3 65.5 + - - +
214F LYS* 3.3 2.0 + - - +
215F MET* 3.0 45.1 + - + +
222F LEU* 4.2 5.8 - - + -
228F ILE* 3.7 40.6 - - + -
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Residues in contact with ALA 212 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116F LEU* 4.0 33.6 - - + +
118F ALA 4.5 0.6 - - - +
121F ILE* 3.8 19.1 - - + -
126F LEU* 4.4 3.8 - - + -
208F ALA 2.9 18.7 + - - +
209F VAL 3.2 4.7 + - - +
211F LEU* 1.3 74.8 - - - +
213F ARG* 1.3 62.0 + - - +
215F MET* 4.0 1.9 - - - +
216F ALA* 3.1 25.1 + - - +
222F LEU* 4.0 15.5 + - + +
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Residues in contact with ARG 213 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B MET* 2.5 52.0 - - - +
118F ALA 4.5 2.0 - - - -
119F THR* 3.4 25.4 - - - +
120F ASP 4.0 0.6 - - - -
121F ILE* 2.8 33.5 + - + +
122F THR* 4.3 4.6 - - - +
123F PHE 5.2 0.6 - - - +
209F VAL* 3.1 34.1 + - - +
210F TRP* 3.6 9.1 - - + +
212F ALA* 1.3 72.6 - - - +
214F LYS* 1.3 65.7 + - - +
216F ALA* 3.2 6.7 + - - +
217F SER* 2.9 25.1 + - - -
87G CYS 4.7 8.1 + - - -
92G GLU* 6.0 0.2 + - - -
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Residues in contact with LYS 214 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39F TYR* 4.3 24.5 + - - -
76F GLN* 4.4 20.6 - - - +
79F PHE* 4.5 7.3 - - + -
210F TRP* 3.1 37.2 + - + +
211F LEU* 3.6 9.9 - - - +
213F ARG* 1.3 78.2 - - - +
215F MET* 1.3 73.4 + - + +
217F SER* 3.0 13.3 + - - +
218F LEU* 2.9 46.8 + - + +
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Residues in contact with MET 215 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59F ARG* 3.7 33.2 - - - -
79F PHE* 3.2 48.2 - - + -
211F LEU* 3.0 27.1 + - + +
212F ALA 4.0 3.1 - - - +
214F LYS* 1.3 84.1 - - + +
216F ALA* 1.3 60.0 + - - +
218F LEU* 3.2 14.1 + - + +
220F GLU* 2.9 50.0 + - - +
222F LEU* 3.9 30.5 - - + +
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Residues in contact with ALA 216 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116F LEU 3.9 4.7 - - - +
117F PRO 3.3 29.2 - - - +
118F ALA 3.8 9.4 - - - +
119F THR* 3.8 14.2 - - + +
212F ALA 3.1 19.7 + - - +
213F ARG 3.5 4.3 - - - +
214F LYS 3.2 0.2 - - - -
215F MET* 1.3 75.6 - - - +
217F SER* 1.3 63.0 + - - +
219F GLY* 3.2 13.7 + - - -
221F PRO* 4.2 13.1 - - - +
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Residues in contact with SER 217 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119F THR* 3.9 17.5 - - - +
213F ARG 2.9 14.0 + - - -
214F LYS* 3.0 18.9 + - - +
216F ALA* 1.3 75.3 - - - +
218F LEU* 1.3 67.3 + - - +
219F GLY 3.2 3.4 + - - -
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Residues in contact with LEU 218 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39F TYR* 6.0 2.0 - - + -
79F PHE* 4.0 17.9 - - + -
214F LYS* 2.9 29.2 + - + +
215F MET* 3.2 33.3 + - + +
217F SER* 1.3 84.1 + - - +
219F GLY* 1.3 60.3 + - - +
220F GLU* 3.5 20.3 + - + +
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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