Contacts of the helix formed by residues 203 - 218 (chain O) 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 O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90M ASP* 3.6 34.1 - - + +
168M GLY* 5.4 5.5 - - - -
123O PHE* 3.8 12.5 - + - -
127O TYR* 4.5 6.5 + - - -
178O LEU* 3.6 28.3 + - + +
179O LYS* 3.6 20.8 + - + +
197O GLY 3.9 1.8 + - - -
200O CYS 3.0 11.3 + - - +
201O LEU 3.1 1.8 + - - -
202O GLY* 1.3 78.2 - - - +
204O PRO* 1.3 67.4 - - + +
205O LEU* 3.1 46.7 + - + +
206O ASN* 2.8 39.4 + - - +
207O ALA 3.7 0.3 + - - -
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Residues in contact with PRO 204 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108O ILE* 3.8 26.7 - - + -
110O LEU* 6.1 0.2 - - + -
178O LEU* 3.4 28.9 - - + +
179O LYS* 4.9 0.2 - - - -
197O GLY* 3.4 19.7 - - - +
200O CYS* 4.0 16.6 - - + +
203O HIS* 1.3 89.8 - - + +
205O LEU* 1.3 65.5 + - + +
207O ALA* 3.2 8.3 + - - +
208O ALA 3.2 15.4 + - - -
230O THR* 3.7 26.8 - - + +
233O LEU* 4.9 1.1 - - + -
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Residues in contact with LEU 205 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110O LEU* 3.7 21.8 - - + -
123O PHE* 3.5 25.4 - - + +
126O LEU* 3.8 12.3 - - + -
127O TYR* 3.6 50.5 - - + -
130O ILE* 3.5 24.7 - - + -
178O LEU* 4.2 12.1 - - + -
203O HIS* 3.1 16.6 + - + +
204O PRO* 1.3 75.3 - - + +
206O ASN* 1.3 59.5 + - - +
208O ALA* 3.6 4.6 - - - +
209O VAL* 2.8 32.2 + - - +
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Residues in contact with ASN 206 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89M GLY* 3.4 10.9 - - - -
90M ASP 2.9 26.2 + - - -
91M ASN 4.6 0.2 - - - -
92M GLU* 3.5 25.1 + - - +
123O PHE* 3.4 20.1 - - - -
201O LEU* 3.0 34.1 + - + +
202O GLY* 4.1 0.4 - - - -
203O HIS* 2.8 19.3 + - - +
205O LEU* 1.3 74.6 - - - +
207O ALA* 1.3 59.6 + - - +
209O VAL* 3.3 6.9 + - - +
210O TRP* 2.9 30.0 + - - +
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Residues in contact with ALA 207 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61O VAL* 3.9 20.9 - - + +
64O THR* 4.5 4.0 - - + -
200O CYS* 4.6 4.0 - - - -
201O LEU* 3.9 18.1 - - + +
203O HIS 3.7 1.8 + - - -
204O PRO 3.2 9.1 + - - +
206O ASN* 1.3 78.5 - - - +
208O ALA* 1.3 56.4 + - - +
210O TRP* 3.4 3.8 + - - +
211O LEU* 3.0 30.0 + - - +
230O THR* 3.1 29.8 - - - +
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Residues in contact with ALA 208 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110O LEU* 3.8 22.7 - - + -
126O LEU* 3.4 30.5 - - + +
204O PRO 3.2 7.0 + - - +
205O LEU* 3.6 2.9 - - - +
206O ASN 3.3 0.2 - - - -
207O ALA* 1.3 76.9 - - - +
209O VAL* 1.3 59.8 + - - +
211O LEU* 3.3 5.2 + - - +
212O ALA* 2.9 30.8 + - - +
228O ILE* 4.6 15.9 - - + +
230O THR* 4.5 3.5 - - + +
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Residues in contact with VAL 209 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121O ILE* 3.7 11.8 - - + +
122O THR 4.3 1.1 - - - -
123O PHE* 3.8 33.7 - - + +
126O LEU* 4.1 19.5 - - + -
205O LEU 2.8 25.4 + - - +
206O ASN* 3.7 6.7 - - - +
208O ALA* 1.3 68.7 - - - +
210O TRP* 1.3 68.2 + - - +
212O ALA* 3.2 4.6 + - - +
213O ARG* 3.1 60.0 + - - +
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Residues in contact with TRP 210 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39O TYR* 4.4 6.1 - - - -
61O VAL* 4.2 5.6 - - + -
76O GLN* 3.7 31.4 + - - +
77O PRO* 3.5 39.1 - - + +
78O ASP* 3.6 37.9 - - - -
79O PHE* 4.2 13.0 - + + -
201O LEU* 4.5 7.4 - - + -
206O ASN 2.9 17.0 + - - +
207O ALA* 3.6 8.3 - - - +
209O VAL* 1.3 78.7 - - - +
211O LEU* 1.3 91.4 + - + +
213O ARG* 3.5 9.8 + - - +
214O LYS* 3.1 46.1 + - + +
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Residues in contact with LEU 211 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59O ARG* 3.7 25.1 - - + -
61O VAL* 3.9 13.0 - - + -
79O PHE* 3.8 29.8 - - + -
207O ALA 3.0 17.4 + - - +
208O ALA* 3.7 3.6 - - - +
210O TRP* 1.3 82.4 - - + +
212O ALA* 1.3 66.5 + - - +
214O LYS* 3.2 2.7 + - - +
215O MET* 2.9 45.4 + - + +
222O LEU* 4.1 5.8 - - + -
228O ILE* 3.7 40.8 - - + -
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Residues in contact with ALA 212 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116O LEU* 4.0 34.0 - - + +
118O ALA 4.6 1.1 - - - +
121O ILE* 3.9 18.2 - - + -
126O LEU* 4.4 4.3 - - + -
208O ALA 2.9 18.5 + - - +
209O VAL 3.2 4.2 + - - +
211O LEU* 1.3 75.4 - - - +
213O ARG* 1.3 62.2 + - - +
215O MET* 3.6 1.7 + - - +
216O ALA* 3.1 25.1 + - - +
222O LEU* 3.9 15.7 + - + +
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Residues in contact with ARG 213 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84M ALA 5.3 3.2 + - - -
87M CYS 4.8 11.3 + - - -
92M GLU* 5.9 0.6 + - - -
118O ALA 4.6 1.8 - - - -
119O THR* 3.4 24.9 - - - +
120O ASP* 4.0 8.1 + - - +
121O ILE* 2.7 42.5 + - + +
122O THR* 4.2 7.5 - - - +
123O PHE 5.2 0.6 - - - +
209O VAL* 3.1 37.2 + - - +
210O TRP* 3.7 8.3 - - - +
212O ALA* 1.3 73.1 - - - +
214O LYS* 1.3 65.9 + - - +
216O ALA* 3.2 6.2 + - - +
217O SER* 2.9 25.6 + - - -
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Residues in contact with LYS 214 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39O TYR* 4.2 24.9 + - - -
76O GLN* 4.4 20.5 - - - +
79O PHE* 4.5 7.3 - - + -
210O TRP* 3.1 37.1 + - + +
211O LEU* 3.2 10.3 + - - +
213O ARG* 1.3 76.2 - - - +
215O MET* 1.3 74.7 + - + +
217O SER* 3.0 12.4 + - - +
218O LEU* 2.9 47.0 + - + +
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Residues in contact with MET 215 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59O ARG* 3.8 33.4 - - - -
79O PHE* 3.1 47.1 - - + -
211O LEU* 2.9 25.8 + - + +
212O ALA 4.0 3.8 - - - +
214O LYS* 1.3 86.2 - - + +
216O ALA* 1.3 59.7 + - - +
218O LEU* 3.3 13.7 + - + +
220O GLU* 2.9 50.2 + - - +
222O LEU* 3.8 31.6 - - + +
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Residues in contact with ALA 216 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116O LEU 4.0 8.1 - - - +
117O PRO 3.4 24.6 - - - +
118O ALA 3.9 9.2 - - - +
119O THR* 3.8 15.2 - - + +
212O ALA 3.1 19.7 + - - +
213O ARG 3.5 4.5 - - - +
215O MET* 1.3 77.6 - - - +
217O SER* 1.3 60.9 + - - +
219O GLY* 3.2 14.0 + - - -
221O PRO* 4.2 13.9 - - - +
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Residues in contact with SER 217 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119O THR* 3.9 17.5 - - - +
213O ARG 2.9 14.4 + - - -
214O LYS* 3.0 18.6 + - - +
216O ALA* 1.3 73.7 - - - +
218O LEU* 1.3 67.2 + - - +
219O GLY 3.1 6.5 + - - -
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Residues in contact with LEU 218 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39O TYR* 5.9 3.1 - - + -
79O PHE* 3.9 31.4 - - + -
214O LYS* 2.9 26.8 + - + +
215O MET* 3.8 18.6 - - + +
216O ALA 3.2 0.4 - - - -
217O SER* 1.3 84.3 + - - +
219O GLY* 1.3 60.6 + - - +
220O GLU* 3.8 21.1 - - + +
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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