Contacts of the helix formed by residues 203 - 218 (chain P) 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 P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123P PHE* 3.8 13.0 - + - -
127P TYR* 4.5 7.1 + - - -
178P LEU* 3.7 28.3 + - + +
179P LYS* 3.6 21.7 + - + +
197P GLY 3.8 1.8 + - - -
200P CYS 3.0 12.2 + - - +
201P LEU 3.1 1.6 + - - -
202P GLY* 1.3 79.7 - - - +
204P PRO* 1.3 68.2 - - + +
205P LEU* 3.1 46.9 + - + +
206P ASN* 2.8 39.4 + - - +
207P ALA 3.7 0.5 + - - -
90Q ASP* 3.5 33.8 + - + +
168Q GLY* 5.4 4.6 - - - -
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Residues in contact with PRO 204 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108P ILE* 3.8 27.4 - - + -
110P LEU* 6.0 0.2 - - + -
178P LEU* 3.4 28.7 - - + +
197P GLY* 3.3 19.7 - - - +
200P CYS* 4.0 17.3 - - + +
203P HIS* 1.3 89.2 - - + +
205P LEU* 1.3 65.5 + - + +
207P ALA* 3.2 7.0 + - - +
208P ALA 3.2 15.6 + - - -
230P THR* 3.7 28.7 - - + +
233P LEU* 4.8 1.8 - - + -
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Residues in contact with LEU 205 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110P LEU* 3.6 22.9 - - + -
123P PHE* 3.5 21.8 - - + +
126P LEU* 3.7 12.1 - - + -
127P TYR* 3.6 51.6 - - + -
130P ILE* 3.5 25.4 - - + -
178P LEU* 4.2 11.0 - - + -
203P HIS* 3.1 16.4 + - + +
204P PRO* 1.3 76.1 - - + +
206P ASN* 1.3 61.5 + - - +
207P ALA 3.3 0.2 - - - -
208P ALA* 3.7 4.4 - - - +
209P VAL* 2.8 32.1 + - - +
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Residues in contact with ASN 206 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123P PHE* 3.3 21.8 - - - -
201P LEU* 2.9 34.9 + - + +
202P GLY* 4.1 0.6 - - - -
203P HIS* 2.8 17.4 + - - +
205P LEU* 1.3 75.6 - - - +
207P ALA* 1.3 60.5 + - - +
209P VAL* 3.3 6.6 + - - +
210P TRP* 2.8 30.8 + - - +
89Q GLY* 3.5 10.2 - - - -
90Q ASP 2.8 26.0 + - - -
91Q ASN 4.4 0.4 + - - -
92Q GLU* 3.6 25.9 + - + +
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Residues in contact with ALA 207 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61P VAL* 3.9 20.1 - - + +
64P THR* 4.5 4.3 - - + -
200P CYS* 4.5 4.0 - - - -
201P LEU* 3.9 17.3 - - + +
203P HIS 3.7 1.8 + - - -
204P PRO* 3.2 9.6 + - + +
206P ASN* 1.3 79.4 - - - +
208P ALA* 1.3 55.3 + - - +
210P TRP* 3.4 4.4 + - - +
211P LEU* 3.0 29.6 + - - +
230P THR* 3.2 31.0 - - - +
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Residues in contact with ALA 208 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110P LEU* 3.8 23.3 - - + -
126P LEU* 3.5 31.0 - - + +
204P PRO 3.2 6.8 + - - +
205P LEU 3.7 2.2 - - - +
206P ASN 3.3 0.2 - - - -
207P ALA* 1.3 75.4 - - - +
209P VAL* 1.3 59.6 + - - +
211P LEU* 3.3 6.2 + - - +
212P ALA* 2.8 31.7 + - - +
228P ILE* 4.5 17.6 - - + +
230P THR* 4.5 2.8 - - + +
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Residues in contact with VAL 209 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121P ILE* 3.7 11.7 - - + +
122P THR 4.3 1.3 - - - -
123P PHE* 3.8 33.2 - - + +
126P LEU* 4.0 20.6 - - + -
205P LEU 2.8 29.1 + - - +
206P ASN* 3.7 6.5 - - - +
208P ALA* 1.3 70.9 - - - +
210P TRP* 1.3 66.2 + - - +
212P ALA* 3.2 4.7 + - - +
213P ARG* 3.1 60.3 + - - +
92Q GLU* 6.0 2.7 - - - +
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Residues in contact with TRP 210 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39P TYR* 4.4 7.0 - - - -
61P VAL* 4.2 8.5 - - + -
76P GLN* 3.7 31.6 + - - +
77P PRO* 3.5 37.4 - - + +
78P ASP 3.6 38.4 - - - -
79P PHE* 4.2 12.3 - + + -
201P LEU* 4.5 7.6 - - + -
206P ASN 2.8 18.7 + - - +
207P ALA* 3.6 5.6 - - - +
209P VAL* 1.3 79.0 - - - +
211P LEU* 1.3 90.9 + - + +
213P ARG* 3.4 10.1 + - + +
214P LYS* 3.1 46.7 + - + +
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Residues in contact with LEU 211 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59P ARG* 3.7 26.2 - - + -
61P VAL* 3.9 13.9 - - + -
79P PHE* 3.8 29.6 - - + -
207P ALA 3.0 16.8 + - - +
208P ALA* 3.7 3.6 - - - +
209P VAL 3.2 0.2 - - - -
210P TRP* 1.3 82.3 - - + +
212P ALA* 1.3 66.6 + - - +
214P LYS* 3.2 2.6 + - - +
215P MET* 2.9 46.6 + - + +
222P LEU* 4.1 5.4 - - + -
228P ILE* 3.7 40.2 - - + -
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Residues in contact with ALA 212 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116P LEU* 4.0 33.1 - - + +
118P ALA 4.9 0.4 - - - -
121P ILE* 3.8 18.6 - - + -
126P LEU* 4.4 4.7 - - + -
208P ALA 2.8 21.2 + - - +
209P VAL 3.6 4.7 - - - +
211P LEU* 1.3 72.4 - - - +
213P ARG* 1.3 57.0 + - - +
215P MET* 4.0 1.9 - - - +
216P ALA* 3.1 30.1 + - - +
222P LEU* 3.9 14.6 + - + +
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Residues in contact with ARG 213 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118P ALA 4.6 0.4 - - - -
119P THR* 3.4 27.1 - - - +
120P ASP* 4.0 8.0 + - - +
121P ILE* 2.7 42.6 + - + +
122P THR* 4.2 7.1 - - - +
123P PHE 5.2 0.4 - - - +
209P VAL* 3.1 33.0 + - - +
210P TRP* 3.6 11.0 - - - +
212P ALA* 1.3 73.8 - - - +
214P LYS* 1.3 66.7 + - - +
216P ALA* 3.2 6.6 + - - +
217P SER* 2.9 25.4 + - - -
84Q ALA 5.5 2.4 + - - -
87Q CYS 4.8 11.1 + - - -
92Q GLU* 5.7 2.6 + - - -
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Residues in contact with LYS 214 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39P TYR* 4.3 24.5 + - - -
76P GLN* 4.4 20.7 - - - +
79P PHE* 4.5 7.5 - - + -
210P TRP* 3.1 38.6 + - + +
211P LEU* 3.5 10.1 - - - +
213P ARG* 1.3 75.7 - - - +
215P MET* 1.3 69.1 + - + +
217P SER* 3.0 12.6 + - - +
218P LEU* 2.9 51.9 + - + +
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Residues in contact with MET 215 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59P ARG* 3.8 31.4 - - - -
79P PHE* 3.1 48.5 - - + -
211P LEU* 2.9 26.8 + - + +
212P ALA 4.0 3.1 - - - +
214P LYS* 1.3 85.1 - - + +
216P ALA* 1.3 60.8 + - - +
218P LEU* 3.3 14.0 + - + +
220P GLU* 2.9 49.9 + - - +
222P LEU* 3.9 30.3 - - + +
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Residues in contact with ALA 216 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116P LEU 4.0 3.8 - - - +
117P PRO 3.4 28.8 - - - +
118P ALA 3.9 9.6 - - - +
119P THR* 3.8 13.8 - - + +
212P ALA 3.1 19.0 + - - +
213P ARG 3.5 4.3 - - - +
215P MET* 1.3 76.6 - - - +
217P SER* 1.3 61.2 + - - +
219P GLY* 3.1 14.6 + - - -
221P PRO* 4.2 14.3 - - - +
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Residues in contact with SER 217 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119P THR* 3.9 17.5 - - - +
213P ARG 2.9 14.6 + - - -
214P LYS* 3.0 19.2 + - - +
216P ALA* 1.3 76.9 - - - +
218P LEU* 1.3 67.0 + - - +
219P GLY 3.2 1.6 + - - -
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Residues in contact with LEU 218 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39P TYR* 5.9 2.9 - - + -
79P PHE* 3.9 17.7 - - + -
214P LYS* 2.9 27.9 + - + +
215P MET* 3.7 32.3 - - + +
216P ALA 3.2 0.2 - - - -
217P SER* 1.3 85.2 - - - +
219P GLY* 1.3 60.2 - - - +
220P GLU* 3.5 20.6 + - + +
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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