Contacts of the helix formed by residues 203 - 218 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123L PHE* 3.8 12.6 - + - -
127L TYR* 4.5 6.9 + - - -
178L LEU* 3.6 22.8 + - + +
179L LYS* 3.6 36.5 + - + +
197L GLY 3.9 2.6 + - - -
200L CYS 3.1 11.6 + - - +
201L LEU 3.1 2.0 + - - -
202L GLY* 1.3 79.1 - - - +
204L PRO* 1.3 62.5 - - + +
205L LEU* 3.1 46.9 + - + +
206L ASN* 2.8 43.7 + - - +
207L ALA 3.7 0.7 + - - -
90O ASP* 3.8 26.2 + - + +
168O GLY* 5.7 4.9 - - - -
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Residues in contact with PRO 204 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108L ILE* 3.9 27.1 - - + -
110L LEU* 6.1 0.2 - - + -
178L LEU* 3.3 29.6 - - + +
197L GLY* 3.4 18.8 - - - +
200L CYS* 3.7 17.5 - - + +
203L HIS* 1.3 89.8 - - + +
205L LEU* 1.3 64.3 + - + +
207L ALA* 3.2 7.8 + - - +
208L ALA 3.2 15.2 + - - -
230L THR* 3.7 28.1 - - + +
233L LEU* 4.9 1.3 - - + -
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Residues in contact with LEU 205 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110L LEU* 3.7 21.3 - - + -
123L PHE* 3.5 24.2 - - + +
126L LEU* 3.8 12.1 - - + -
127L TYR* 3.6 52.0 - - + +
130L ILE* 3.5 26.2 - - + -
178L LEU* 4.2 11.7 - - + -
203L HIS* 3.0 15.1 + - + +
204L PRO* 1.3 74.8 - - + +
206L ASN* 1.3 60.7 + - - +
207L ALA 3.3 0.2 - - - -
208L ALA* 3.7 4.1 - - - +
209L VAL* 2.8 32.4 + - - +
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Residues in contact with ASN 206 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123L PHE* 3.3 22.2 - - - -
201L LEU* 3.0 33.5 + - + +
202L GLY* 4.1 0.8 - - - -
203L HIS* 2.8 19.9 + - - +
205L LEU* 1.3 75.8 - - - +
207L ALA* 1.3 58.7 + - - +
209L VAL* 3.3 6.2 + - - +
210L TRP* 2.9 30.7 + - - +
89O GLY* 3.6 5.2 - - - -
90O ASP 3.0 25.0 + - - -
91O ASN 4.7 0.4 - - - -
92O GLU* 3.5 30.2 + - - +
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Residues in contact with ALA 207 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61L VAL* 3.9 20.3 - - + +
64L THR* 4.6 4.3 - - + -
200L CYS* 4.6 3.6 - - - -
201L LEU* 3.9 18.7 - - + +
203L HIS 3.7 2.0 + - - -
204L PRO 3.2 9.3 + - - +
206L ASN* 1.3 77.7 - - - +
208L ALA* 1.3 58.1 + - - +
210L TRP* 3.4 3.5 + - - +
211L LEU* 2.9 29.6 + - - +
230L THR* 3.1 31.6 - - - +
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Residues in contact with ALA 208 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110L LEU* 3.8 23.3 - - + -
126L LEU* 3.4 30.8 - - + +
204L PRO 3.2 7.6 + - - +
205L LEU* 3.7 2.7 - - - +
207L ALA* 1.3 76.3 - - - +
209L VAL* 1.3 61.0 + - - +
211L LEU* 3.4 5.8 + - - +
212L ALA* 2.9 30.5 + - - +
228L ILE* 4.5 16.0 - - + +
230L THR* 4.5 3.5 - - + +
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Residues in contact with VAL 209 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121L ILE* 3.6 13.2 - - + +
122L THR 4.2 1.1 - - - +
123L PHE* 3.8 35.0 - - + +
126L LEU* 4.0 19.3 - - + -
205L LEU 2.8 23.1 + - - +
206L ASN* 3.7 5.8 - - - +
208L ALA* 1.3 71.9 - - - +
210L TRP* 1.3 68.5 + - - +
211L LEU 3.2 0.2 + - - -
212L ALA* 3.2 3.7 + - - +
213L ARG* 3.1 58.3 + - - +
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Residues in contact with TRP 210 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39L TYR* 4.5 3.8 - - - -
61L VAL* 4.2 8.7 - - + -
76L GLN* 3.7 31.4 + - - +
77L PRO* 3.5 36.7 - - + +
78L ASP 3.7 38.1 - - - -
79L PHE* 4.3 15.7 - + + -
201L LEU* 4.5 8.1 - - + -
206L ASN 2.9 17.4 + - - +
207L ALA* 3.7 5.4 - - - +
209L VAL* 1.3 79.2 - - - +
211L LEU* 1.3 89.8 + - + +
213L ARG* 3.4 9.3 + - + +
214L LYS* 3.1 48.2 + - + +
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Residues in contact with LEU 211 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59L ARG* 3.7 26.2 - - + +
61L VAL* 3.9 14.1 - - + -
79L PHE* 3.8 29.2 - - + -
207L ALA 2.9 18.9 + - - +
208L ALA 3.8 2.9 - - - +
210L TRP* 1.3 83.2 - - + +
212L ALA* 1.3 65.8 + - - +
214L LYS* 3.2 2.9 + - - +
215L MET* 2.9 45.7 + - + +
222L LEU* 4.2 5.4 - - + -
228L ILE* 3.7 39.3 - - + -
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Residues in contact with ALA 212 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116L LEU* 4.0 34.3 - - + +
118L ALA 4.6 0.6 - - - +
121L ILE* 3.8 19.5 - - + -
126L LEU* 4.4 3.6 - - + -
208L ALA 2.9 17.9 + - - +
209L VAL 3.2 4.2 + - - +
211L LEU* 1.3 75.8 - - - +
213L ARG* 1.3 61.9 + - - +
215L MET* 3.6 2.3 + - - +
216L ALA* 3.1 24.4 + - - +
222L LEU* 3.9 14.5 - - + +
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Residues in contact with ARG 213 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118L ALA 4.5 1.3 - - - -
119L THR* 3.4 24.5 - - - +
120L ASP* 3.9 11.0 + - - +
121L ILE* 2.8 40.0 + - + -
122L THR* 4.2 7.7 - - - +
123L PHE 5.2 0.6 - - - +
209L VAL* 3.1 37.0 + - - +
210L TRP* 3.6 8.3 - - - +
212L ALA* 1.3 73.7 - - - +
214L LYS* 1.3 66.1 + - - +
216L ALA* 3.2 6.6 + - - +
217L SER* 2.9 25.7 + - - -
84O ALA 5.6 2.4 + - - -
87O CYS 5.0 9.1 + - - -
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Residues in contact with LYS 214 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39L TYR* 4.4 24.7 + - - -
76L GLN* 4.4 21.1 - - - +
79L PHE* 4.6 6.7 - - + -
210L TRP* 3.1 39.1 + - + +
211L LEU* 3.5 9.9 - - - +
213L ARG* 1.3 77.6 - - - +
215L MET* 1.3 73.5 + - + +
217L SER* 3.1 12.1 + - - +
218L LEU* 2.9 46.0 + - + +
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Residues in contact with MET 215 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59L ARG* 3.8 33.7 - - - -
79L PHE* 3.2 45.5 - - + -
211L LEU* 2.9 26.6 + - + +
212L ALA 4.0 3.4 - - - +
214L LYS* 1.3 84.0 - - + +
216L ALA* 1.3 61.2 + - - +
218L LEU* 3.3 14.6 + - + +
220L GLU* 2.9 50.8 + - - +
222L LEU* 3.8 31.4 - - + +
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Residues in contact with ALA 216 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116L LEU 3.9 4.0 - - - +
117L PRO 3.4 29.1 - - - +
118L ALA 3.9 9.6 - - - +
119L THR* 3.8 15.0 - - + +
212L ALA 3.1 19.8 + - - +
213L ARG 3.2 4.2 + - - +
215L MET* 1.3 78.9 - - - +
217L SER* 1.3 60.8 + - - +
219L GLY* 3.2 14.0 + - - -
221L PRO* 4.2 13.3 - - - +
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Residues in contact with SER 217 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119L THR* 3.8 17.5 - - - +
213L ARG 2.9 14.5 + - - -
214L LYS* 3.1 18.4 + - - +
216L ALA* 1.3 73.1 - - - +
218L LEU* 1.3 67.2 + - - +
219L GLY 3.1 5.7 + - - -
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Residues in contact with LEU 218 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39L TYR* 6.0 1.6 - - + -
79L PHE* 4.0 17.7 - - + -
214L LYS* 2.9 32.8 + - + +
215L MET* 3.7 27.1 - - + +
216L ALA 3.3 0.4 - - - -
217L SER* 1.3 85.6 + - - +
219L GLY* 1.3 61.6 + - - +
220L GLU* 3.5 22.6 + - + +
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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