Contacts of the helix formed by residues 203 - 218 (chain M) 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 M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123M PHE* 3.8 13.5 - + + -
127M TYR* 4.5 6.9 + - - -
178M LEU* 3.6 25.5 + - + +
179M LYS* 3.6 36.5 + - + +
197M GLY 3.8 2.4 + - - -
200M CYS 3.0 12.5 + - - +
201M LEU 3.1 1.6 + - - -
202M GLY* 1.3 79.3 - - - +
204M PRO* 1.3 67.7 - - + +
205M LEU* 3.1 43.5 + - + +
206M ASN* 2.8 39.5 + - - +
207M ALA 3.7 0.5 + - - -
90N ASP* 3.6 26.7 + - + +
168N GLY* 5.7 3.4 + - - -
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Residues in contact with PRO 204 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108M ILE* 3.8 27.4 - - + -
110M LEU* 6.1 0.2 - - + -
178M LEU* 3.3 29.6 - - + +
197M GLY* 3.3 20.0 - - - +
200M CYS* 4.1 17.7 - - + +
203M HIS* 1.3 88.7 - - + +
205M LEU* 1.3 66.1 + - + +
207M ALA* 3.2 15.2 + - - +
208M ALA 3.2 8.3 + - - -
230M THR* 3.7 27.7 - - + +
233M LEU* 4.9 1.1 - - + -
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Residues in contact with LEU 205 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110M LEU* 3.7 23.1 - - + -
123M PHE* 3.5 24.7 - - + +
126M LEU* 3.8 12.6 - - + -
127M TYR* 3.6 50.7 - - + -
130M ILE* 3.5 24.7 - - + -
178M LEU* 4.2 11.4 - - + -
203M HIS* 3.1 17.2 + - + +
204M PRO* 1.3 76.1 - - + +
206M ASN* 1.3 59.6 + - - +
208M ALA* 3.6 4.1 - - - +
209M VAL* 2.8 32.2 + - - +
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Residues in contact with ASN 206 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123M PHE* 3.3 21.2 - - - -
201M LEU* 3.0 34.3 + - + +
202M GLY* 4.1 0.8 - - - -
203M HIS* 2.8 18.9 + - - +
205M LEU* 1.3 74.9 - - - +
207M ALA* 1.3 60.3 + - - +
209M VAL* 3.3 6.5 + - - +
210M TRP* 2.9 30.1 + - - +
89N GLY* 3.5 5.2 - - - -
90N ASP 3.0 24.0 + - - -
91N ASN 4.5 0.4 + - - -
92N GLU* 3.3 32.1 + - - +
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Residues in contact with ALA 207 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61M VAL* 4.0 19.6 - - + +
64M THR* 4.5 3.8 - - + -
200M CYS* 4.6 4.3 - - - -
201M LEU* 3.9 17.5 - - + +
203M HIS 3.7 1.8 + - - -
204M PRO 3.2 9.5 + - - +
206M ASN* 1.3 78.1 - - - +
208M ALA* 1.3 57.1 + - - +
210M TRP* 3.4 4.2 + - - +
211M LEU* 2.9 30.0 + - - +
230M THR* 3.1 31.6 - - - +
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Residues in contact with ALA 208 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110M LEU* 3.7 23.6 - - + -
126M LEU* 3.4 30.3 - - + +
204M PRO 3.2 6.6 + - - +
205M LEU 3.6 2.7 - - - +
206M ASN 3.3 0.2 - - - -
207M ALA* 1.3 81.0 - - - +
209M VAL* 1.3 57.3 + - - +
211M LEU* 3.3 5.8 + - - +
212M ALA* 2.9 31.2 + - - +
228M ILE* 4.6 16.6 - - + +
230M THR* 4.5 3.1 - - + +
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Residues in contact with VAL 209 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121M ILE* 3.7 11.2 - - + +
122M THR 4.3 0.9 - - - -
123M PHE* 3.8 33.7 - - + +
126M LEU* 4.0 20.9 - - + -
205M LEU 2.8 26.2 + - - +
206M ASN* 3.6 6.5 - - - +
208M ALA* 1.3 71.1 - - - +
210M TRP* 1.3 65.2 + - - +
212M ALA* 3.2 4.7 + - - +
213M ARG* 3.0 60.0 + - - +
92N GLU* 6.1 1.3 - - - +
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Residues in contact with TRP 210 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39M TYR* 4.4 7.0 - - - -
61M VAL* 4.2 9.2 - - + -
76M GLN* 3.7 27.1 + - - +
77M PRO* 3.5 45.0 - - + +
78M ASP 3.6 38.4 - - - -
79M PHE* 4.3 13.2 - + + -
201M LEU* 4.5 8.1 - - + -
206M ASN 2.9 17.6 + - - +
207M ALA* 3.6 5.4 - - - +
209M VAL* 1.3 78.3 - - - +
211M LEU* 1.3 90.7 + - + +
213M ARG* 3.4 10.1 + - - +
214M LYS* 3.1 46.7 + - + +
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Residues in contact with LEU 211 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59M ARG* 3.8 24.7 - - + -
61M VAL* 3.8 13.9 - - + -
79M PHE* 3.7 29.4 - - + -
207M ALA 2.9 18.1 + - - +
208M ALA 3.7 2.7 - - - +
210M TRP* 1.3 82.6 - - + +
212M ALA* 1.3 66.4 + - - +
214M LYS* 3.2 2.8 + - - +
215M MET* 2.9 49.8 + - + +
222M LEU* 4.1 5.6 - - + -
228M ILE* 3.7 41.1 - - + -
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Residues in contact with ALA 212 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116M LEU* 4.0 33.0 - - + +
118M ALA 4.6 0.8 - - - +
121M ILE* 3.9 19.3 - - + -
126M LEU* 4.4 4.3 - - + -
208M ALA 2.9 20.8 + - - +
209M VAL 3.6 4.3 - - - +
211M LEU* 1.3 73.7 - - - +
213M ARG* 1.3 61.4 + - - +
215M MET* 4.0 1.4 - - - +
216M ALA* 3.1 25.2 + - - +
222M LEU* 3.9 15.2 + - + +
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Residues in contact with ARG 213 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1E MET* 2.6 51.6 - - - +
118M ALA 4.6 0.4 - - - -
119M THR* 3.4 26.2 - - - +
120M ASP 4.0 0.4 - - - -
121M ILE* 2.8 33.5 + - + +
122M THR* 4.2 4.8 - - - +
123M PHE 5.1 0.4 - - - +
209M VAL* 3.0 33.4 + - - +
210M TRP* 3.6 11.4 - - + +
212M ALA* 1.3 74.6 - - - +
214M LYS* 1.3 65.7 + - - +
216M ALA* 3.2 6.2 + - - +
217M SER* 2.9 25.0 + - - -
87N CYS 4.9 7.1 + - - -
92N GLU* 6.0 0.2 + - - -
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Residues in contact with LYS 214 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39M TYR* 4.3 24.2 + - - -
76M GLN* 4.3 20.9 - - - +
79M PHE* 4.6 6.9 - - + -
210M TRP* 3.1 36.9 + - + +
211M LEU* 3.2 10.1 + - - +
213M ARG* 1.3 77.8 - - - +
215M MET* 1.3 74.1 + - + +
217M SER* 3.0 11.7 + - - +
218M LEU* 2.9 46.5 + - + +
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Residues in contact with MET 215 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59M ARG* 3.8 32.3 - - - -
79M PHE* 3.2 48.5 - - + -
211M LEU* 2.9 26.2 + - + +
212M ALA 4.0 2.9 - - - +
214M LYS* 1.3 85.4 - - + +
216M ALA* 1.3 60.9 + - - +
218M LEU* 3.3 13.5 + - + +
220M GLU* 2.9 49.6 + - - +
222M LEU* 3.9 30.7 - - + +
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Residues in contact with ALA 216 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116M LEU 4.0 4.3 - - - +
117M PRO 3.4 28.5 - - - +
118M ALA 3.9 9.2 - - - +
119M THR* 3.8 15.0 - - + +
212M ALA 3.1 19.5 + - - +
213M ARG 3.5 4.9 - - - +
215M MET* 1.3 77.4 - - - +
217M SER* 1.3 56.6 + - - +
219M GLY* 3.2 17.3 + - - -
221M PRO* 4.2 13.5 - - - +
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Residues in contact with SER 217 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119M THR* 3.9 17.5 - - - +
213M ARG 2.9 14.6 + - - -
214M LYS* 3.0 19.9 + - - +
216M ALA* 1.3 72.0 - - - +
218M LEU* 1.3 68.6 + - - +
219M GLY 3.1 5.7 + - - -
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Residues in contact with LEU 218 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39M TYR* 5.9 2.7 - - + -
79M PHE* 3.9 17.7 - - + -
214M LYS* 2.9 32.8 + - + +
215M MET* 3.7 29.6 - - + +
216M ALA 3.3 0.4 - - - -
217M SER* 1.3 85.0 + - - +
219M GLY* 1.3 61.3 + - - +
220M GLU* 3.5 20.7 + - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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