Contacts of the helix formed by residues 203 - 218 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90H ASP* 3.5 34.7 + - + +
168H GLY* 5.4 5.1 + - - -
123J PHE* 3.8 14.1 - + + -
127J TYR* 4.5 6.7 + - - -
178J LEU* 3.7 22.3 + - + +
179J LYS* 3.6 26.9 + - + +
197J GLY 3.8 2.2 + - - -
200J CYS 3.0 11.7 + - - +
201J LEU 3.1 1.2 - - - -
202J GLY* 1.3 78.9 - - - +
204J PRO* 1.3 67.8 - - + +
205J LEU* 3.1 46.3 + - + +
206J ASN* 2.8 39.4 + - - +
207J ALA 3.7 0.5 + - - -
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Residues in contact with PRO 204 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108J ILE* 3.9 26.9 - - + -
110J LEU* 6.1 0.4 - - + -
178J LEU* 3.4 29.6 - - + +
197J GLY* 3.3 20.6 - - - +
200J CYS* 4.0 17.9 - - + +
203J HIS* 1.3 89.4 - - + +
205J LEU* 1.3 65.2 + - + +
207J ALA* 3.2 15.1 + - - +
208J ALA 3.2 8.5 + - - -
230J THR* 3.7 27.9 - - + +
233J LEU* 4.9 1.3 - - + -
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Residues in contact with LEU 205 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110J LEU* 3.7 21.8 - - + -
123J PHE* 3.5 25.6 - - + +
126J LEU* 3.7 12.5 - - + +
127J TYR* 3.6 51.1 - - + -
130J ILE* 3.6 25.1 - - + -
178J LEU* 4.2 11.4 - - + -
203J HIS* 3.1 16.2 + - + +
204J PRO* 1.3 76.5 - - + +
206J ASN* 1.3 59.0 + - - +
207J ALA 3.3 0.2 - - - -
208J ALA* 3.6 3.9 - - - +
209J VAL* 2.8 32.2 + - - +
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Residues in contact with ASN 206 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89H GLY* 3.4 23.7 - - - -
90H ASP 2.9 26.0 + - - -
92H GLU* 3.5 26.5 + - - +
123J PHE* 3.4 8.2 - - - -
201J LEU* 3.0 33.9 + - + +
202J GLY* 4.1 0.6 - - - -
203J HIS* 2.8 18.1 + - - +
205J LEU* 1.3 75.3 - - - +
207J ALA* 1.3 60.5 + - - +
209J VAL* 3.3 6.6 + - - +
210J TRP* 2.9 30.3 + - - +
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Residues in contact with ALA 207 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61J VAL* 3.9 22.1 - - + +
64J THR* 4.5 4.3 - - + -
200J CYS* 4.6 3.6 - - - -
201J LEU* 3.9 17.5 - - + +
203J HIS 3.7 1.6 + - - -
204J PRO* 3.2 9.7 + - + +
206J ASN* 1.3 76.9 - - - +
208J ALA* 1.3 59.5 + - - +
210J TRP* 3.4 3.7 + - - +
211J LEU* 3.0 29.6 + - - +
230J THR* 3.1 29.6 - - - +
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Residues in contact with ALA 208 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110J LEU* 3.8 23.3 - - + -
126J LEU* 3.5 30.5 - - + +
204J PRO 3.2 7.9 + - - +
205J LEU* 3.6 3.1 - - - +
206J ASN 3.3 0.4 - - - -
207J ALA* 1.3 79.2 - - - +
209J VAL* 1.3 56.5 + - - +
211J LEU* 3.4 6.1 + - - +
212J ALA* 2.9 30.3 + - - +
228J ILE* 4.6 17.4 - - + +
230J THR* 4.5 3.3 - - + +
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Residues in contact with VAL 209 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121J ILE* 3.6 13.2 - - + +
122J THR 4.3 0.9 - - - -
123J PHE* 3.8 34.3 - - + +
126J LEU* 4.1 20.0 - - + -
205J LEU 2.8 23.3 + - - +
206J ASN* 3.7 7.0 - - - +
207J ALA 3.3 0.2 - - - -
208J ALA* 1.3 71.7 - - - +
210J TRP* 1.3 67.8 + - - +
212J ALA* 3.2 4.9 + - - +
213J ARG* 3.0 58.0 + - - +
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Residues in contact with TRP 210 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39J TYR* 4.4 6.1 - - - -
61J VAL* 4.2 8.7 - - + -
76J GLN* 3.7 27.2 + - - +
77J PRO* 3.5 43.8 - - + +
78J ASP* 3.6 38.4 - - - -
79J PHE* 4.2 13.2 - + + -
201J LEU* 4.5 7.0 - - + -
206J ASN 2.9 17.6 + - - +
207J ALA* 3.6 5.8 - - - +
209J VAL* 1.3 78.7 - - - +
211J LEU* 1.3 90.0 + - + +
213J ARG* 3.5 9.5 + - - +
214J LYS* 3.1 45.7 + - + +
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Residues in contact with LEU 211 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59J ARG* 3.7 24.7 - - + +
61J VAL* 3.8 14.4 - - + -
79J PHE* 3.7 29.8 - - + -
207J ALA 3.0 17.2 + - - +
208J ALA 3.7 3.1 - - - +
210J TRP* 1.3 82.2 - - + +
212J ALA* 1.3 65.2 + - - +
214J LYS* 3.2 2.4 + - - +
215J MET* 2.9 46.2 + - + +
222J LEU* 4.1 5.2 - - + -
228J ILE* 3.7 40.8 - - + -
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Residues in contact with ALA 212 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116J LEU* 4.0 33.0 - - + +
118J ALA 4.6 0.8 - - - +
121J ILE* 3.9 18.8 - - + -
126J LEU* 4.4 4.3 - - + -
208J ALA 2.9 18.1 + - - +
209J VAL 3.2 4.5 + - - +
211J LEU* 1.3 75.2 - - - +
213J ARG* 1.3 63.1 + - - +
215J MET* 3.6 1.7 + - - +
216J ALA* 3.1 24.3 + - - +
222J LEU* 3.9 15.0 + - + +
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Residues in contact with ARG 213 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84H ALA 5.3 3.2 + - - -
87H CYS 4.7 11.7 + - - -
92H GLU* 5.9 1.0 + - - -
118J ALA 4.6 1.6 - - - -
119J THR* 3.4 24.8 - - - +
120J ASP* 4.0 11.4 + - - +
121J ILE* 2.8 38.0 + - + -
122J THR* 4.3 7.7 - - - +
123J PHE 5.2 0.4 - - - +
209J VAL* 3.0 32.6 + - - +
210J TRP* 3.6 11.8 - - - +
212J ALA* 1.3 74.3 - - - +
214J LYS* 1.3 66.3 + - - +
216J ALA* 3.2 6.7 + - - +
217J SER* 2.9 25.1 + - - -
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Residues in contact with LYS 214 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39J TYR* 4.2 25.5 + - - -
76J GLN* 4.4 20.9 - - - +
79J PHE* 4.5 6.9 - - + -
210J TRP* 3.1 37.4 + - + +
211J LEU* 3.5 10.1 - - - +
213J ARG* 1.3 78.8 - - - +
215J MET* 1.3 67.6 + - + +
217J SER* 3.0 13.9 + - - +
218J LEU* 2.9 52.0 + - + +
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Residues in contact with MET 215 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59J ARG* 3.8 32.8 - - - -
79J PHE* 3.2 47.3 - - + -
211J LEU* 2.9 29.1 + - + +
212J ALA 4.0 3.4 - - - +
214J LYS* 1.3 85.3 - - + +
216J ALA* 1.3 60.3 + - - +
218J LEU* 3.2 14.5 + - + +
220J GLU* 2.9 49.2 + - - +
222J LEU* 3.9 27.1 - - + +
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Residues in contact with ALA 216 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116J LEU 4.0 4.7 - - - +
117J PRO 3.4 28.9 - - - +
118J ALA 3.9 9.4 - - - +
119J THR* 3.8 14.2 - - + +
212J ALA 3.1 19.5 + - - +
213J ARG 3.5 4.3 - - - +
215J MET* 1.3 76.2 - - - +
217J SER* 1.3 60.7 + - - +
219J GLY* 3.2 14.0 + - - -
221J PRO* 4.2 13.5 - - - +
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Residues in contact with SER 217 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119J THR* 4.0 17.4 - - - +
213J ARG 2.9 14.9 + - - -
214J LYS* 3.0 19.9 + - - +
216J ALA* 1.3 75.0 - - - +
218J LEU* 1.3 66.2 + - - +
219J GLY 3.2 3.3 + - - -
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Residues in contact with LEU 218 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39J TYR* 5.9 2.5 - - + -
79J PHE* 3.9 32.5 - - + -
214J LYS* 2.9 27.7 + - + +
215J MET* 3.7 17.9 - - + +
216J ALA 3.2 0.4 - - - -
217J SER* 1.3 84.7 + - - +
219J GLY* 1.3 60.9 + - - +
220J GLU* 3.4 20.8 + - + +
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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