Contacts of the helix formed by residues 203 - 218 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123K PHE* 3.8 13.5 - + - -
127K TYR* 4.5 6.3 + - - -
178K LEU* 3.6 28.7 + - + +
179K LYS* 3.6 20.1 + - + +
197K GLY 3.9 1.6 - - - -
200K CYS 3.0 11.7 + - - +
201K LEU 3.1 2.0 + - - -
202K GLY* 1.3 79.0 - - - +
204K PRO* 1.4 68.4 - - + +
205K LEU* 3.1 47.3 + - + +
206K ASN* 2.8 30.8 + - - +
207K ALA 3.7 0.3 + - - -
90L ASP* 3.5 43.6 + - + +
168L GLY* 5.4 4.8 + - - -
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Residues in contact with PRO 204 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108K ILE* 3.8 27.6 - - + -
110K LEU* 6.0 0.2 - - + -
178K LEU* 3.4 28.5 - - + +
197K GLY* 3.4 19.5 - - - +
200K CYS* 4.1 17.3 - - + +
203K HIS* 1.4 90.5 - - + +
205K LEU* 1.3 65.3 + - + +
207K ALA* 3.2 8.5 + - - +
208K ALA 3.2 15.4 + - - -
230K THR* 3.7 25.6 - - + +
233K LEU* 4.9 1.3 - - + -
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Residues in contact with LEU 205 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110K LEU* 3.7 22.4 - - + -
123K PHE* 3.5 24.2 - - + +
126K LEU* 3.7 12.8 - - + -
127K TYR* 3.6 50.7 - - + -
130K ILE* 3.5 25.4 - - + -
178K LEU* 4.2 11.7 - - + -
203K HIS* 3.1 16.7 + - + +
204K PRO* 1.3 76.2 - - + +
206K ASN* 1.3 59.6 + - - +
208K ALA* 3.6 4.5 - - - +
209K VAL* 2.9 31.9 + - - +
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Residues in contact with ASN 206 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123K PHE* 3.4 7.3 - - - -
201K LEU* 3.0 32.8 + - + +
202K GLY* 4.1 0.6 - - - -
203K HIS* 2.8 18.1 + - - +
205K LEU* 1.3 76.3 - - - +
207K ALA* 1.3 59.8 + - - +
209K VAL* 3.2 6.4 + - - +
210K TRP* 2.9 30.0 + - - +
89L GLY* 3.3 24.3 - - - -
90L ASP 2.8 26.5 + - - -
91L ASN 4.5 0.4 - - - -
92L GLU* 3.4 27.0 + - + +
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Residues in contact with ALA 207 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61K VAL* 4.0 22.0 - - + +
64K THR* 4.5 3.8 - - + -
200K CYS* 4.6 4.0 - - - -
201K LEU* 3.9 18.2 - - + +
203K HIS 3.7 1.6 + - - -
204K PRO 3.2 9.1 + - - +
206K ASN* 1.3 76.2 - - - +
208K ALA* 1.3 64.5 + - - +
210K TRP* 3.4 3.8 + - - +
211K LEU* 3.0 24.9 + - - +
230K THR* 3.1 29.8 - - - +
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Residues in contact with ALA 208 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110K LEU* 3.7 22.0 - - + -
126K LEU* 3.5 31.6 - - + +
204K PRO 3.2 8.1 + - - +
205K LEU* 3.6 2.9 - - - +
206K ASN 3.3 0.2 - - - -
207K ALA* 1.3 79.1 - - - +
209K VAL* 1.3 56.3 + - - +
211K LEU* 3.4 5.7 + - - +
212K ALA* 2.9 30.0 + - - +
228K ILE* 4.5 17.4 - - + +
230K THR* 4.5 3.3 - - + +
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Residues in contact with VAL 209 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121K ILE* 3.6 13.7 - - + +
122K THR 4.3 0.9 - - - -
123K PHE* 3.8 33.7 - - + +
126K LEU* 4.0 20.9 - - + -
205K LEU 2.9 26.1 + - - +
206K ASN* 3.7 6.7 - - - +
208K ALA* 1.3 74.7 - - - +
210K TRP* 1.3 65.1 + - - +
212K ALA* 3.2 4.5 + - - +
213K ARG* 3.1 57.5 + - - +
92L GLU* 6.1 0.7 - - - +
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Residues in contact with TRP 210 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39K TYR* 4.3 6.1 - - - -
61K VAL* 4.2 8.5 - - + -
76K GLN* 3.7 30.4 + - - +
77K PRO* 3.5 40.2 - - + +
78K ASP* 3.7 38.6 - - - -
79K PHE* 4.2 12.8 - + + -
201K LEU* 4.5 7.9 - - + -
206K ASN 2.9 17.5 + - - +
207K ALA* 3.6 5.8 - - - +
209K VAL* 1.3 79.2 - - - +
211K LEU* 1.3 88.5 + - + +
213K ARG* 3.5 10.5 + - + +
214K LYS* 3.1 48.7 + - + +
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Residues in contact with LEU 211 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59K ARG* 3.7 27.6 - - + -
61K VAL* 3.9 14.4 - - + -
79K PHE* 3.7 29.2 - - + -
207K ALA 3.0 16.8 + - - +
208K ALA* 3.7 3.1 - - - +
210K TRP* 1.3 82.9 - - + +
212K ALA* 1.3 66.1 + - - +
214K LYS* 3.2 2.4 + - - +
215K MET* 2.9 43.5 + - + +
222K LEU* 4.2 4.9 - - + -
228K ILE* 3.6 42.0 - - + -
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Residues in contact with ALA 212 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116K LEU* 4.0 33.7 - - + +
118K ALA 5.0 0.9 - - - +
121K ILE* 3.8 18.4 - - + -
126K LEU* 4.4 4.0 - - + -
208K ALA 2.9 18.1 + - - +
209K VAL 3.6 4.9 - - - +
211K LEU* 1.3 75.2 - - - +
213K ARG* 1.3 57.4 + - - +
215K MET* 4.0 1.4 - - - +
216K ALA* 3.1 29.1 + - - +
222K LEU* 4.0 15.5 + - + +
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Residues in contact with ARG 213 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118K ALA 4.6 1.8 - - - -
119K THR* 3.4 24.7 - - - +
120K ASP 4.0 0.4 - - - -
121K ILE* 2.8 35.1 + - + +
122K THR* 4.3 4.0 - - - +
123K PHE 5.2 0.2 - - - +
209K VAL* 3.1 33.0 + - - +
210K TRP* 3.6 11.7 - - - +
212K ALA* 1.3 74.2 - - - +
214K LYS* 1.3 65.3 + - - +
216K ALA* 3.3 6.4 + - - +
217K SER* 2.9 26.0 + - - -
87L CYS 4.8 7.3 + - - -
92L GLU* 5.9 0.8 + - - -
1T MET* 2.6 53.7 - - - +
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Residues in contact with LYS 214 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39K TYR* 4.2 24.7 + - - -
76K GLN* 4.4 20.6 - - - +
79K PHE* 4.5 7.1 - - + -
210K TRP* 3.1 37.4 + - + +
211K LEU* 3.2 9.8 + - - +
213K ARG* 1.3 76.8 - - - +
215K MET* 1.3 69.9 + - + +
217K SER* 3.1 12.7 + - - +
218K LEU* 2.9 52.3 + - + +
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Residues in contact with MET 215 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59K ARG* 3.8 31.9 - - - -
79K PHE* 3.2 46.7 - - + -
211K LEU* 2.9 26.2 + - + +
212K ALA 4.0 3.8 - - - +
214K LYS* 1.3 84.9 - - + +
216K ALA* 1.3 60.5 + - - +
218K LEU* 3.3 13.9 + - + +
220K GLU* 2.9 51.5 + - - +
222K LEU* 3.8 30.3 - - + +
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Residues in contact with ALA 216 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116K LEU 4.0 8.1 - - - +
117K PRO 3.4 25.1 - - - +
118K ALA 3.9 9.4 - - - +
119K THR* 3.9 14.5 - - + +
212K ALA 3.1 19.9 + - - +
213K ARG 3.5 4.7 - - - +
214K LYS 3.2 0.2 - - - -
215K MET* 1.3 77.0 - - - +
217K SER* 1.3 58.9 + - - +
219K GLY* 3.2 14.0 + - - -
221K PRO* 4.2 13.8 - - - +
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Residues in contact with SER 217 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119K THR* 3.9 16.6 - - - +
213K ARG 2.9 15.0 + - - -
214K LYS* 3.1 18.7 + - - +
216K ALA* 1.3 74.7 - - - +
218K LEU* 1.3 66.9 + - - +
219K GLY 3.2 3.5 + - - -
0T LEU* 6.5 0.4 - - - -
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Residues in contact with LEU 218 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39K TYR* 5.9 2.0 - - + -
79K PHE* 4.0 18.2 - - + -
214K LYS* 2.9 32.2 + - + +
215K MET* 3.7 28.0 - - + +
216K ALA 3.2 0.4 - - - -
217K SER* 1.3 84.2 + - - +
219K GLY* 1.3 61.0 + - - +
220K GLU* 3.5 21.0 + - + +
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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