Contacts of the helix formed by residues 204 - 216 (chain C) in PDB entry 1WUR
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 ASN 204 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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200C VAL* 2.9 30.3 + - + +
203C GLU* 1.3 73.0 - - + +
205C GLN* 1.3 63.3 + - - +
206C LYS* 2.8 37.9 + - - +
207C THR* 3.1 23.0 + - - +
208C ARG* 3.2 23.5 + - - +
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Residues in contact with GLN 205 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203C GLU 3.4 5.8 + - - +
204C ASN* 1.3 72.1 + - - +
206C LYS* 1.3 66.5 + - + +
208C ARG* 2.9 36.8 + - - +
209C GLU* 3.0 65.7 + - - +
204D ASN* 5.6 0.6 + - - -
206D LYS* 3.9 48.6 - - + +
209D GLU* 5.5 0.2 - - - +
210D GLU* 4.7 4.2 - - - +
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Residues in contact with LYS 206 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205B GLN* 3.9 34.6 + - + +
206B LYS* 5.1 10.1 - - - +
209B GLU* 3.8 21.5 - - - +
204C ASN* 2.8 12.4 + - - +
205C GLN* 1.3 81.9 - - + +
207C THR* 1.3 60.8 + - - +
209C GLU* 3.7 17.3 + - + +
210C GLU* 3.0 30.5 + - - +
206D LYS* 4.5 16.2 - - - +
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Residues in contact with THR 207 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96C MET* 3.5 15.7 - - + +
124C ILE* 3.7 31.6 - - + +
200C VAL* 3.8 13.3 - - + +
201C PHE* 3.9 20.4 - - + -
204C ASN* 3.1 30.6 + - - +
205C GLN 3.3 0.2 - - - -
206C LYS* 1.3 75.4 - - - +
208C ARG* 1.3 65.0 + - - +
210C GLU* 3.3 5.9 + - - -
211C PHE* 3.0 19.1 + - - +
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Residues in contact with ARG 208 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197C MET* 3.7 30.7 - - + +
201C PHE* 3.0 39.7 + - - +
202C ARG* 3.2 22.4 + - - +
204C ASN 3.2 8.8 + - - +
205C GLN* 2.9 40.7 + - - +
206C LYS 3.4 0.2 - - - -
207C THR* 1.3 79.6 - - - +
209C GLU* 1.3 57.1 + - - +
211C PHE* 3.2 7.7 + - - +
212C LEU* 2.9 45.7 + - + +
95D GLU* 4.6 5.0 + - - -
210D GLU* 2.9 28.8 + - - +
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Residues in contact with GLU 209 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209B GLU* 5.5 3.3 - - - +
205C GLN* 3.0 52.4 + - - +
206C LYS* 3.7 17.2 + - - +
208C ARG* 1.3 77.6 - - + +
210C GLU* 1.3 56.5 + - - +
212C LEU* 3.2 9.3 + - + +
213C SER* 2.8 36.8 + - - +
216C ARG* 5.1 0.2 + - - -
206D LYS* 4.1 12.5 + - - +
209D GLU* 3.9 17.6 - - - +
210D GLU* 5.8 2.2 - - - +
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Residues in contact with GLU 210 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195B SER* 5.7 1.0 + - - -
197B MET* 6.1 0.3 - - - +
205B GLN* 4.5 5.7 + - - +
208B ARG* 3.0 34.9 + - - +
209B GLU* 5.8 1.6 - - + +
212B LEU* 3.9 27.5 - - + +
95C GLU* 4.6 8.0 - - - +
96C MET* 3.9 25.6 - - + +
206C LYS 3.0 18.1 + - - +
207C THR* 3.6 6.7 - - - +
209C GLU* 1.3 75.7 - - - +
211C PHE* 1.3 62.7 + - - +
213C SER* 3.4 8.2 + - - -
214C HIS* 3.2 36.1 + - + -
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Residues in contact with PHE 211 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96C MET* 3.8 10.3 - - - +
98C VAL* 4.1 19.1 - - + -
120C HIS 3.8 14.1 - - - -
121C ILE* 3.7 5.4 - - - -
122C GLY* 3.4 27.4 - - - -
170C GLY* 3.4 33.0 - - - -
172C VAL* 3.9 18.6 - - + -
197C MET* 3.9 13.2 - - + -
201C PHE* 3.6 30.5 - + + -
207C THR 3.0 9.4 + - - +
208C ARG 3.5 6.5 - - - +
210C GLU* 1.3 76.8 - - - +
212C LEU* 1.3 67.0 + - + +
214C HIS* 3.2 17.6 + - - +
215C LEU* 3.5 20.4 + - + +
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Residues in contact with LEU 212 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172C VAL* 3.8 29.6 - - + -
197C MET* 4.2 6.3 - - + -
208C ARG* 2.9 33.3 + - + +
209C GLU* 3.8 6.7 - - + +
211C PHE* 1.3 85.6 - - + +
213C SER* 1.3 61.6 + - - +
215C LEU* 3.2 23.2 + - + +
216C ARG* 3.5 19.7 + - - +
210D GLU* 4.0 34.3 - - + +
213D SER* 6.3 1.6 - - - -
214D HIS* 4.2 21.8 - - + +
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Residues in contact with SER 213 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212B LEU* 6.3 2.0 - - - -
216B ARG* 3.5 40.2 + - - +
209C GLU* 2.8 20.8 + - - +
210C GLU* 3.7 8.7 - - - -
211C PHE 3.2 0.2 - - - -
212C LEU* 1.3 74.0 - - - +
214C HIS* 1.3 65.9 + - - +
216C ARG* 3.2 39.2 + - - +
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Residues in contact with HIS 214 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172B VAL* 4.9 8.0 - - + +
193B VAL* 4.0 26.8 - - + +
195B SER* 5.5 5.3 + - - -
212B LEU* 4.0 35.1 - - + +
215B LEU* 6.2 0.4 - - + -
96C MET* 4.3 5.5 - - - +
98C VAL* 4.2 33.0 - - + -
100C LYS* 2.9 28.2 + - - +
210C GLU* 3.2 34.1 + - + +
211C PHE 3.2 9.7 + - - +
213C SER* 1.3 76.3 - - - +
215C LEU* 1.3 61.8 + - - +
216C ARG 3.5 3.5 + - - -
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Residues in contact with LEU 215 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98C VAL* 4.2 13.5 - - + -
100C LYS* 4.0 23.4 + - + +
120C HIS* 3.6 47.3 - - + +
172C VAL* 4.0 27.1 - - + -
211C PHE* 3.6 19.5 - - + +
212C LEU* 3.5 16.2 - - + +
213C SER 3.1 0.6 - - - -
214C HIS* 1.3 75.6 - - - +
216C ARG* 1.3 63.4 + - - +
214D HIS* 6.1 0.7 - - + -
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Residues in contact with ARG 216 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216B ARG* 3.4 47.7 - - - +
209C GLU 5.1 0.2 + - - -
212C LEU* 3.5 14.4 + - - +
213C SER* 3.2 51.0 + - - +
214C HIS 4.4 3.5 - - - +
215C LEU* 1.3 82.8 - - - +
213D SER* 3.5 38.0 + - - -
216D ARG* 3.4 46.9 - - + +
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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