Contacts of the helix formed by residues 204 - 215 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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200B VAL* 2.8 32.1 + - + +
201B PHE 4.1 0.3 - - - +
203B GLU* 1.3 72.0 - - + +
205B GLN* 1.3 63.7 + - - +
206B LYS* 3.0 23.5 + - - +
207B THR* 3.1 23.9 + - - +
208B ARG* 3.2 23.4 + - - +
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Residues in contact with GLN 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203B GLU 3.9 3.6 + - - -
204B ASN* 1.3 72.4 + - - +
206B LYS* 1.3 62.6 + - + +
208B ARG* 2.6 40.5 + - - +
209B GLU* 2.9 70.3 + - - +
206C LYS* 3.9 41.3 + - + +
210C GLU* 4.5 5.9 + - - +
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Residues in contact with LYS 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205A GLN* 3.6 35.6 - - + +
206A LYS* 4.1 16.6 - - - +
209A GLU* 3.5 26.7 + - - +
204B ASN* 3.0 10.6 + - - +
205B GLN* 1.3 78.1 - - + +
207B THR* 1.3 60.5 + - - +
209B GLU* 3.6 28.3 + - + +
210B GLU* 2.9 31.2 + - - +
206C LYS* 5.1 9.6 - - - +
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Residues in contact with THR 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96B MET* 3.5 13.1 - - + +
124B ILE* 3.6 31.9 - - + +
200B VAL* 3.8 8.5 - - + +
201B PHE* 4.0 19.1 - - + -
204B ASN* 3.1 37.7 + - - +
206B LYS* 1.3 74.9 - - - +
208B ARG* 1.3 63.8 + - - +
210B GLU* 3.3 8.8 + - - +
211B PHE* 3.1 19.9 + - - +
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Residues in contact with ARG 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197B MET* 3.8 35.0 - - + +
201B PHE* 3.0 40.0 + - - +
202B ARG* 3.3 21.4 + - - +
204B ASN 3.2 8.4 + - - +
205B GLN* 2.6 43.0 + - - +
207B THR* 1.3 79.9 - - - +
209B GLU* 1.3 56.9 + - - +
211B PHE* 3.2 7.8 + - - +
212B LEU* 2.9 37.0 + - + +
95C GLU* 4.7 5.7 + - - -
210C GLU* 3.0 27.2 + - - +
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Residues in contact with GLU 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209A GLU* 5.0 4.7 - - - +
205B GLN* 2.9 52.9 + - - +
206B LYS* 3.6 28.8 + - - +
208B ARG* 1.3 76.1 - - + +
210B GLU* 1.3 57.9 + - - +
212B LEU* 3.3 8.5 + - + +
213B SER* 2.8 37.6 + - - +
206C LYS* 3.8 14.0 - - - +
209C GLU* 5.5 3.5 - - - +
210C GLU* 5.8 1.6 - - + +
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Residues in contact with GLU 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205A GLN* 4.6 5.2 - - - +
208A ARG* 3.0 40.7 + - - +
209A GLU* 5.8 2.3 - - + +
212A LEU* 3.9 22.4 - - + +
95B GLU* 4.5 9.5 - - - +
96B MET* 4.1 24.3 - - + +
206B LYS 2.9 17.9 + - - +
207B THR* 3.5 7.8 - - - +
209B GLU* 1.3 77.6 - - - +
211B PHE* 1.3 60.7 + - - +
213B SER* 3.4 6.4 + - - -
214B HIS* 3.2 32.0 + - + -
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Residues in contact with PHE 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96B MET* 3.8 10.3 - - - -
98B VAL* 4.1 18.6 - - + -
120B HIS 3.8 12.6 - - - -
121B ILE* 3.7 5.4 - - - -
122B GLY* 3.4 26.5 - - - -
170B GLY 3.5 31.9 - - - -
172B VAL* 3.8 24.7 - - + -
197B MET* 3.9 14.4 - - + -
201B PHE* 3.5 31.0 - + + -
207B THR 3.1 8.7 + - - +
208B ARG 3.5 7.2 - - - +
210B GLU* 1.3 76.5 - - - +
212B LEU* 1.3 64.6 + - + +
214B HIS* 3.1 18.3 + - - +
215B LEU* 3.5 17.9 + - + +
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Residues in contact with LEU 212 (chain B).
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* 3.8 29.4 - - + -
197B MET* 4.3 5.6 - - + -
208B ARG* 2.9 31.1 + - + +
209B GLU* 3.8 7.2 - - + +
211B PHE* 1.3 84.2 - - + +
213B SER* 1.3 61.7 + - - +
215B LEU* 3.1 23.9 + - + +
216B ARG* 3.6 21.1 + - - +
210C GLU* 3.9 35.9 - - + +
213C SER* 6.3 2.2 - - - -
214C HIS* 4.0 22.2 - - + +
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Residues in contact with SER 213 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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212A LEU* 6.3 2.0 - - - -
216A ARG* 3.3 34.3 + - - -
209B GLU* 2.8 21.9 + - - +
210B GLU* 3.8 7.9 - - - -
212B LEU* 1.3 72.0 - - - +
214B HIS* 1.3 65.2 + - - +
215B LEU 3.1 2.0 - - - -
216B ARG* 3.1 45.2 + - - +
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Residues in contact with HIS 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A VAL* 4.9 7.2 - - + -
193A VAL* 4.1 26.6 - - + +
195A SER* 5.5 5.1 + - - -
212A LEU* 4.0 36.3 - - + +
215A LEU* 6.2 0.4 - - + -
216A ARG* 6.1 0.2 - - - -
96B MET* 4.2 6.3 - - - +
98B VAL* 4.1 31.6 - - + -
100B LYS* 3.0 27.8 + - - +
210B GLU* 3.2 33.2 + - + +
211B PHE 3.1 10.4 + - - +
213B SER* 1.3 76.5 - - - +
215B LEU* 1.3 61.5 + - - +
216B ARG 3.5 4.7 + - - +
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Residues in contact with LEU 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B VAL* 4.2 12.6 - - + -
100B LYS* 4.1 22.4 - - + -
120B HIS* 3.6 47.1 - - + +
172B VAL* 3.9 28.5 - - + -
211B PHE* 3.5 20.2 - - + +
212B LEU* 3.1 17.2 + - + +
213B SER 3.1 0.8 - - - -
214B HIS* 1.3 79.4 - - - +
216B ARG* 1.3 59.0 + - + +
214C HIS* 6.2 0.2 - - + -
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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