Contacts of the helix formed by residues 194 - 206 (chain B) in PDB entry 1WG8
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 ALA 194 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113B TYR* 4.3 9.6 - - + -
178B ALA* 3.7 25.8 - - + +
181B VAL* 4.0 21.8 - - + +
193B PRO* 1.3 79.5 - - + +
195B ARG* 1.3 55.8 + - - +
196B LYS 3.6 0.4 - - - -
197B THR* 3.4 5.2 + - - -
198B PHE* 2.9 59.9 + - + -
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Residues in contact with ARG 195 (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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113B TYR* 3.7 31.5 - - + +
190B ALA* 3.2 27.7 + - - +
191B GLY* 3.3 10.9 - - - -
192B HIS* 3.6 26.4 - - - +
193B PRO 2.6 7.3 + - - -
194B ALA* 1.3 72.1 - - - +
196B LYS* 1.3 74.4 + - + +
198B PHE* 2.9 15.4 + - - +
199B GLN* 3.0 12.4 + - + +
273B ARG* 4.5 22.5 - - - +
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Residues in contact with LYS 196 (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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150B GLY* 3.0 26.3 - - - +
151B GLU* 2.5 36.2 + - - +
152B GLU* 3.9 24.0 - - + -
153B PRO* 4.2 7.9 - - + +
188B ARG* 5.4 14.6 - - - +
192B HIS 5.4 2.0 - - - +
193B PRO 3.8 5.5 + - - +
194B ALA 3.6 0.2 - - - -
195B ARG* 1.3 87.7 - - + +
197B THR* 1.3 56.8 + - - +
199B GLN* 3.3 10.1 + - - +
200B ALA* 3.0 27.7 + - - +
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Residues in contact with THR 197 (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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146B LEU* 3.6 29.3 - - + +
152B GLU* 4.5 4.6 - - - +
158B ILE* 3.7 28.8 - - + +
162B ILE* 5.2 3.1 - - + -
177B LEU* 4.6 9.0 - - + -
181B VAL* 4.3 17.4 - - + +
193B PRO 4.7 1.1 + - - -
194B ALA* 3.4 14.6 + - - +
195B ARG 3.1 0.8 - - - -
196B LYS* 1.3 75.8 - - - +
198B PHE* 1.3 68.9 + - + +
200B ALA* 3.3 2.6 + - - +
201B LEU* 3.1 37.0 + - + +
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Residues in contact with PHE 198 (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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110B GLY 4.7 1.6 - - - -
111B PHE 3.8 18.4 - - - +
112B SER 3.8 1.6 - - - -
113B TYR* 3.4 42.6 - + + -
119B LEU* 4.5 2.9 - - + -
121B MET* 3.1 25.9 - - + +
174B THR* 3.5 36.1 - - + -
177B LEU* 3.6 33.4 - - + -
178B ALA 4.4 0.4 - - - -
194B ALA* 2.9 46.1 + - + +
195B ARG 2.9 4.2 + - - +
197B THR* 1.3 79.4 - - + +
199B GLN* 1.3 57.8 + - - +
201B LEU* 3.4 5.3 + - + +
202B ARG* 3.0 23.4 + - - +
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Residues in contact with GLN 199 (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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149B LEU 3.6 16.8 - - - +
150B GLY* 4.5 6.6 - - - +
195B ARG* 3.0 12.5 + - + +
196B LYS* 3.6 11.9 - - - +
197B THR 3.2 0.2 - - - -
198B PHE* 1.3 75.3 - - - +
200B ALA* 1.3 65.4 + - - +
202B ARG* 3.3 12.3 + - - +
203B ILE* 3.1 32.5 + - + +
235B HIS* 3.2 39.3 + - + +
237B LEU* 5.5 1.4 - - - +
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Residues in contact with ALA 200 (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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145B LEU* 3.5 25.4 - - + +
146B LEU* 4.2 8.3 - - + -
149B LEU* 3.9 16.9 + - - +
150B GLY* 3.6 18.4 - - - +
196B LYS 3.0 14.7 + - - +
197B THR 3.5 9.6 - - - +
199B GLN* 1.3 76.6 - - - +
201B LEU* 1.3 58.1 - - - +
203B ILE* 3.4 2.6 + - - +
204B TYR* 3.0 29.3 + - - +
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Residues in contact with LEU 201 (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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121B MET* 3.7 20.9 - - - -
130B ALA* 4.7 9.9 - - + +
133B VAL* 4.1 20.4 - - + -
134B VAL* 3.8 24.9 - - + -
142B LEU* 5.8 3.8 - - + -
145B LEU* 4.1 17.3 - - + -
146B LEU* 5.3 3.4 - - + -
177B LEU* 3.7 30.1 - - + -
197B THR* 3.1 25.9 + - + +
198B PHE* 3.7 3.4 - - + +
199B GLN 3.3 0.2 - - - -
200B ALA* 1.3 77.7 - - - +
202B ARG* 1.3 55.7 + - - +
204B TYR* 3.7 3.1 - - + +
205B VAL* 2.8 39.5 + - + +
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Residues in contact with ARG 202 (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 GLY* 3.7 34.9 - - - +
99B VAL* 3.9 23.0 - - - +
111B PHE* 3.9 16.8 - - + -
121B MET* 3.9 14.3 - - + -
123B MET* 4.0 6.9 - - - +
198B PHE 3.0 17.3 + - - +
199B GLN* 3.3 12.9 + - - +
201B LEU* 1.3 74.9 - - - +
203B ILE* 1.3 65.6 + - - +
205B VAL* 4.8 0.2 - - - -
206B ASN* 2.9 42.0 + - - +
208B GLU* 2.8 45.7 + - - +
235B HIS* 3.6 23.6 - - - -
238B GLU* 4.5 3.0 + - - -
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Residues in contact with ILE 203 (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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149B LEU* 3.6 40.8 - - + +
199B GLN* 3.1 17.8 + - + +
200B ALA 3.6 6.1 - - - +
202B ARG* 1.3 79.3 - - - +
204B TYR* 1.3 53.4 + - - +
207B ASP* 2.8 29.6 + - - -
208B GLU* 3.0 28.3 + - + +
209B LEU* 3.5 28.5 - - + +
235B HIS* 3.5 41.5 - - + +
237B LEU* 4.3 4.9 - - + -
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Residues in contact with TYR 204 (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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133B VAL* 3.8 34.8 - - + -
137B LEU* 4.0 20.9 - - + +
145B LEU* 3.5 33.9 - - + -
149B LEU* 4.0 17.3 - - + -
200B ALA 3.0 18.2 + - - +
201B LEU* 3.7 4.5 - - + +
203B ILE* 1.3 73.6 - - - +
205B VAL* 1.3 69.7 + - + +
207B ASP* 3.1 14.2 + - - +
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Residues in contact with VAL 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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120B ASP 4.1 3.6 - - - +
121B MET* 4.0 14.4 - - + +
122B ARG* 3.7 23.6 - - + -
126B GLU 4.2 13.4 - - - +
127B GLY* 5.7 0.5 - - - -
128B PRO 3.7 19.4 - - - +
129B THR 4.2 2.5 - - - -
130B ALA* 3.7 33.9 - - + +
133B VAL* 4.2 14.1 - - + -
201B LEU* 2.8 26.4 + - + +
202B ARG 4.1 2.0 - - - +
204B TYR* 1.3 76.2 - - + +
206B ASN* 1.3 60.1 + - - +
207B ASP* 5.3 0.5 - - - +
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Residues in contact with ASN 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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52B GLN* 4.4 7.2 + - - +
74B ASN* 5.1 6.2 + - - -
76B ARG* 4.8 1.9 + - - -
121B MET 2.9 23.0 + - - -
122B ARG* 3.8 3.5 - - - +
123B MET* 2.9 59.3 + - + +
124B GLY 4.4 1.6 + - - -
202B ARG* 2.9 34.2 + - - +
205B VAL* 1.3 79.8 - - - +
207B ASP* 1.3 71.7 + - - +
208B GLU* 2.9 7.9 + - + +
211B ALA* 4.7 5.5 - - - +
3141B SAM 5.9 0.3 + - - -
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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