Contacts of the helix formed by residues 168 - 182 (chain A) in PDB entry 1O0W
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 ASP 168 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96A MET* 4.0 13.4 - - + +
100A LYS* 3.1 37.0 + - - +
167A PHE* 1.3 72.1 - - - +
169A TYR* 1.3 64.8 + - - +
170A LYS* 3.5 4.2 + - - +
171A THR* 2.6 40.7 + - + +
172A ALA* 3.2 20.4 + - - +
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Residues in contact with TYR 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155A PHE* 3.9 22.4 - + - -
159A LYS* 3.6 8.5 - - - +
165A MET 2.7 29.3 + - - -
166A LEU* 3.5 18.4 - - + +
167A PHE* 2.8 53.0 + + - -
168A ASP* 1.3 71.3 + - - +
170A LYS* 1.3 64.2 + - - +
172A ALA* 3.2 2.6 + - - +
173A LEU* 2.9 24.9 + - - +
225A LYS* 3.5 43.2 - - + +
228A ALA* 3.7 9.7 - - + +
229A ARG* 3.4 42.6 - - + +
232A TYR* 5.2 1.5 - - + +
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Residues in contact with LYS 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A LYS* 5.2 7.9 - - - +
168A ASP* 3.4 7.2 + - - +
169A TYR* 1.3 76.0 - - - +
171A THR* 1.3 63.2 + - - +
173A LEU* 3.5 1.4 + - - +
174A GLN* 3.1 24.9 + - - +
185A PRO* 5.4 0.2 - - - +
187A TYR* 3.9 36.7 + - + +
221A LYS* 5.1 3.4 - - - +
224A GLU* 2.6 41.0 + - + +
225A LYS* 4.3 20.9 - - + +
228A ALA* 3.9 14.6 - - + -
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Residues in contact with THR 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A LYS* 4.8 1.7 + - - -
168A ASP* 2.6 36.1 + - + +
170A LYS* 1.3 78.9 - - - +
172A ALA* 1.3 63.3 + - - +
174A GLN* 3.5 7.0 + - - +
175A GLU* 3.2 23.1 + - + +
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Residues in contact with ALA 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A PHE* 3.6 27.8 - - + -
168A ASP 3.2 8.1 + - - +
169A TYR 3.7 3.8 - - - +
171A THR* 1.3 77.7 - - - +
173A LEU* 1.3 64.0 + - - +
175A GLU* 3.3 14.3 + - - +
176A ILE* 3.1 17.7 + - - +
232A TYR* 3.6 32.0 - - + +
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Residues in contact with LEU 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169A TYR 2.9 16.4 + - - +
170A LYS 3.9 3.6 - - - +
172A ALA* 1.3 73.9 - - - +
174A GLN* 1.3 61.4 + - - +
176A ILE* 3.3 6.5 + - + +
177A VAL* 2.8 54.0 + - + +
185A PRO* 4.1 6.7 - - + -
187A TYR* 3.4 20.4 - - - +
205A VAL* 3.6 23.8 - - + -
207A VAL* 6.5 0.2 - - + -
228A ALA* 3.8 21.1 - - + +
231A ALA* 4.0 7.2 - - + -
232A TYR* 3.9 21.4 - - + +
235A LEU* 3.8 20.0 - - + -
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Residues in contact with GLN 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170A LYS 3.1 18.1 + - - +
171A THR* 3.8 7.8 - - - +
173A LEU* 1.3 76.8 - - - +
175A GLU* 1.3 58.1 + - - +
177A VAL* 4.0 0.2 - - - +
178A GLN* 2.9 36.0 + - + +
184A PRO* 3.8 25.2 - - + +
185A PRO* 3.8 23.5 + - + +
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Residues in contact with GLU 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A THR* 3.2 11.8 + - + +
172A ALA* 3.5 15.7 - - - +
173A LEU 3.2 0.2 - - - -
174A GLN* 1.3 80.8 - - - +
176A ILE* 1.3 58.4 + - + +
178A GLN* 4.1 3.5 - - - +
179A SER* 2.9 38.4 + - - +
232A TYR* 5.7 1.9 + - - -
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Residues in contact with ILE 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A ALA 3.1 10.9 + - - +
173A LEU* 3.4 26.0 - - + +
175A GLU* 1.3 83.5 - - + +
177A VAL* 1.3 64.7 + - + +
179A SER* 3.8 6.5 - - - -
180A GLU* 3.0 43.0 + - + +
232A TYR* 4.4 12.6 - - + +
235A LEU* 4.3 9.9 - - + -
236A LEU* 4.0 24.2 - - + -
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Residues in contact with VAL 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173A LEU* 2.8 45.6 + - + +
174A GLN 4.0 2.0 - - - +
176A ILE* 1.3 78.1 - - + +
178A GLN* 1.3 60.8 + - - +
180A GLU* 4.0 5.6 - - - +
181A HIS* 2.8 31.4 + - + +
183A VAL 3.2 16.6 - - - +
185A PRO* 4.0 17.5 - - + -
207A VAL* 3.6 39.5 - - + -
235A LEU* 4.2 10.3 - - + -
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Residues in contact with GLN 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A GLN* 2.9 22.2 + - + +
175A GLU* 4.1 3.6 - - - +
177A VAL* 1.3 76.4 - - - +
179A SER* 1.3 62.3 + - - +
182A LYS* 2.8 65.6 + - - +
183A VAL* 3.6 20.2 + - - +
184A PRO* 3.8 10.8 - - + +
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Residues in contact with SER 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A GLU* 2.9 28.6 + - - +
176A ILE* 3.8 10.5 - - - -
177A VAL 3.3 0.2 - - - -
178A GLN* 1.3 78.9 - - - +
180A GLU* 1.3 57.4 + - - +
182A LYS* 3.2 22.6 + - - +
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Residues in contact with GLU 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176A ILE* 3.0 39.3 + - + +
177A VAL* 3.8 1.9 - - - +
179A SER* 1.3 81.0 - - - +
181A HIS* 1.3 94.9 + - + +
182A LYS* 3.8 12.1 + - - +
235A LEU* 3.9 30.6 - - - +
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Residues in contact with HIS 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A VAL* 2.8 19.1 + - + +
180A GLU* 1.3 114.2 + - + +
182A LYS* 1.3 76.3 + - - +
183A VAL* 3.1 24.9 + - + +
207A VAL* 3.6 25.7 - - + +
208A ASN* 4.1 15.6 + - - +
235A LEU* 5.9 3.8 - - + +
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Residues in contact with LYS 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178A GLN* 2.8 45.5 + - - +
179A SER 3.2 22.8 + - - -
180A GLU* 3.8 10.1 + - - +
181A HIS* 1.3 77.2 - - - +
183A VAL* 1.3 62.9 + - - +
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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