Contacts of the helix formed by residues 170 - 183 (chain A) in PDB entry 1W6J
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 170 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132A ARG* 3.0 35.5 + - - -
166A VAL* 3.5 18.9 - - + +
167A GLY* 3.2 19.4 + - - +
169A ASP* 1.3 77.3 - - - +
171A PRO* 1.3 70.0 - - - +
172A ASP* 3.0 27.2 + - - +
173A LEU* 3.0 10.0 + - + +
174A VAL* 2.9 24.4 + - - +
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Residues in contact with PRO 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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169A ASP 3.2 7.6 - - - +
170A ASP* 1.3 91.0 - - - +
172A ASP* 1.3 64.6 + - - +
174A VAL* 3.6 9.1 + - + +
175A ARG* 3.3 31.3 + - - +
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Residues in contact with ASP 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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132A ARG* 2.9 40.0 + - + +
135A GLN* 2.9 40.3 + - - +
161A LEU* 5.9 1.8 - - + -
170A ASP* 3.0 10.2 + - - +
171A PRO* 1.3 80.6 - - - +
173A LEU* 1.3 63.2 + - + +
175A ARG* 2.9 22.2 + - - +
176A ALA* 3.1 14.6 + - - +
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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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132A ARG* 5.9 0.2 - - - +
141A TRP* 4.7 1.6 - - + -
158A TYR* 3.3 33.2 - - + -
161A LEU* 3.6 33.9 - - + -
162A ARG* 3.4 37.7 - - + -
166A VAL* 3.7 25.4 - - + -
167A GLY 3.6 15.9 - - - +
168A PRO 4.5 3.8 - - - +
170A ASP* 3.0 9.8 + - - +
172A ASP* 1.3 81.5 - - + +
174A VAL* 1.3 56.3 + - - +
176A ALA* 4.1 4.7 - - + -
177A ARG* 2.8 32.3 + - - +
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Residues in contact with VAL 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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168A PRO 3.7 14.6 + - - +
169A ASP* 3.9 14.6 - - - +
170A ASP 2.9 19.1 + - - +
171A PRO* 3.7 11.7 - - + +
173A LEU* 1.3 76.4 - - - +
175A ARG* 1.3 58.9 + - + +
177A ARG* 3.4 19.0 + - - +
178A ASN* 3.0 52.7 + - - +
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Residues in contact with ARG 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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135A GLN* 3.8 10.5 + - - +
136A LEU 3.4 23.6 + - - -
137A PRO* 3.6 18.8 + - - +
138A ASP 4.2 3.4 - - - +
139A GLY* 3.8 14.9 - - - -
171A PRO* 3.3 13.2 + - - +
172A ASP* 2.9 43.1 + - - +
173A LEU 3.3 0.2 - - - -
174A VAL* 1.3 80.3 - - + +
176A ALA* 1.3 61.9 + - - +
178A ASN* 3.5 7.9 + - - +
179A ILE* 3.1 25.3 + - - +
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Residues in contact with ALA 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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135A GLN* 3.9 0.2 - - - +
139A GLY 3.2 22.8 + - - +
141A TRP* 3.7 21.3 - - + -
154A THR* 3.5 6.7 - - + +
158A TYR* 4.0 14.6 - - + -
172A ASP 3.1 16.3 + - - +
173A LEU* 3.6 7.0 - - - +
175A ARG* 1.3 74.2 - - - +
177A ARG* 1.3 66.2 + - - +
179A ILE* 3.3 4.7 - - - +
180A LEU* 3.0 24.1 + - - +
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Residues in contact with ARG 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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158A TYR* 2.8 46.3 + - + +
168A PRO* 3.0 36.2 + - - +
169A ASP* 4.7 5.1 + - - -
173A LEU 2.8 22.7 + - - +
174A VAL* 3.7 24.4 - - - +
176A ALA* 1.3 72.5 - - - +
178A ASN* 1.3 65.6 + - - +
180A LEU* 3.3 8.2 - - + +
181A HIS* 3.0 49.4 + - + +
262A GLU* 3.4 35.4 - - - +
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Residues in contact with ASN 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 VAL* 3.0 42.0 + - - +
175A ARG* 3.9 6.7 - - - +
177A ARG* 1.3 83.8 + - - +
179A ILE* 1.3 65.1 + - - +
181A HIS* 3.4 8.3 + - - +
182A LYS* 3.0 23.6 + - - +
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Residues in contact with ILE 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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138A ASP* 3.2 50.9 - - + +
139A GLY 3.9 0.2 - - - -
140A GLY* 3.8 18.6 - - - +
149A SER* 3.4 12.6 - - - +
154A THR* 3.9 12.6 - - + +
175A ARG 3.1 15.8 + - - +
176A ALA 3.3 10.5 - - - +
178A ASN* 1.3 76.6 - - - +
180A LEU* 1.3 58.5 + - - +
182A LYS* 3.2 15.7 + - + +
183A LYS* 3.0 42.3 + - + +
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Residues in contact with LEU 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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151A VAL* 4.0 22.4 - - + -
154A THR* 4.1 15.0 - - + -
155A ALA* 4.3 17.5 - - + -
158A TYR* 5.7 3.6 - - + -
176A ALA 3.0 12.8 + - - +
177A ARG* 3.3 13.0 - - - +
179A ILE* 1.3 77.7 - - - +
181A HIS* 1.3 66.1 + - + +
183A LYS* 3.2 13.1 + - - +
184A GLY 3.3 0.5 + - - -
185A GLY 2.8 43.1 + - - +
186A ALA* 3.8 1.1 - - + +
262A GLU 4.8 0.9 - - - +
263A LEU* 3.5 45.1 - - + +
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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
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177A ARG* 3.0 35.1 + - + +
178A ASN* 3.8 8.5 - - - +
179A ILE 3.3 0.2 - - - -
180A LEU* 1.3 77.2 - - + +
182A LYS* 1.3 62.4 + - - +
184A GLY* 2.9 17.8 + - - -
185A GLY 4.0 0.7 - - - +
261A GLN 5.3 1.6 + - - -
262A GLU 2.9 28.9 + - - -
263A LEU* 3.9 16.2 + - - -
264A TYR 3.5 16.9 + - - -
265A VAL* 3.5 31.9 - - + +
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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 ASN 3.0 14.6 + - - +
179A ILE* 3.3 20.0 - - + +
181A HIS* 1.3 76.9 - - - +
183A LYS* 1.3 61.6 + - + +
184A GLY* 3.2 1.1 + - - -
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Residues in contact with LYS 183 (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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149A SER* 3.0 53.2 + - - -
150A THR* 3.7 19.7 - - - +
151A VAL* 3.5 24.3 - - + +
154A THR* 4.4 3.6 - - - +
179A ILE* 3.0 35.3 + - + +
180A LEU* 3.5 9.4 - - - +
181A HIS 3.1 0.6 - - - -
182A LYS* 1.3 76.5 - - + +
184A GLY* 1.3 56.0 + - - +
185A GLY 3.6 0.2 - - - -
188A ALA* 4.9 3.1 - - - +
281A ALA* 4.7 9.5 - - - +
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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