Contacts of the helix formed by residues 165 - 186 (chain A) in PDB entry 1AV1
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 PRO 165 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A THR 3.2 19.3 - - - +
162A HIS 4.2 8.3 - - - +
163A LEU 2.9 13.0 - - - +
164A ALA* 1.3 83.7 - - + +
166A TYR* 1.3 66.8 + - + +
168A ASP* 3.1 12.2 + - + +
169A GLU* 2.6 34.6 + - - +
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Residues in contact with TYR 166 (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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162A HIS 4.6 14.6 - - - -
163A LEU* 2.6 20.3 + - + +
165A PRO* 1.3 83.0 - - + +
167A SER* 1.3 69.8 + - - +
169A GLU* 2.9 32.0 + - - +
170A LEU* 2.7 24.6 + - + +
93B VAL* 5.1 12.6 - - + -
96B LYS* 3.2 55.5 + - + +
97B VAL* 4.2 18.8 - - + -
100B TYR* 6.0 4.3 - + - -
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Residues in contact with SER 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A LEU* 3.5 4.8 + - - +
164A ALA* 3.4 19.4 + - - -
165A PRO 3.3 0.2 - - - -
166A TYR* 1.3 81.6 - - - +
168A ASP* 1.3 55.7 + - - +
170A LEU* 3.5 2.9 - - - +
171A ARG* 2.7 54.9 + - - +
215D ARG* 5.1 3.7 + - - +
218D LEU* 3.1 38.0 - - - +
219D LEU* 5.2 5.9 - - - +
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Residues in contact with ASP 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A ALA 3.1 11.1 + - - +
165A PRO* 3.1 16.2 + - + +
167A SER* 1.3 81.0 - - - +
169A GLU* 1.3 57.9 + - - +
171A ARG* 3.4 28.2 + - - +
172A GLN* 3.2 26.0 + - - +
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Residues in contact with GLU 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A PRO 2.6 16.6 + - - +
166A TYR* 2.9 35.9 + - - +
168A ASP* 1.3 75.7 - - - +
170A LEU* 1.3 60.7 + - + +
172A GLN* 3.7 4.6 + - - +
173A ARG* 2.9 61.0 + - + +
93B VAL* 5.8 4.0 - - - +
96B LYS* 5.7 3.6 + - - +
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Residues in contact with LEU 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A TYR* 2.7 19.2 + - + +
167A SER* 3.7 3.1 - - - +
169A GLU* 1.3 72.0 - - + +
171A ARG* 1.3 62.5 + - - +
173A ARG* 2.8 15.4 + - + +
174A LEU* 2.7 44.7 + - + +
177A ARG* 5.2 1.6 - - - +
86B MET* 5.0 9.4 - - + -
89B ASP* 3.4 34.5 - - + +
90B LEU* 5.5 7.0 - - + +
93B VAL* 4.4 25.6 - - + -
214D LEU* 4.5 22.4 - - + -
218D LEU* 6.2 1.6 - - + -
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Residues in contact with ARG 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A SER* 2.7 46.8 + - - +
168A ASP* 3.4 24.2 + - - +
170A LEU* 1.3 75.5 - - - +
172A GLN* 1.3 62.5 + - - +
173A ARG 3.0 0.3 + - - -
174A LEU* 5.4 0.4 - - - -
175A ALA* 3.1 28.9 + - - +
211D LEU* 4.9 14.6 + - + +
212D GLU* 4.8 3.2 + - - -
214D LEU* 3.6 23.1 - - + +
215D ARG* 3.3 50.5 - - - +
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Residues in contact with GLN 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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168A ASP 3.2 15.3 + - - +
169A GLU* 3.7 6.3 - - - +
170A LEU 3.2 0.4 - - - -
171A ARG* 1.3 78.5 - - - +
173A ARG* 1.3 62.2 + - + +
175A ALA* 4.8 1.9 - - - +
176A ALA* 3.9 14.8 + - - +
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Residues in contact with ARG 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 GLU* 2.9 50.3 + - - +
170A LEU* 2.8 23.6 + - + +
172A GLN* 1.3 77.5 - - + +
174A LEU* 1.3 66.0 + - - +
175A ALA 3.1 1.9 + - - -
176A ALA* 3.2 15.1 + - - +
177A ARG* 3.2 15.8 + - - +
89B ASP* 4.3 15.3 + - - +
92B GLU* 5.3 5.5 + - - -
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Residues in contact with LEU 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 LEU* 2.7 24.3 + - + +
171A ARG* 4.7 1.3 - - - +
173A ARG* 1.3 74.3 - - - +
175A ALA* 1.3 62.7 + - - +
177A ARG* 2.9 36.1 - - + +
178A LEU* 3.4 19.5 + - + +
86B MET* 3.5 38.4 - - + -
52C SER* 3.7 24.9 - - - +
56C THR* 5.6 6.3 - - + -
57C PHE* 5.3 2.9 - - + -
210D ALA* 6.5 1.1 - - + -
211D LEU* 5.4 11.2 - - + -
214D LEU* 5.7 13.7 - - + -
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Residues in contact with ALA 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 ARG 3.1 20.2 + - - +
172A GLN* 4.8 2.9 - - - +
173A ARG 3.1 0.2 + - - -
174A LEU* 1.3 75.1 - - - +
176A ALA* 1.3 58.2 + - - +
178A LEU* 2.9 29.1 + - - +
179A GLU* 3.4 7.3 + - - +
211D LEU* 4.4 24.0 - - + +
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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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172A GLN* 3.9 13.6 + - - +
173A ARG* 3.2 10.0 + - - +
175A ALA* 1.3 78.2 - - - +
177A ARG* 1.3 62.7 + - - +
179A GLU* 3.0 22.6 + - + +
180A ALA* 3.1 11.6 + - - +
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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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170A LEU* 5.2 0.6 - - - +
173A ARG* 3.2 14.5 + - - +
174A LEU* 2.9 39.0 + - + +
175A ALA 3.0 0.2 - - - -
176A ALA* 1.3 77.4 - - - +
178A LEU* 1.3 61.8 + - + +
180A ALA* 3.1 25.5 - - - +
181A LEU* 3.5 4.9 + - - +
82B LEU* 4.2 18.4 + - + +
85B GLU* 2.5 44.1 + - - +
86B MET* 2.8 46.6 - - - +
89B ASP* 3.1 19.2 + - - -
57C PHE* 5.3 4.5 - - - -
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Residues in contact with LEU 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 LEU* 3.6 21.1 - - + +
175A ALA* 2.9 9.5 + - - +
177A ARG* 1.3 83.0 - - + +
179A GLU* 1.3 60.9 + - - +
180A ALA 3.0 1.8 - - - -
181A LEU* 2.8 35.0 + - + +
182A LYS* 3.3 7.3 + - - +
56C THR* 3.7 33.7 - - + -
57C PHE* 4.2 26.5 - - + -
203D LEU* 4.5 13.0 - - + +
207D ALA* 4.8 21.8 - - + -
211D LEU* 6.4 2.0 - - + -
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Residues in contact with GLU 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 ALA 3.4 4.1 + - - +
176A ALA* 3.0 18.9 + - + +
178A LEU* 1.3 77.6 - - - +
180A ALA* 1.3 62.6 + - - +
181A LEU 3.0 0.2 - - - -
182A LYS* 3.4 7.1 + - + +
183A GLU* 3.1 27.7 + - + +
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Residues in contact with ALA 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 ALA 3.1 9.5 + - - +
177A ARG* 3.1 16.4 - - - +
178A LEU 3.0 0.2 - - - -
179A GLU* 1.3 79.1 - - - +
181A LEU* 1.3 54.7 + - - -
183A GLU* 3.6 11.9 - - - +
184A ASN* 2.8 42.1 + - - +
82B LEU* 5.4 8.8 - - + +
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Residues in contact with LEU 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 3.5 3.2 + - - +
178A LEU* 2.8 29.2 + - + +
180A ALA* 1.3 77.0 - - - +
182A LYS* 1.3 51.7 + - - +
184A ASN* 3.3 1.2 + - + -
185A GLY* 2.6 33.4 + - - -
188A ARG* 6.3 0.7 - - - +
78B GLU* 5.1 7.2 - - + +
79B THR* 4.7 16.6 - - - +
82B LEU* 4.8 17.3 - - + -
56C THR 4.5 10.8 - - - +
57C PHE* 4.7 15.7 - - + -
60C LEU* 3.5 37.2 - - + +
200D LEU* 4.8 1.2 - - - +
203D LEU* 3.5 17.9 - - + -
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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 LEU 3.3 6.3 + - - +
179A GLU* 3.4 9.2 + - + +
181A LEU* 1.3 77.7 - - - +
183A GLU* 1.3 66.2 + - - +
185A GLY* 2.9 12.0 + - - -
186A GLY* 3.0 10.6 + - - -
200D LEU* 3.2 43.7 - - + +
201D SER* 3.9 26.9 + - - +
203D LEU* 4.1 12.5 - - + +
204D SER* 4.3 27.9 + - - +
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Residues in contact with GLU 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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179A GLU* 3.1 19.3 + - + +
180A ALA* 3.2 11.3 - - - +
182A LYS* 1.3 78.5 - - - +
184A ASN* 1.3 93.3 + - - +
186A GLY* 3.3 10.6 + - - -
187A ALA* 3.4 11.8 + - - +
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Residues in contact with ASN 184 (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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180A ALA* 2.8 33.2 + - - +
181A LEU* 3.9 3.4 - - + +
183A GLU* 1.3 92.9 + - - +
185A GLY* 1.3 65.0 + - - +
186A GLY 3.1 1.8 - - - -
187A ALA* 3.1 20.8 + - - +
188A ARG* 3.2 24.5 + - - -
78B GLU* 3.3 36.5 + - - +
82B LEU* 5.8 1.4 - - - +
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Residues in contact with GLY 185 (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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181A LEU* 2.6 21.5 + - - -
182A LYS 2.9 3.9 + - - -
184A ASN* 1.3 72.7 - - - +
186A GLY* 1.3 56.5 + - - +
188A ARG* 3.4 8.1 + - - +
189A LEU* 3.0 29.5 + - - +
71B PHE* 5.1 0.3 - - - -
60C LEU* 5.9 3.6 - - - -
200D LEU* 4.0 18.8 - - - -
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Residues in contact with GLY 186 (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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182A LYS 3.0 11.5 + - - -
183A GLU* 3.3 5.6 + - - -
184A ASN 3.1 0.4 - - - -
185A GLY* 1.3 74.9 - - - +
187A ALA* 1.3 57.6 + - - +
189A LEU* 3.9 6.9 - - - +
190A ALA* 2.9 33.1 + - - +
200D LEU* 4.0 8.4 - - - +
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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