Contacts of the helix formed by residues 164 - 180 (chain A) in PDB entry 2J0M
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 164 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162A GLN 4.2 0.4 + - - -
163A VAL* 1.3 75.1 - - - +
165A GLN* 1.3 60.8 + - - +
166A GLU* 3.3 34.3 - - - +
167A ILE* 3.0 43.8 + - + +
168A ALA 3.2 4.3 + - - -
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Residues in contact with GLN 165 (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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161A ASP 5.8 2.8 + - - +
163A VAL 3.2 9.6 + - - +
164A ASP* 1.3 74.3 + - - +
166A GLU* 1.3 57.8 + - - +
168A ALA* 3.2 10.2 + - + +
169A LEU* 2.8 23.9 + - + +
208A PRO* 6.6 0.2 - - + -
210A SER* 4.3 17.7 + - - +
211A LEU* 3.7 29.2 - - + +
214A SER* 3.8 30.6 + - - -
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Residues in contact with GLU 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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164A ASP* 3.3 19.1 + - - +
165A GLN* 1.3 73.4 - - - +
167A ILE* 1.3 61.9 + - + +
169A LEU* 3.5 17.6 - - + +
170A LYS* 2.9 52.5 + - - +
227A THR* 6.3 0.9 - - + -
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Residues in contact with ILE 167 (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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163A VAL* 4.4 15.5 - - + -
164A ASP* 3.0 34.3 + - + +
166A GLU* 1.3 76.9 - - + +
168A ALA* 1.3 65.5 - - - +
170A LYS* 3.2 16.0 + - - +
171A LEU* 3.0 43.0 + - + +
246A ILE* 3.9 35.9 - - + +
250A VAL* 4.8 9.6 - - + -
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Residues in contact with ALA 168 (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 TYR* 3.4 23.4 + - - +
160A ALA 4.3 0.2 - - - +
163A VAL* 3.7 16.9 - - + +
164A ASP 3.2 2.8 + - - -
165A GLN* 3.2 15.1 + - + +
167A ILE* 1.3 79.5 - - - +
169A LEU* 1.3 60.6 + - - +
172A GLY* 3.2 18.7 + - - -
206A PHE 4.6 1.4 - - - +
207A PHE* 3.5 11.4 - - - -
208A PRO* 4.0 24.1 - - + +
211A LEU* 4.6 5.2 - - + -
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Residues in contact with LEU 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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165A GLN 2.8 12.3 + - - +
166A GLU* 3.5 20.6 - - + +
167A ILE 3.1 0.2 - - - -
168A ALA* 1.3 74.8 - - - +
170A LYS* 1.3 66.1 + - - +
173A CYS* 3.2 30.9 + - - -
207A PHE* 3.5 23.6 - - + -
211A LEU* 4.1 23.1 - - + -
220A LEU* 5.8 0.2 - - + -
223A LEU* 4.3 26.5 - - + -
224A ILE* 4.3 18.2 - - + +
227A THR* 3.8 32.1 - - + +
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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
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166A GLU* 2.9 47.8 + - + +
167A ILE* 3.2 12.9 + - + +
169A LEU* 1.3 72.5 - - - +
171A LEU* 1.3 62.0 + - - +
173A CYS* 3.7 0.5 + - - +
174A LEU* 3.1 29.4 + - - +
227A THR* 4.2 10.5 - - - +
230A GLN* 4.7 16.3 + - - +
231A PHE* 3.4 35.6 - - + -
246A ILE* 4.3 25.6 - - + -
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Residues in contact with LEU 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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155A TYR* 3.4 43.5 - - + +
167A ILE* 3.0 31.2 + - + +
168A ALA 4.2 2.7 - - - +
170A LYS* 1.3 73.8 - - - +
172A GLY* 1.3 60.6 + - - +
174A LEU* 2.9 21.6 + - + +
175A GLU* 3.0 12.0 + - - +
243A PHE* 3.4 57.7 - - + +
246A ILE* 3.8 19.7 - - + -
247A LEU* 4.1 15.5 - - + +
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Residues in contact with GLY 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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155A TYR* 5.5 0.4 + - - -
168A ALA 3.2 8.5 + - - -
171A LEU* 1.3 78.1 - - - +
173A CYS* 1.3 62.3 + - - +
175A GLU* 2.9 8.2 + - - +
176A ILE* 2.9 24.6 + - - +
206A PHE* 3.2 31.2 + - - +
207A PHE* 3.5 16.2 - - - -
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Residues in contact with CYS 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 LEU* 3.2 27.1 + - - +
170A LYS 3.8 4.7 - - - +
172A GLY* 1.3 74.1 - - - +
174A LEU* 1.3 52.0 + - - +
176A ILE* 3.2 12.4 + - - +
177A ARG* 2.8 35.6 + - - +
207A PHE* 3.6 15.1 - - - -
224A ILE* 3.8 33.2 - - - -
227A THR* 4.1 11.4 - - - +
228A PHE* 3.7 23.2 - - + -
231A PHE* 4.4 8.1 - - + -
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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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148A TYR* 4.7 1.8 - - - -
170A LYS 3.1 24.0 + - - +
171A LEU* 2.9 15.5 + - + +
173A CYS* 1.3 77.9 - - - +
175A GLU* 1.3 54.9 + - - +
177A ARG* 3.4 5.8 + - + +
178A ARG* 2.9 28.6 + - - +
231A PHE* 3.7 33.7 - - + -
234A LEU* 4.4 6.5 - - + -
239A SER* 3.8 34.4 - - - +
242A LYS* 4.1 2.7 - - + -
243A PHE* 3.8 32.5 - - + +
246A ILE* 3.8 23.8 - - + -
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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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148A TYR* 2.9 15.3 + - - +
149A GLN* 4.4 0.7 + - - -
152A LYS* 3.2 37.0 + - + +
171A LEU 3.0 9.1 + - - +
172A GLY* 2.9 12.3 + - - +
174A LEU* 1.3 73.0 - - - +
176A ILE* 1.3 61.1 + - - +
178A ARG* 2.7 45.3 + - - -
179A SER* 2.8 34.0 + - - -
205A ARG 4.7 2.0 - - - +
206A PHE* 3.6 22.4 - - + -
243A PHE* 5.5 0.4 - - + -
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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 GLY 2.9 17.6 + - - +
173A CYS* 3.4 13.0 - - - +
175A GLU* 1.3 76.3 - - - +
177A ARG* 1.3 64.1 + - - +
180A TYR* 3.0 34.9 + - + +
183A MET* 3.8 24.4 - - + +
188A LEU* 4.3 9.4 - - + -
197A LEU* 3.7 29.8 - - + -
203A LEU* 5.3 1.8 - - + -
206A PHE* 3.6 36.1 - - + -
207A PHE* 4.2 15.3 - - + -
224A ILE* 4.6 7.0 - - + -
228A PHE* 4.1 6.5 - - + -
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Residues in contact with ARG 177 (chain A).
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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173A CYS 2.8 20.1 + - - +
174A LEU* 3.6 9.6 - - + +
176A ILE* 1.3 73.6 - - - +
178A ARG* 1.3 60.8 + - - +
180A TYR 3.2 26.9 + - - +
181A GLY* 3.3 20.6 + - - -
183A MET* 3.0 32.5 + - - +
184A ARG* 4.9 3.4 - - - +
185A GLY* 3.6 14.8 - - - +
228A PHE* 4.2 18.1 - - + -
231A PHE* 3.3 30.1 - - + +
232A ALA* 2.8 22.5 + - - +
234A LEU* 3.5 18.3 + - + +
235A ASN 5.6 1.0 - - - +
236A ARG* 5.4 0.7 - - - +
239A SER* 3.5 17.4 + - - +
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Residues in contact with ARG 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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44A GLU* 2.7 42.3 + - - -
145A ASN* 4.3 11.6 - - - +
148A TYR* 3.2 22.8 - - + +
149A GLN* 3.2 11.1 - - - +
174A LEU 2.9 18.3 + - - +
175A GLU* 2.7 39.6 + - - +
176A ILE 3.2 0.2 - - - -
177A ARG* 1.3 78.4 - - - +
179A SER* 1.3 79.0 + - - +
180A TYR 3.2 0.9 + - - -
181A GLY 3.5 7.3 + - - -
236A ARG* 3.7 34.4 - - + +
239A SER* 4.0 13.7 + - - -
240A ILE* 3.8 26.5 - - + -
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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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44A GLU* 4.1 4.3 + - - -
175A GLU* 2.8 28.4 + - - -
176A ILE* 4.0 1.8 - - - -
178A ARG* 1.3 97.7 + - - +
180A TYR* 1.3 72.8 + - - +
181A GLY 3.6 2.8 + - - -
206A PHE* 5.1 3.3 - - - -
597B ARG* 2.4 42.2 + - - +
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Residues in contact with TYR 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 27.6 + - + +
177A ARG* 3.2 18.5 + - - +
179A SER* 1.3 85.4 + - - +
181A GLY* 1.3 64.0 + - - +
182A GLU 3.1 5.0 + - - -
183A MET* 3.4 18.3 - - + +
197A LEU* 3.6 22.0 - - + -
201A VAL* 3.5 32.9 - - - +
205A ARG* 5.4 1.7 + - - -
206A PHE* 3.9 14.9 - + - -
595B ASN 3.4 16.2 - - - +
596B PHE* 3.6 44.9 - + + -
597B ARG* 3.6 26.9 - - - +
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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