Contacts of the helix formed by residues 166 - 185 (chain A) in PDB entry 3AXJ
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 GLU 166 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A ASP* 3.3 6.9 - - - +
165A TYR* 1.3 81.7 - - - +
167A ARG* 1.3 66.2 + - - +
168A PRO* 3.3 1.6 - - - -
169A LEU* 3.2 18.2 + - - +
170A ASN* 3.3 11.9 + - - +
218A LEU 4.5 1.0 - - - +
219A SER* 3.5 12.1 + - - -
220A SER* 2.6 49.1 + - - +
221A LYS* 3.3 37.7 + - + +
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Residues in contact with ARG 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A LEU* 5.9 0.6 - - - +
55A ILE* 4.6 11.1 - - - +
108A TYR* 2.9 45.7 + - - -
109A LEU* 4.7 12.1 + - - +
112A GLY* 6.1 0.4 - - - -
155A PHE* 3.4 33.1 - - + -
159A SER* 3.5 19.5 - - - +
164A ASP* 3.3 28.9 + - - +
166A GLU* 1.3 78.2 - - - +
168A PRO* 1.4 68.3 - - + +
170A ASN* 3.2 15.1 + - - +
171A ILE* 2.9 34.7 + - + +
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Residues in contact with PRO 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A ALA* 4.0 20.4 - - + +
160A VAL* 3.5 27.1 - - + -
164A ASP 3.7 7.6 - - - +
165A TYR 3.5 13.0 - - - +
166A GLU 3.4 5.4 - - - -
167A ARG* 1.4 93.2 - - + +
169A LEU* 1.3 56.2 + - - +
171A ILE* 3.2 3.4 + - + +
172A SER* 2.8 29.1 + - - -
206A ILE* 4.0 2.5 - - + +
209A VAL* 3.5 22.4 - - + -
210A VAL* 3.5 17.7 - - + +
213A VAL* 4.6 3.8 - - + -
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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
----------------------------------------------------------
165A TYR 5.1 1.5 + - - +
166A GLU* 3.2 12.2 + - - +
168A PRO* 1.3 79.4 - - - +
170A ASN* 1.3 63.6 + - - +
172A SER* 3.2 7.4 + - - +
173A HIS* 3.0 54.7 + - + +
210A VAL* 3.8 29.1 - - + +
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Residues in contact with ASN 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A TYR* 2.5 41.8 + - - +
112A GLY* 5.5 3.8 + - - -
166A GLU 3.3 8.7 + - - +
167A ARG* 3.2 19.5 + - - +
169A LEU* 1.3 79.8 - - - +
171A ILE* 1.3 59.2 + - - +
173A HIS* 3.5 9.5 + - - +
174A PHE* 3.1 19.3 + - - +
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Residues in contact with ILE 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A TYR* 3.3 24.5 - - + +
152A LEU* 3.6 41.7 - - + +
155A PHE* 3.8 12.1 - - + -
156A ALA* 3.7 19.1 - - + +
167A ARG* 2.9 34.3 + - + +
168A PRO* 3.6 7.4 - - + +
170A ASN* 1.3 72.2 - - - +
172A SER* 1.3 60.6 + - - +
174A PHE* 3.2 4.3 + - - -
175A ILE* 2.8 33.0 + - + +
206A ILE* 3.9 24.5 - - + -
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Residues in contact with SER 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A PRO 2.8 14.1 + - - -
169A LEU* 3.2 15.8 + - - +
171A ILE* 1.3 77.7 - - - +
173A HIS* 1.3 59.1 - - - +
175A ILE* 3.9 2.3 - - - +
176A GLY* 2.9 27.0 + - - -
206A ILE* 3.8 11.0 - - - -
207A GLU* 2.4 34.1 + - - +
210A VAL* 3.8 13.9 - - - +
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Residues in contact with HIS 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* 3.0 47.0 + - + +
170A ASN* 3.7 10.5 - - - +
171A ILE 3.3 0.2 - - - -
172A SER* 1.3 79.7 - - - +
174A PHE* 1.3 61.6 + - - +
176A GLY* 3.5 1.2 + - - -
177A ASP* 3.1 34.3 + - - +
23B GLN* 6.1 2.6 + - - -
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Residues in contact with PHE 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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104A ALA 5.3 0.4 - - - -
108A TYR* 3.7 32.8 - + + -
112A GLY 3.8 11.2 - - - +
113A PHE* 3.6 27.4 - - - -
114A LEU* 3.6 22.4 - - + -
148A LEU* 3.6 32.1 - - + -
152A LEU* 3.6 26.7 - - + -
170A ASN* 3.1 17.5 + - - +
171A ILE 3.2 3.6 + - - +
173A HIS* 1.3 77.4 - - - +
175A ILE* 1.3 65.3 + - + +
177A ASP* 3.4 9.6 + - + +
178A LEU* 3.1 28.9 + - + +
30B ILE* 5.7 0.2 - - - +
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Residues in contact with ILE 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 LEU* 4.6 0.7 - - + -
149A ALA* 4.0 21.1 - - + +
152A LEU* 3.8 12.8 - - + -
171A ILE* 2.8 29.0 + - + +
172A SER* 4.3 2.7 - - - +
174A PHE* 1.3 90.9 - - + +
176A GLY* 1.3 57.2 + - - +
178A LEU* 3.5 16.1 - - + +
179A ASN* 2.8 28.1 + - - +
199A LEU* 4.2 13.9 - - + -
203A VAL* 3.7 26.9 - - + -
206A ILE* 3.9 28.3 - - + -
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Residues in contact with GLY 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 SER 2.9 19.8 + - - -
173A HIS* 3.5 2.2 + - - -
174A PHE 3.3 0.2 - - - -
175A ILE* 1.3 73.5 - - - +
177A ASP* 1.3 60.2 + - - +
179A ASN* 3.4 8.4 + - - +
180A THR* 3.0 31.9 + - - -
203A VAL* 6.0 1.1 - - - -
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Residues in contact with ASP 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A HIS* 3.1 19.8 + - - +
174A PHE* 3.4 8.4 + - + +
176A GLY* 1.3 72.7 - - - +
178A LEU* 1.3 60.7 + - - +
180A THR* 3.2 3.3 + - - -
181A GLY 2.9 24.4 + - - -
24B LEU* 3.4 41.9 - - + +
30B ILE* 3.9 22.3 - - + +
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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
----------------------------------------------------------
114A LEU* 3.6 36.3 - - + -
145A ILE* 3.7 41.5 - - + +
146A LEU* 5.0 1.6 - - - -
148A LEU* 4.8 5.6 - - + -
149A ALA 5.3 0.9 - - - +
174A PHE* 3.1 17.4 + - + +
175A ILE* 3.5 28.5 - - + +
176A GLY 3.4 0.2 - - - -
177A ASP* 1.3 73.9 - - - +
179A ASN* 1.3 57.7 + - - +
181A GLY* 3.2 3.0 + - - -
182A PHE* 2.9 46.9 + - + -
199A LEU* 4.7 15.7 - - + -
30B ILE* 4.2 5.5 - - - +
34B PHE* 4.3 2.4 - - + -
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Residues in contact with ASN 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A ILE 2.8 18.7 + - - +
176A GLY* 3.5 9.8 - - - +
178A LEU* 1.3 76.3 - - - +
180A THR* 1.3 62.3 + - - +
182A PHE* 3.2 2.4 + - - +
183A ARG* 3.0 67.8 + - - +
196A PHE* 3.5 8.8 - - - -
199A LEU* 3.4 27.5 - - + +
203A VAL* 4.6 17.6 - - + +
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Residues in contact with THR 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 GLY 3.0 16.0 + - - -
177A ASP* 3.2 9.0 + - - -
179A ASN* 1.3 74.3 - - - +
181A GLY* 1.3 64.3 - - - +
183A ARG* 3.3 9.8 + - - +
184A LEU* 3.1 32.3 + - + +
24B LEU* 3.9 27.0 - - + +
31B VAL* 4.9 7.6 - - + -
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Residues in contact with GLY 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 ASP 2.9 14.3 + - - -
178A LEU 3.2 3.3 + - - -
180A THR* 1.3 76.1 - - - +
182A PHE* 1.3 62.2 + - - +
184A LEU* 3.0 25.4 - - - +
185A LEU 3.4 2.9 + - - -
24B LEU* 5.6 0.2 - - - +
30B ILE* 5.3 2.7 - - - -
31B VAL* 6.2 0.7 - - - -
34B PHE* 3.3 40.8 - - - -
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Residues in contact with PHE 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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142A LEU* 3.6 35.0 - - + -
145A ILE* 3.7 25.8 - - + -
146A LEU* 3.5 41.3 - - + -
178A LEU* 2.9 37.8 + - + +
179A ASN* 3.2 2.2 + - - +
181A GLY* 1.3 74.6 - - - +
183A ARG* 1.3 58.6 + - - +
185A LEU* 3.1 38.5 + - + +
186A ASN 3.8 2.1 + - - -
187A LEU* 4.3 14.7 + - + +
192A LEU* 4.6 5.6 - - + -
196A PHE* 3.4 37.3 - + + -
199A LEU* 4.9 2.0 - - + -
34B PHE* 3.9 7.9 - + - -
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Residues in contact with ARG 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 ASN* 3.0 50.6 + - - +
180A THR* 3.9 7.0 - - - +
181A GLY 3.3 0.2 - - - -
182A PHE* 1.3 73.8 - - - +
184A LEU* 1.3 67.2 + - + +
186A ASN* 3.2 21.4 + - - +
196A PHE* 3.8 26.9 - - + -
200A LYS* 5.3 11.3 - - - +
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Residues in contact with LEU 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 THR* 3.1 25.7 + - + +
181A GLY* 3.0 15.5 - - - +
183A ARG* 1.3 78.0 - - + +
185A LEU* 1.3 60.3 + - + +
186A ASN* 3.3 8.5 + - - +
31B VAL* 3.7 47.1 - - + +
34B PHE* 4.3 14.1 - - + -
35B ARG* 3.9 39.1 + - + +
38B SER* 4.2 9.1 + - - -
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Residues in contact with LEU 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A LEU* 3.9 26.2 - - + -
181A GLY 3.7 6.7 - - - +
182A PHE* 3.1 35.9 + - + +
184A LEU* 1.3 73.6 - - - +
186A ASN* 1.3 71.9 + - - +
187A LEU* 3.2 24.6 + - + +
34B PHE* 3.4 43.5 - - + +
37B TYR* 4.2 4.5 - - + -
38B SER* 3.5 29.4 + - - +
41B LEU* 4.1 5.5 - - + +
42B ILE* 5.7 4.0 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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