Contacts of the helix formed by residues 166 - 183 (chain A) in PDB entry 1JDP
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 ARG 166 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A TYR* 3.0 23.6 + - + -
160A SER 5.5 0.4 - - - -
161A ASP* 2.9 38.7 + - - +
162A ASP* 3.6 17.2 + - - +
163A LYS* 3.6 24.8 - - - +
164A LEU 3.3 21.1 - - - +
165A GLU* 1.3 80.3 - - - +
167A ASN* 1.3 65.4 + - - +
168A CYS 3.3 2.5 - - - -
169A TYR* 3.0 45.4 + - + +
170A PHE* 3.0 18.7 + - + -
11H LEU* 5.7 2.0 - - - +
14H ILE* 2.9 28.7 - - - +
18H SER* 5.5 4.1 + - - +
22H CYS* 4.8 9.3 - - - +
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Residues in contact with ASN 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A PHE* 6.3 1.6 - - - -
91A CYS* 6.1 0.9 - - - -
92A GLU* 5.0 9.0 - - - +
136A TYR* 4.0 14.9 + - - +
162A ASP* 4.9 2.6 + - - -
165A GLU* 3.1 30.8 + - - +
166A ARG* 1.3 76.4 - - - +
168A CYS* 1.3 57.9 + - - +
170A PHE* 3.4 5.5 + - - +
171A THR* 2.7 36.7 + - - +
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Residues in contact with CYS 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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159A TYR* 4.1 3.8 - - + +
160A SER* 3.4 20.5 + - - +
166A ARG 3.3 0.6 - - - -
167A ASN* 1.3 78.3 - - - +
169A TYR* 1.3 64.7 + - - +
171A THR* 3.6 1.0 - - - -
172A LEU* 3.1 24.9 + - - +
193A GLU* 5.9 0.7 - - - -
216A CYS* 2.0 67.5 - - + +
217A ALA* 3.2 13.5 - - - -
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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
----------------------------------------------------------
159A TYR* 3.7 31.2 - + + -
160A SER 3.8 3.2 + - - +
161A ASP* 3.9 16.8 - - + +
166A ARG* 3.0 42.4 + - + +
168A CYS* 1.3 78.9 - - - +
170A PHE* 1.3 76.0 + + - +
172A LEU 3.4 0.2 + - - -
173A GLU* 3.0 35.8 + - - +
6H CYS* 4.7 10.6 + - + -
7H PHE* 3.1 48.1 - + - -
11H LEU* 3.9 19.1 - - - +
14H ILE* 3.3 31.1 - - + +
22H CYS* 5.6 1.5 - - + +
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Residues in contact with PHE 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A GLU* 3.5 29.8 - - + -
93A TYR* 4.0 15.5 - + - -
116A ALA* 3.5 18.1 - - + -
117A ALA 5.4 0.7 + - - -
136A TYR* 3.3 30.2 - - + +
165A GLU 3.6 16.8 - - - -
166A ARG* 3.0 28.8 + - + -
167A ASN* 3.9 4.5 - - - +
169A TYR* 1.3 78.2 - + - +
171A THR* 1.3 67.3 + - - +
173A GLU* 3.3 22.8 + - - +
174A GLY 3.2 14.0 + - - -
14H ILE* 3.2 52.9 - - + -
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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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136A TYR* 3.4 32.6 + - + +
139A MET* 3.4 36.2 - - + +
167A ASN* 2.7 24.6 + - - +
168A CYS* 3.6 7.2 - - - -
169A TYR 3.2 0.2 - - - -
170A PHE* 1.3 76.1 - - - +
172A LEU* 1.3 61.5 + - + +
174A GLY* 3.1 19.8 + - - -
175A VAL 3.6 0.7 + - - -
216A CYS* 4.0 15.1 - - - -
244A ILE* 3.7 20.2 - - + -
246A LEU* 4.9 0.7 - - + -
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Residues in contact with LEU 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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157A LEU* 4.2 13.0 - - + +
158A VAL 3.8 6.7 - - - +
159A TYR* 3.3 44.4 - - + -
168A CYS 3.1 12.0 + - - +
169A TYR 4.2 1.8 - - - +
171A THR* 1.3 74.1 - - - +
173A GLU* 1.3 54.8 + - - +
174A GLY 3.1 1.8 - - - -
175A VAL* 3.1 10.2 + - + +
176A HIS* 2.8 33.4 + - - +
214A ILE* 3.6 30.5 - - + +
216A CYS* 4.0 14.1 - - + +
244A ILE* 3.4 33.7 - - + -
7H PHE* 4.0 6.3 - - + -
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Residues in contact with GLU 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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116A ALA* 4.4 0.7 - - - +
117A ALA* 3.8 25.0 + - + +
118A GLY 4.9 1.6 + - - -
169A TYR* 3.0 23.5 + - - +
170A PHE* 3.4 34.0 - - - +
171A THR 3.2 0.2 - - - -
172A LEU* 1.3 77.3 - - - +
174A GLY* 1.3 59.4 + - - +
176A HIS* 3.8 1.7 - - + +
177A GLU* 2.8 50.7 + - + +
7H PHE* 3.2 33.3 - - + -
10H LYS 4.5 11.6 - - - +
11H LEU* 4.9 5.4 - - - +
14H ILE* 5.2 4.4 - - - +
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Residues in contact with GLY 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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117A ALA* 5.4 4.7 - - - +
136A TYR* 3.7 30.7 - - - -
137A ALA* 3.9 6.2 - - - -
140A GLY* 3.7 2.2 - - - -
170A PHE 3.2 3.4 + - - -
171A THR 3.1 11.0 + - - -
173A GLU* 1.3 82.2 - - - +
175A VAL* 1.3 59.3 + - - +
177A GLU* 4.1 4.1 - - - +
178A VAL* 3.2 27.5 + - - +
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Residues in contact with VAL 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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139A MET* 3.8 35.0 - - + -
140A GLY* 4.0 7.4 - - - -
143A MET* 4.3 10.3 - - + -
157A LEU* 4.1 11.2 - - + -
171A THR 3.6 2.8 + - - +
172A LEU* 3.1 18.2 + - + +
174A GLY* 1.3 74.0 - - - +
176A HIS* 1.3 66.0 + - - +
178A VAL* 3.2 2.6 + - - -
179A PHE* 2.9 58.2 + - + +
214A ILE* 4.0 18.2 - - + -
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Residues in contact with HIS 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A LEU* 4.0 9.4 - - + +
172A LEU 2.8 20.8 + - - +
173A GLU 3.8 3.6 - - - +
175A VAL* 1.3 73.9 - - - +
177A GLU* 1.3 65.3 + - + +
179A PHE* 3.8 4.8 - - - +
180A GLN* 2.9 63.1 + - + +
186A THR* 3.3 18.8 + - - -
188A ILE* 4.3 10.8 - - + +
5H GLY* 6.1 1.1 - - - -
7H PHE* 3.1 41.5 - + + +
8H GLY* 3.1 24.6 + - - -
9H LEU* 3.9 9.4 - - + -
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Residues in contact with GLU 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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117A ALA* 4.0 21.9 - - + +
120A GLN* 6.1 1.1 - - - +
121A HIS* 5.6 5.7 - - - -
137A ALA* 5.8 3.8 - - + -
173A GLU* 2.8 40.9 + - + +
174A GLY* 4.1 4.9 - - - +
176A HIS* 1.3 76.2 - - + +
178A VAL* 1.3 64.3 + - + +
180A GLN* 3.4 3.7 + - - +
181A GLU* 3.1 27.8 + - - +
9H LEU* 2.7 47.8 - - - +
10H LYS 4.4 3.6 + - - +
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Residues in contact with VAL 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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137A ALA* 3.8 26.2 - - + +
140A GLY 3.8 22.2 - - - +
141A GLU* 3.8 13.2 - - + +
144A LEU* 3.9 26.0 - - + -
174A GLY 3.2 17.3 - - - +
175A VAL 3.2 6.1 + - - +
177A GLU* 1.3 76.2 - - + +
179A PHE* 1.3 64.2 + - + +
181A GLU* 3.2 9.2 + - + +
182A GLU* 3.1 22.9 + - + +
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Residues in contact with PHE 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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140A GLY 4.2 1.8 - - - -
143A MET* 3.9 8.7 - - + -
144A LEU* 3.6 29.8 - - + -
147A PHE* 3.7 53.2 - + - -
155A ALA* 4.2 4.0 - - + -
175A VAL* 2.9 41.2 + - + +
176A HIS 3.9 2.2 - - - +
178A VAL* 1.3 83.6 - - + +
180A GLN* 1.3 58.4 + - - +
182A GLU* 3.4 3.1 + - - +
183A GLY 2.9 9.0 + - - -
184A LEU* 2.9 51.4 + - + +
185A HIS 5.0 0.4 - - - -
186A THR* 3.7 31.0 - - + -
214A ILE* 4.1 5.4 - - + -
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Residues in contact with GLN 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 HIS* 2.9 46.9 + - - +
177A GLU 3.8 1.6 - - - +
179A PHE* 1.3 72.5 - - - +
181A GLU* 1.3 70.1 + - - +
183A GLY* 3.1 11.5 + - - +
184A LEU 3.4 22.2 + - - +
185A HIS* 4.9 0.2 - - - +
186A THR* 3.3 29.9 + - - +
9H LEU* 3.3 27.9 - - + +
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Residues in contact with GLU 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 GLU* 3.1 17.5 + - - +
178A VAL* 3.4 11.9 - - + +
180A GLN* 1.3 79.6 - - - +
182A GLU* 1.3 69.7 + - + +
183A GLY 3.4 0.3 + - - -
9H LEU* 5.4 11.9 - - + +
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Residues in contact with GLU 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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144A LEU* 3.6 42.4 - - + +
148A ARG* 4.1 24.2 + - - +
178A VAL* 3.1 16.5 + - + +
179A PHE 4.0 3.1 - - - +
181A GLU* 1.3 84.4 - - + +
183A GLY* 1.3 59.0 + - - +
184A LEU* 4.4 3.1 - - + +
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Residues in contact with GLY 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 PHE 2.9 5.2 + - - -
180A GLN* 3.1 11.2 + - - -
181A GLU 3.3 1.0 - - - -
182A GLU* 1.3 78.2 - - - +
184A LEU* 1.3 67.9 + - - +
185A HIS* 3.9 1.0 + - - +
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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
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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