Contacts of the helix formed by residues 170 - 185 (chain A) in PDB entry 4X2Q
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 PHE 170 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106A GLU* 3.8 3.6 - - - -
112A LYS* 3.5 19.3 - - - -
121A ASP* 3.6 22.0 - - - +
169A ASN* 1.3 89.8 - - + +
171A PRO* 1.3 60.5 - - - +
172A LEU 3.0 2.8 + - - -
173A LEU* 3.0 28.5 + - + -
174A MET* 2.6 51.7 + - + +
177A TRP* 5.3 8.5 - + + -
296A PHE* 3.9 14.1 - + - -
297A ASN* 3.4 27.4 - - + -
301A CYS* 3.7 29.2 - - + -
302A CYS* 5.4 3.8 - - - -
303A THR* 4.1 15.3 - - + -
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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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106A GLU* 3.3 19.7 - - + +
110A GLY* 5.0 6.3 - - - -
121A ASP* 5.4 0.7 - - - +
166A ILE* 4.6 6.1 - - + +
167A PRO 4.6 9.9 - - - +
168A TRP 3.3 13.0 - - - +
169A ASN 3.6 3.6 - - - +
170A PHE* 1.3 85.8 - - - +
172A LEU* 1.3 56.7 + - - +
174A MET* 4.0 3.3 - - + +
175A PHE* 3.2 24.9 + - - +
193A PRO* 6.1 0.7 - - - +
197A THR* 3.3 42.2 - - + +
200A SER* 3.3 20.4 - - - +
201A ALA* 5.4 3.8 - - - +
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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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102A LEU* 3.8 26.5 - - + +
106A GLU* 2.9 20.9 + - - +
121A ASP* 6.3 0.9 - - + -
122A LEU* 3.7 35.2 - - + -
125A VAL* 3.8 19.3 - - + -
171A PRO* 1.3 73.7 - - - +
173A LEU* 1.3 62.1 + - - +
174A MET 3.3 0.2 - - - -
175A PHE* 3.2 10.2 + - + +
176A ALA* 2.8 29.8 + - - +
200A SER* 3.8 17.7 - - - +
204A MET* 3.5 35.0 - - + -
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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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106A GLU* 4.3 1.2 + - - -
120A VAL* 4.9 4.3 - - + +
121A ASP* 3.4 44.3 - - + +
124A GLY* 3.8 10.3 - - - -
125A VAL* 3.7 28.3 - - + +
170A PHE* 3.0 25.9 + - + +
172A LEU* 1.3 77.5 - - - +
174A MET* 1.3 53.1 + - - +
176A ALA* 3.1 3.0 + - + +
177A TRP* 2.7 82.5 + - + +
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Residues in contact with MET 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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166A ILE* 3.8 24.0 - - + +
167A PRO* 4.3 15.5 - - + +
169A ASN* 5.2 1.1 - - + -
170A PHE* 2.6 41.2 + - + +
171A PRO* 4.0 3.4 - - + +
173A LEU* 1.3 73.2 - - - +
175A PHE* 1.3 61.6 + - - +
177A TRP* 3.6 30.1 + - + +
178A LYS* 3.2 43.0 + - + +
244A THR* 3.7 38.8 - - + +
268A GLU* 4.0 6.5 - - - +
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Residues in contact with PHE 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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129A PHE* 5.1 0.2 - + - -
166A ILE* 4.7 6.0 - - + +
171A PRO 3.2 14.4 + - - +
172A LEU* 3.3 13.9 - - + +
173A LEU 3.2 0.4 - - - -
174A MET* 1.3 78.4 - - - +
176A ALA* 1.3 58.1 + - + +
178A LYS* 3.3 1.4 + - - +
179A ILE* 2.8 57.6 + - + +
191A ILE* 3.6 43.5 - - + -
193A PRO* 5.6 0.2 - - + -
201A ALA* 3.9 29.6 - - + -
204A MET* 3.7 39.3 - - + -
208A ILE* 4.5 9.0 - - + -
220A ILE* 3.9 26.0 - - + -
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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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125A VAL* 3.9 14.8 - - + -
128A THR* 3.7 19.7 + - - +
129A PHE* 3.8 29.2 - - + -
172A LEU* 2.8 17.0 + - + +
173A LEU* 3.4 5.4 - - - +
175A PHE* 1.3 76.4 - - + +
177A TRP* 1.3 58.4 + - + +
180A ALA* 3.1 36.6 + - - +
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Residues in contact with TRP 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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124A GLY* 5.8 0.2 - - - -
128A THR* 3.4 33.7 - - + +
132A TYR* 5.6 4.9 - + - -
170A PHE* 5.3 9.0 - + - -
173A LEU* 2.7 55.8 + - + +
174A MET* 3.7 33.4 - - + +
176A ALA* 1.3 72.2 - - - +
178A LYS* 1.3 61.5 + - + +
180A ALA* 5.4 0.2 - - - -
181A PRO* 3.3 21.4 - - - +
268A GLU* 5.8 3.6 - - - -
303A THR* 5.0 18.8 - - + -
485A TYR* 5.3 1.0 - - - -
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Residues in contact with LYS 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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164A GLN* 2.7 45.3 + - + +
166A ILE* 3.6 19.7 - - + -
174A MET* 3.2 24.3 + - + +
175A PHE 4.0 1.8 - - - +
176A ALA 3.1 0.6 - - - -
177A TRP* 1.3 83.0 - - + +
179A ILE* 1.3 64.2 + - - +
180A ALA 3.5 0.2 - - - -
181A PRO* 3.6 7.0 - - - +
182A ALA* 3.6 3.8 + - - +
191A ILE* 4.5 1.3 - - + -
242A ALA* 3.5 40.2 - - - +
243A PHE 4.6 0.8 + - - -
244A THR* 2.6 29.2 + - - -
266A THR* 6.4 0.7 - - - -
268A GLU* 3.3 13.3 + - - +
485A TYR* 3.7 9.2 + - + +
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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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91A LEU* 5.2 3.4 - - + -
129A PHE* 4.1 17.0 - - + -
164A GLN* 3.7 3.4 - - - +
175A PHE* 2.8 46.9 + - + +
176A ALA 4.4 0.9 - - - +
178A LYS* 1.3 75.4 - - - +
180A ALA* 1.3 66.5 + - - +
182A ALA* 3.2 4.2 + - - +
183A LEU* 3.1 44.5 + - + +
189A VAL* 3.5 33.0 - - + -
191A ILE* 4.0 12.3 - - + -
208A ILE* 5.5 1.3 - - + -
218A ILE* 3.8 24.7 - - + -
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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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88A LEU* 3.9 17.1 - - + +
128A THR* 4.3 4.7 - - - +
129A PHE* 3.9 20.4 - - + -
132A TYR* 3.8 28.3 - - + -
176A ALA 3.1 19.4 + - - +
179A ILE* 1.3 77.6 - - - +
181A PRO* 1.4 66.8 - - + +
183A LEU* 3.5 0.5 + - - -
184A CYS* 3.0 23.0 + - - +
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Residues in contact with PRO 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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132A TYR* 3.9 39.0 - - + +
177A TRP 3.3 26.7 - - - +
178A LYS 3.6 5.6 - - - +
180A ALA* 1.4 93.9 - - + +
182A ALA* 1.3 63.3 + - - +
184A CYS* 3.1 12.5 + - + +
185A CYS* 3.2 18.0 + - - -
481A GLY 4.8 2.9 - - - +
482A LEU* 4.6 10.8 - - + -
485A TYR* 3.7 22.4 - - + -
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Residues in contact with ALA 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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162A CYS* 5.0 0.7 - - - -
164A GLN* 3.5 28.3 - - - +
178A LYS 3.6 0.8 + - - +
179A ILE 3.2 8.0 + - - +
181A PRO* 1.3 81.8 - - - +
183A LEU* 1.3 60.2 + - - +
185A CYS 3.4 2.6 + - - -
187A ASN* 3.0 36.8 + - + -
189A VAL* 3.6 15.7 - - + -
485A TYR* 3.7 24.8 - - + -
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Residues in contact with LEU 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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76A TRP* 3.6 17.8 - - + -
84A ARG* 3.6 7.3 + - - +
88A LEU* 4.5 16.2 - - + -
91A LEU* 5.4 0.4 - - + -
179A ILE* 3.1 36.9 + - + +
180A ALA 4.1 2.5 - - - +
182A ALA* 1.3 71.3 - - - +
184A CYS* 1.3 61.2 + - - +
185A CYS 3.0 2.2 - - - -
186A GLY* 2.9 19.6 + - - +
187A ASN 3.7 18.2 - - - +
189A VAL* 3.9 13.0 - - + -
213A PHE* 4.0 17.5 - - + -
217A VAL* 3.7 12.6 - - + -
218A ILE* 3.6 36.1 - - + -
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Residues in contact with CYS 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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84A ARG* 2.6 22.2 + - - +
88A LEU* 4.0 8.7 - - + +
132A TYR* 3.2 33.7 - - + +
135A TRP* 3.5 14.8 - - - -
136A ALA* 3.5 24.5 - - - -
139A ILE* 3.5 16.7 - - - +
180A ALA 3.0 15.5 + - - +
181A PRO* 3.1 16.6 + - + +
183A LEU* 1.3 77.6 - - - +
185A CYS* 1.3 51.1 + - - +
482A LEU* 4.7 3.6 - - - -
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Residues in contact with CYS 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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84A ARG* 3.6 8.0 + - - +
139A ILE* 3.9 22.7 - - + -
157A GLU 4.5 0.2 - - - -
158A PRO* 3.2 27.7 - - - +
181A PRO 3.2 14.1 + - - +
182A ALA 3.4 0.2 + - - -
183A LEU 3.0 0.8 - - - -
184A CYS* 1.3 76.3 - - - +
186A GLY* 1.3 58.9 + - - +
187A ASN* 3.5 6.5 - - - +
482A LEU* 3.6 34.1 - - - -
485A TYR* 3.4 25.8 - - - +
486A SER* 4.2 11.0 - - - -
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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