Contacts of the helix formed by residues 157 - 174 (chain A) in PDB entry 2C8U
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 THR 157 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A HIS 5.5 0.4 - - - +
84A MET* 3.2 18.6 - - - +
86A GLY* 4.1 13.7 - - - +
95A VAL* 3.5 27.4 - - + +
152A VAL* 4.2 17.3 + - + +
155A LYS* 3.7 10.5 - - + +
156A VAL* 1.3 82.6 - - - +
158A LEU* 1.3 64.1 - - - +
159A ALA* 3.4 16.1 + - - +
160A ASP* 3.0 30.1 + - - +
161A LEU* 3.7 8.2 + - - +
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Residues in contact with LEU 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A SER* 4.4 4.9 - - - +
23A THR* 3.5 23.3 - - - +
72A LEU* 4.6 4.3 - - + +
75A ALA* 3.9 15.3 - - + +
76A ARG* 3.5 47.8 - - + +
79A ALA* 3.9 6.1 - - + -
84A MET* 2.8 17.5 + - - +
85A MET* 3.8 9.9 - - - -
95A VAL* 4.5 0.4 - - + -
99A ILE* 3.8 18.2 - - + -
157A THR* 1.3 72.5 - - - +
159A ALA* 1.3 62.7 + - - +
161A LEU* 3.1 11.7 + - + -
162A VAL* 3.0 37.1 + - + +
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Residues in contact with ALA 159 (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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95A VAL* 3.8 32.1 - - + +
98A LEU* 3.5 27.0 - - + +
99A ILE* 4.0 11.7 - - - +
151A ALA* 4.2 5.6 - - + -
152A VAL* 4.6 1.6 - - + -
157A THR* 3.4 11.9 + - - +
158A LEU* 1.3 78.9 - - - +
160A ASP* 1.3 62.6 + - - +
162A VAL* 4.0 1.1 - - - +
163A LEU* 3.0 25.3 + - - +
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Residues in contact with ASP 160 (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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150A LEU* 3.6 13.6 - - - +
151A ALA* 3.0 21.0 + - - +
152A VAL 5.1 0.3 + - - -
155A LYS 3.9 0.9 - - - +
156A VAL* 3.5 8.8 - - - -
157A THR* 3.0 34.6 + - - +
159A ALA* 1.3 78.6 - - - +
161A LEU* 1.3 62.1 + - + +
163A LEU 3.4 0.2 + - - -
164A ILE* 3.2 22.0 + - - +
188A HIS* 2.4 42.7 + - - +
192A LEU* 3.7 25.0 - - + +
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Residues in contact with LEU 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A SER* 4.8 5.2 - - - +
22A MET* 3.7 18.2 - - + +
23A THR* 3.5 45.5 - - + +
26A ALA* 4.4 9.2 - - + -
84A MET* 4.9 2.7 - - - -
156A VAL* 4.2 18.4 - - + -
157A THR 3.8 12.1 - - - +
158A LEU* 3.1 13.2 + - + +
160A ASP* 1.3 74.8 - - - +
162A VAL* 1.3 66.9 + - - +
163A LEU 3.2 0.2 - - - -
164A ILE* 3.2 9.1 - - + +
165A ALA* 3.2 24.7 + - - +
192A LEU* 4.3 3.6 - - + -
199A LEU* 3.9 34.1 - - + -
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Residues in contact with VAL 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A SER* 3.8 18.8 - - - +
72A LEU* 3.9 15.7 - - + -
99A ILE* 4.3 22.0 - - + +
102A ALA* 3.7 19.3 - - + -
103A GLU* 3.6 23.3 - - - +
158A LEU* 3.0 39.9 + - + +
159A ALA 4.0 2.9 - - - +
161A LEU* 1.3 75.2 - - - +
163A LEU* 1.3 63.0 + - - +
165A ALA* 3.5 2.5 + - - +
166A VAL* 3.1 29.6 + - + +
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Residues in contact with LEU 163 (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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98A LEU* 4.1 10.5 - - + -
102A ALA* 4.5 11.8 - - + +
139A ILE* 3.7 33.9 - - + -
143A LEU* 3.9 33.9 - - + -
159A ALA 3.0 19.2 + - - +
160A ASP 3.6 4.9 - - - +
161A LEU 3.2 0.2 - - - -
162A VAL* 1.3 78.4 - - - +
164A ILE* 1.3 58.3 + - + +
166A VAL* 3.3 2.9 + - + -
167A ILE* 2.9 53.2 + - + +
185A ILE* 5.3 3.4 - - + -
188A HIS* 3.7 25.1 - - + +
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Residues in contact with ILE 164 (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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22A MET* 3.7 20.2 - - + -
160A ASP 3.2 6.7 + - - +
161A LEU* 3.2 19.1 - - - +
163A LEU* 1.3 78.2 - - + +
165A ALA* 1.3 62.2 + - - +
167A ILE* 3.4 3.0 + - + +
168A ASP* 3.1 31.5 + - - +
188A HIS* 4.3 12.6 - - + +
189A ARG* 3.6 38.7 + - + +
192A LEU* 3.4 33.4 - - + -
199A LEU* 3.5 19.7 - - + -
203A LEU* 3.9 13.7 - - + -
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Residues in contact with ALA 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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18A GLU* 3.8 23.2 - - + +
19A SER* 4.4 12.6 - - - +
22A MET* 4.3 14.4 - - + -
106A GLU* 5.8 0.9 - - - +
161A LEU 3.2 17.0 + - - +
162A VAL* 3.7 4.9 - - - +
164A ILE* 1.3 79.9 - - - +
166A VAL* 1.3 63.1 + - + +
168A ASP* 3.5 6.9 + - - +
169A HIS* 3.3 29.3 + - + +
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Residues in contact with VAL 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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102A ALA* 3.5 38.6 - - + +
103A GLU* 4.4 2.7 - - - +
105A LEU* 3.7 21.3 - - + -
106A GLU* 3.5 36.8 - - + +
109A TYR* 5.9 0.9 - - + -
162A VAL* 3.1 24.0 + - + +
163A LEU* 3.9 3.6 - - + +
165A ALA* 1.3 77.3 - - + +
167A ILE* 1.3 65.3 + - + +
169A HIS* 3.0 17.7 + - + +
170A VAL* 3.2 12.2 + - + +
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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
----------------------------------------------------------
105A LEU* 4.3 7.4 - - + -
136A LEU* 3.6 31.6 - - + -
139A ILE* 5.2 0.7 - - + -
163A LEU* 2.9 44.5 + - + +
164A ILE* 4.0 3.8 - - - +
166A VAL* 1.3 73.9 - - - +
168A ASP* 1.3 59.2 + - - +
170A VAL* 3.0 7.6 + - + +
171A THR* 3.0 30.5 + - + +
178A LEU* 3.7 23.8 - - + -
185A ILE* 4.0 25.4 - - + -
189A ARG* 4.4 15.3 - - - +
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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
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14A ARG* 3.5 18.1 - - - +
18A GLU* 5.8 1.3 - - - +
22A MET* 5.7 2.6 - - - +
164A ILE* 3.1 14.4 + - - +
165A ALA* 3.7 6.5 - - - +
167A ILE* 1.3 75.7 - - - +
169A HIS* 1.3 55.6 + - - +
171A THR* 3.1 10.3 + - - +
172A ASP* 2.9 33.6 + - - +
189A ARG* 2.7 37.9 + - - -
203A LEU* 5.2 8.1 - - - +
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Residues in contact with HIS 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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14A ARG* 2.7 46.8 + - + -
15A GLY 4.8 2.4 + - - -
18A GLU* 3.7 15.2 + - - -
106A GLU* 2.7 39.3 + - - +
109A TYR* 3.4 46.9 + + + -
165A ALA* 3.3 13.0 + - - +
166A VAL* 3.0 9.5 + - - +
168A ASP* 1.3 75.1 - - - +
170A VAL* 1.3 61.4 + - - +
172A ASP* 2.9 25.0 + - - +
173A LEU* 3.2 11.6 + - - +
1209A BME 4.2 3.4 - - - -
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Residues in contact with VAL 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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105A LEU* 3.9 37.9 - - + +
109A TYR* 5.6 4.0 - - + -
128A LEU* 4.7 4.2 - - + +
132A VAL* 4.3 15.3 - - + -
136A LEU* 4.7 5.2 - - + -
166A VAL* 3.2 12.1 + - + +
167A ILE* 3.0 11.0 + - - +
169A HIS* 1.3 76.0 - - + +
171A THR* 1.3 58.3 + - - +
173A LEU* 2.8 30.6 + - + +
174A ASP* 3.1 10.0 + - - +
177A PHE* 4.2 19.1 - - + -
178A LEU* 3.7 24.0 - - + -
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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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167A ILE* 3.0 17.8 + - + +
168A ASP* 3.1 25.3 + - - +
170A VAL* 1.3 73.4 - - - +
172A ASP* 1.3 62.0 + - - +
174A ASP 3.1 11.6 - - - +
175A LYS* 2.9 42.7 + - - +
178A LEU* 3.6 28.5 - - + -
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Residues in contact with ASP 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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14A ARG* 2.7 42.4 + - - +
109A TYR* 4.3 13.2 + - + -
168A ASP 2.9 21.9 + - - +
169A HIS* 2.9 22.2 + - - +
171A THR* 1.3 76.8 + - - +
173A LEU* 1.3 60.3 + - + +
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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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109A TYR* 4.0 24.9 - - + -
112A THR* 3.5 30.3 - - + +
120A LYS* 5.5 3.1 - - - -
124A ILE* 3.8 42.5 - - + +
127A ILE* 3.7 30.7 - - + -
128A LEU* 4.7 11.2 - - + -
132A VAL* 5.6 0.9 - - + -
169A HIS 3.6 9.6 - - - +
170A VAL* 2.8 23.3 + - + +
172A ASP* 1.3 76.3 - - + +
174A ASP* 1.3 59.7 + - - +
175A LYS 4.2 0.2 - - - -
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Residues in contact with ASP 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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128A LEU* 3.7 21.5 - - + +
170A VAL 3.1 5.0 + - - +
171A THR* 3.1 12.2 - - - +
173A LEU* 1.3 79.6 - - - +
175A LYS* 1.3 60.2 + - - +
176A GLU* 3.0 26.0 + - - +
177A PHE* 3.0 46.2 + - + +
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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
------------------------------------------------------------
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