Contacts of the helix formed by residues 162 - 183 (chain C) in PDB entry 5B2G
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 ALA 162 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C LEU* 5.4 0.7 - - + -
29C MET* 3.3 42.4 - - + -
47C TRP* 4.7 5.0 - - + -
161C GLY* 1.3 72.3 - - - +
163C SER* 1.3 56.4 + - - +
164C LEU 2.8 1.3 + - - -
165C TYR* 2.7 47.9 + - - +
166C VAL* 3.5 7.0 + - - +
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Residues in contact with SER 163 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C CYS* 3.4 35.4 - - - -
27C LEU* 4.3 15.1 - - - +
29C MET 2.5 23.4 + - - -
30C TRP* 3.1 22.8 + - - -
162C ALA* 1.3 76.7 - - - +
164C LEU* 1.3 58.1 + - - +
165C TYR 3.2 0.2 - - - -
166C VAL* 3.0 15.0 + - - +
167C GLY 2.8 26.0 + - - -
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Residues in contact with LEU 164 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C TRP* 3.3 69.1 - - + +
136C VAL* 3.4 21.9 - - + +
139C THR* 4.1 4.3 - - - +
140C ALA* 3.9 21.8 - - + -
143C ILE* 4.0 9.6 - - + -
160C MET* 3.4 29.8 - - + -
161C GLY 3.9 4.6 + - - +
162C ALA 2.8 3.6 + - - +
163C SER* 1.3 78.4 + - - +
165C TYR* 1.3 63.0 + - + +
168C TRP* 3.2 35.3 + - + -
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Residues in contact with TYR 165 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160C MET* 4.1 40.8 + - + +
161C GLY* 4.3 5.6 - - - -
162C ALA* 2.7 32.1 + - - +
164C LEU* 1.3 73.1 - - + +
166C VAL* 1.3 57.5 + - + +
168C TRP* 3.6 24.5 + + + +
169C ALA* 3.1 26.3 + - - +
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Residues in contact with VAL 166 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C ALA* 3.2 32.5 - - + +
23C LEU* 4.4 15.3 - - + -
24C CYS* 4.0 9.6 - - + +
27C LEU* 4.8 11.4 - - + -
162C ALA 4.0 5.2 - - - +
163C SER* 3.0 24.3 + - - +
165C TYR* 1.3 77.0 - - + +
167C GLY* 1.3 54.5 + - - +
169C ALA* 3.0 7.4 + - + +
170C ALA* 2.6 33.8 + - - +
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Residues in contact with GLY 167 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C CYS* 4.0 13.0 - - - -
132C VAL* 3.6 6.6 - - - +
136C VAL* 3.9 20.6 - - - -
163C SER 2.8 18.3 + - - -
166C VAL* 1.3 70.6 - - - +
168C TRP* 1.3 54.4 + - - +
170C ALA* 4.2 6.1 - - - -
171C SER* 2.7 40.6 + - - -
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Residues in contact with TRP 168 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133C ILE* 5.5 3.8 - - + -
136C VAL* 4.0 6.7 - - + +
137C SER* 3.1 38.1 + - - +
140C ALA* 3.5 31.6 - - + -
144C ILE* 5.9 2.2 - - + -
160C MET* 3.8 25.8 - - + -
164C LEU* 3.2 30.1 + - + +
165C TYR* 3.8 21.5 - + + +
166C VAL 3.3 0.2 - - - -
167C GLY* 1.3 76.0 - - - +
169C ALA* 1.3 59.3 + - - +
171C SER* 3.6 8.7 + - - -
172C GLY* 3.4 16.5 + - - -
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Residues in contact with ALA 169 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C ALA* 5.9 0.9 - - + -
165C TYR 3.1 13.7 + - - +
166C VAL* 3.0 12.0 + - + +
168C TRP* 1.3 76.9 - - - +
170C ALA* 1.3 68.4 + - - +
172C GLY* 3.0 9.6 + - - -
173C LEU* 3.0 27.3 + - + +
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Residues in contact with ALA 170 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C GLY* 3.7 7.8 - - - +
20C ALA* 3.4 32.1 - - + +
21C VAL* 3.6 22.2 - - + +
132C VAL* 4.6 1.6 - - + -
166C VAL 2.6 20.5 + - - +
167C GLY* 3.9 6.1 - - - +
169C ALA* 1.3 72.2 - - - +
171C SER* 1.3 53.9 + - - +
172C GLY 3.0 0.7 + - - -
173C LEU* 3.8 2.5 - - - +
174C LEU* 2.7 40.5 + - + +
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Residues in contact with SER 171 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129C GLY 3.3 23.6 - - - -
132C VAL* 3.7 13.4 - - - +
133C ILE* 3.2 24.0 - - - +
167C GLY 2.7 26.0 + - - -
168C TRP* 3.6 10.9 + - - -
170C ALA* 1.3 72.5 - - - +
172C GLY* 1.3 60.4 + - - +
174C LEU* 3.9 8.0 - - - +
175C LEU* 3.1 34.2 + - - +
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Residues in contact with GLY 172 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168C TRP 3.4 9.8 + - - -
169C ALA* 3.0 10.1 + - - -
171C SER* 1.3 82.0 + - - +
173C LEU* 1.3 55.7 + - - -
174C LEU 3.1 0.7 - - - -
175C LEU* 3.1 21.6 + - - +
176C LEU* 3.2 12.7 + - - +
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Residues in contact with LEU 173 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C LEU* 2.9 43.4 - - + +
16C LEU* 3.6 15.9 - - + -
17C GLY* 2.9 42.6 - - - +
20C ALA* 5.6 2.9 - - + -
169C ALA* 3.0 29.8 + - + +
170C ALA* 3.8 1.8 - - - +
172C GLY* 1.3 73.7 - - - +
174C LEU* 1.3 57.2 + - - +
175C LEU 3.2 0.2 - - - -
176C LEU* 4.4 8.7 - - - -
177C GLY* 2.9 24.2 + - - -
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Residues in contact with LEU 174 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C LEU 4.6 2.0 - - - -
14C ALA* 3.2 33.4 - - - +
17C GLY* 3.8 12.3 - - - +
18C TRP* 3.8 10.8 - - + +
21C VAL* 4.9 4.0 - - + -
87C SER* 5.0 0.2 - - - +
91C ALA* 4.8 7.0 - - + -
125C PHE* 3.3 44.7 - - + +
128C ALA* 4.2 9.9 - - + -
129C GLY* 3.6 25.4 - - - +
132C VAL* 4.2 12.3 - - + -
170C ALA 2.7 25.8 + - - +
171C SER* 4.0 4.5 - - - +
173C LEU* 1.3 70.9 - - - +
175C LEU* 1.3 64.8 + - - +
177C GLY 4.3 0.7 - - - -
178C GLY 3.7 2.3 + - - -
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Residues in contact with LEU 175 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126C LEU* 3.1 49.0 - - + +
129C GLY 4.3 3.6 - - - -
130C LEU* 4.0 20.2 - - + +
133C ILE* 3.6 24.2 - - + -
171C SER 3.1 19.8 + - - +
172C GLY* 3.1 10.3 + - - +
174C LEU* 1.3 76.9 - - - +
176C LEU* 1.3 60.5 + - - +
178C GLY 2.9 3.3 + - - -
179C GLY* 2.9 23.2 + - - -
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Residues in contact with LEU 176 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C LEU* 3.7 23.8 - - + -
172C GLY 3.2 10.9 + - - +
173C LEU* 4.1 5.8 - - - +
175C LEU* 1.3 79.2 - - - +
177C GLY* 1.3 57.5 + - - +
179C GLY* 2.9 4.4 + - - +
180C LEU* 2.8 53.6 + - + +
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Residues in contact with GLY 177 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C GLY* 3.0 32.9 - - - +
13C LEU* 3.5 18.3 - - - +
14C ALA* 3.9 9.0 - - - -
173C LEU 2.9 14.5 + - - -
176C LEU* 1.3 76.7 - - - +
178C GLY* 1.3 58.8 + - - +
181C LEU* 3.3 19.9 + - - +
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Residues in contact with GLY 178 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122C GLY* 3.4 31.7 - - - -
125C PHE* 3.8 13.6 - - - +
126C LEU* 4.1 4.0 - - - -
174C LEU 3.7 4.6 + - - -
175C LEU 2.9 10.0 + - - -
177C GLY* 1.3 76.2 - - - +
179C GLY* 1.3 63.0 - - - +
181C LEU* 3.1 17.5 + - - +
182C CYS* 3.5 6.4 + - - -
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Residues in contact with GLY 179 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126C LEU* 3.8 13.1 - - - +
175C LEU 2.9 13.2 + - - -
176C LEU* 2.9 4.9 + - - -
178C GLY* 1.3 71.9 - - - +
180C LEU* 1.3 61.6 + - - +
181C LEU 3.0 4.9 - - - -
182C CYS* 3.1 15.2 + - - +
183C CYS* 3.2 22.8 + - - -
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Residues in contact with LEU 180 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C LEU* 3.7 45.8 - - + +
7C GLN* 4.6 7.7 + - - +
9C MET* 4.3 6.7 - - + -
10C GLY* 3.9 24.0 - - - +
13C LEU* 3.6 30.7 - - + -
176C LEU* 2.8 34.1 + - + +
179C GLY* 1.3 76.0 - - - +
181C LEU* 1.3 59.5 + - - +
183C CYS* 3.3 23.9 - - + +
184C SER* 5.3 0.5 - - - -
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Residues in contact with LEU 181 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7C GLN* 3.7 38.2 - - + +
10C GLY* 4.2 4.5 - - - -
11C ILE* 3.7 19.5 - - + -
98C SER* 5.1 0.2 - - - +
115C ALA 5.3 0.2 - - - +
118C MET* 3.2 39.5 - - + +
119C ILE* 3.6 18.9 + - - +
121C ALA* 4.4 3.1 - - + -
122C GLY* 3.8 3.6 - - - +
125C PHE* 3.6 32.8 - - + -
177C GLY 3.3 19.7 - - - +
178C GLY 3.1 9.6 + - - +
179C GLY 3.0 1.2 - - - -
180C LEU* 1.3 77.8 - - - +
182C CYS* 1.3 61.2 + - - +
183C CYS 4.8 0.4 - - - -
184C SER* 4.4 7.0 + - - -
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Residues in contact with CYS 182 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119C ILE* 3.3 50.9 - - + +
122C GLY* 4.1 1.1 - - - -
123C VAL* 4.0 17.9 - - - -
126C LEU* 4.4 10.8 - - - -
178C GLY 3.7 13.0 - - - -
179C GLY* 3.1 8.5 + - - +
181C LEU* 1.3 77.1 - - - +
183C CYS* 1.3 64.4 + - - +
184C SER* 3.5 6.2 + - - -
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Residues in contact with CYS 183 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C LEU* 4.2 17.8 - - + +
179C GLY 3.2 17.8 + - - +
180C LEU* 3.3 17.9 + - + +
181C LEU 3.4 0.2 - - - -
182C CYS* 1.3 77.4 - - - +
184C SER* 1.3 62.5 + - - +
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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