Contacts of the helix formed by residues 155 - 168 (chain R) in PDB entry 6CNC
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 TYR 155 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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153R SER* 2.9 12.4 - - - +
154R VAL* 1.3 80.9 - - - +
156R SER* 1.3 64.0 + - - +
157R ILE 3.2 0.7 - - - -
158R GLY* 2.8 4.0 + - - +
159R ALA* 2.4 54.0 + - + +
515R LEU* 4.9 5.4 - - + -
413S ARG* 4.6 8.2 + - - -
12X T 3.0 57.2 + - - +
13X A 3.0 42.0 + - - +
44Y T 5.5 7.2 - - - -
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Residues in contact with SER 156 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124R ASN* 3.3 13.9 - - - -
152R VAL* 3.9 21.2 - - - +
153R SER* 4.6 6.5 - - - -
155R TYR* 1.3 84.4 - - - +
157R ILE* 1.3 62.7 + - - +
159R ALA* 3.5 7.2 - - - +
160R THR* 2.9 28.9 + - - -
44Y T 4.9 8.5 + - - -
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Residues in contact with ILE 157 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123R GLN* 6.1 1.3 - - + -
124R ASN* 3.1 27.3 + - - +
127R ALA* 4.1 25.4 - - + -
128R SER* 5.2 2.6 - - - +
143R LEU* 3.5 27.8 - - + -
146R PHE* 4.9 3.8 - - + +
147R SER* 3.6 28.5 - - - +
150R LEU* 5.5 5.8 - - + -
152R VAL* 3.5 30.3 - - + -
154R VAL* 4.9 6.7 - - - +
155R TYR 3.2 1.2 - - - +
156R SER* 1.3 76.7 - - - +
158R GLY* 1.3 62.8 + - - +
160R THR* 3.8 1.7 - - - -
161R PHE* 2.9 24.2 + - + +
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Residues in contact with GLY 158 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143R LEU* 4.0 14.5 - - - +
154R VAL 4.4 1.6 - - - -
155R TYR* 2.8 16.7 + - - +
157R ILE* 1.3 76.7 - - - +
159R ALA* 1.3 60.0 + - - -
161R PHE* 3.4 3.8 - - - +
162R LEU* 2.9 21.5 + - - +
515R LEU* 3.4 35.2 - - - +
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Residues in contact with ALA 159 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155R TYR* 2.4 50.3 + - + +
156R SER* 3.5 8.3 - - - +
158R GLY* 1.3 69.0 - - - +
160R THR* 1.3 66.1 + - - +
162R LEU* 3.1 4.6 + - - +
163R LYS* 2.9 37.7 + - + +
515R LEU* 5.3 0.2 - - - -
13X A 5.5 2.7 - - - -
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Residues in contact with THR 160 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116R PHE* 3.6 22.1 - - + -
120R ARG* 4.8 15.7 - - + +
124R ASN* 3.4 43.7 - - + +
125R VAL* 4.3 9.0 - - + +
128R SER* 4.7 2.0 - - - +
156R SER 2.9 18.7 + - - -
157R ILE 3.9 2.0 - - - -
159R ALA* 1.3 72.4 - - - +
161R PHE* 1.3 64.3 + - - +
163R LYS* 3.0 9.7 + - - +
164R MET* 2.9 20.6 + - - +
43Y A 5.6 0.9 + - - -
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Residues in contact with PHE 161 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128R SER* 3.6 33.0 - - - -
131R TYR* 3.4 37.7 - + - -
132R VAL* 3.5 20.9 - - + -
135R ARG* 4.9 4.9 - - - -
143R LEU* 5.2 7.6 - - + -
157R ILE* 2.9 20.4 + - + +
158R GLY* 3.4 9.6 - - - +
160R THR* 1.3 79.5 - - - +
162R LEU* 1.3 78.4 + - + +
163R LYS 3.0 0.3 + - - -
164R MET* 3.0 19.4 + - + +
165R VAL* 3.2 25.8 + - + +
512R GLU* 4.3 24.0 - - + -
515R LEU* 4.9 7.6 - - + -
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Residues in contact with LEU 162 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158R GLY 2.9 19.6 + - - +
159R ALA* 3.8 4.0 - - - +
161R PHE* 1.3 82.2 - - + +
163R LYS* 1.3 67.6 + - + +
165R VAL* 3.3 21.4 - - + +
166R LYS* 3.5 9.0 + - + +
512R GLU* 4.3 24.0 - - + +
515R LEU* 4.8 14.8 - - + +
520R ILE* 4.0 21.1 - - + -
522R ARG* 4.9 9.0 - - - +
13X A 3.7 19.3 - - - +
14X T 3.1 28.3 - - - +
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Residues in contact with LYS 163 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116R PHE* 3.7 4.5 - - + -
120R ARG* 3.5 30.5 - - - +
159R ALA* 2.9 30.6 + - + +
160R THR* 3.0 8.3 + - - +
162R LEU* 1.3 78.1 - - + +
164R MET* 1.3 57.5 + - - +
165R VAL 2.9 4.7 - - - -
166R LYS* 2.7 43.2 + - + +
167R LYS* 3.0 13.7 + - + +
14X T 3.3 28.0 + - - -
43Y A 5.2 4.9 - - - +
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Residues in contact with MET 164 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107R TRP* 5.5 6.1 - - + +
111R ALA* 4.6 6.1 - - + -
116R PHE* 3.4 33.3 - - + -
125R VAL* 5.9 0.7 - - - -
128R SER* 2.6 35.7 - - - +
129R CYS* 3.8 30.7 - - - -
132R VAL* 5.0 13.2 - - + -
160R THR 2.9 8.9 + - - +
161R PHE* 3.0 20.8 + - + +
163R LYS* 1.3 75.1 - - - +
165R VAL* 1.3 62.8 + - + +
166R LYS 3.3 0.2 - - - -
167R LYS* 3.9 4.5 - - - +
168R LEU* 3.2 49.0 + - + +
170R ILE* 3.7 3.3 - - + +
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Residues in contact with VAL 165 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132R VAL* 5.7 2.9 - - + -
161R PHE* 3.2 37.0 + - + +
162R LEU* 3.3 18.4 - - + +
163R LYS 2.9 0.6 - - - -
164R MET* 1.3 80.5 - - + +
166R LYS* 1.3 53.8 + - + +
168R LEU 2.6 23.4 - - - +
169R HIS* 4.4 1.2 - - - -
170R ILE* 3.4 26.8 + - + +
510R SER* 4.8 17.3 - - - +
512R GLU* 5.1 4.3 - - - +
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Residues in contact with LYS 166 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162R LEU* 3.5 7.8 + - + +
163R LYS* 2.7 37.1 + - + +
165R VAL* 1.3 73.3 - - + +
167R LYS* 1.3 77.4 + - + +
168R LEU 2.6 15.8 - - - +
169R HIS* 4.3 10.6 + - - -
522R ARG* 3.2 45.3 - - - +
14X T 5.3 4.9 - - - +
15X T 4.7 14.0 + - - +
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Residues in contact with LYS 167 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114R ASN* 3.1 28.7 + - + +
116R PHE* 3.6 39.4 - - + -
120R ARG* 4.7 8.1 - - - +
163R LYS* 3.0 9.0 + - + +
164R MET* 4.7 2.0 - - - -
166R LYS* 1.3 95.4 - - + +
168R LEU* 1.3 60.7 + - + +
169R HIS* 4.8 5.8 + - - -
42Y T 4.0 18.0 + - - -
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Residues in contact with LEU 168 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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857B PRO* 5.9 2.9 - - + -
107R TRP* 4.5 14.6 - - + +
110R LEU* 4.2 36.6 - - + +
111R ALA* 4.4 20.4 - - + +
114R ASN* 3.3 27.1 - - + +
116R PHE* 6.5 0.9 - - + -
164R MET* 3.2 38.9 + - + +
165R VAL 2.6 15.5 - - - +
166R LYS 2.6 21.2 - - - +
167R LYS* 1.3 76.2 - - + +
169R HIS* 1.3 71.9 + - - +
170R ILE* 3.6 10.1 - - + -
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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