Contacts of the helix formed by residues 160 - 170 (chain H) in PDB entry 6O81
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 SER 160 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129H ALA* 3.4 11.8 - - - +
130H TYR* 3.3 32.4 + - - +
155H SER* 3.5 1.7 + - - -
158H ASP* 2.6 23.4 + - - -
159H LEU* 1.3 72.7 - - - +
161H GLY* 1.3 58.3 + - - +
162H LYS 3.2 1.3 - - - -
163H LYS* 3.1 20.3 + - - +
164H MET* 2.5 34.0 + - - +
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Residues in contact with GLY 161 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129H ALA* 4.5 5.8 - - - -
130H TYR 4.4 0.4 - - - +
152H VAL* 3.4 14.5 - - - +
153H THR 3.3 26.0 - - - -
154H GLU* 4.4 1.8 - - - -
155H SER* 2.7 17.2 + - - -
160H SER* 1.3 70.6 + - - +
162H LYS* 1.3 60.1 + - - +
164H MET* 3.3 7.8 + - - -
165H ALA* 2.9 25.3 + - - +
177H VAL* 5.3 0.7 - - - -
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Residues in contact with LYS 162 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270G HIS* 6.0 2.4 - - - -
154H GLU* 3.9 11.0 + - - +
159H LEU* 4.2 35.0 - - + +
160H SER* 3.2 0.6 - - - +
161H GLY* 1.3 75.4 - - - +
163H LYS* 1.3 56.5 + - - +
165H ALA* 3.3 6.9 + - + +
166H LYS* 2.9 55.6 + - + +
177H VAL* 4.5 28.0 - - + +
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Residues in contact with LYS 163 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130H TYR* 3.7 40.9 - - + -
159H LEU 3.9 7.8 + - - +
160H SER* 3.1 24.4 + - - +
162H LYS* 1.3 76.8 - - - +
164H MET* 1.3 58.3 + - - +
166H LYS* 3.3 11.3 + - + +
167H ALA* 2.9 29.9 + - + +
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Residues in contact with MET 164 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127H THR* 4.7 16.8 - - + -
128H HIS 4.7 0.9 - - - +
129H ALA 4.3 3.6 - - - +
130H TYR* 3.7 28.0 - - + +
131H SER 3.6 31.9 - - - +
134H VAL* 4.8 3.4 - - + -
135H LEU* 4.2 26.5 - - + +
138H LEU* 5.8 1.6 - - - -
152H VAL* 3.8 18.4 - - + -
160H SER 2.5 19.1 + - - +
161H GLY* 3.5 10.1 - - - +
162H LYS 3.3 0.2 - - - -
163H LYS* 1.3 73.7 - - - +
165H ALA* 1.3 58.0 + - - +
167H ALA* 3.3 2.7 + - - +
168H LEU* 2.9 48.6 + - + +
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Residues in contact with ALA 165 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152H VAL* 3.8 10.3 - - + -
161H GLY 2.9 16.5 + - - +
162H LYS* 3.8 4.3 - - + +
164H MET* 1.3 76.3 - - - +
166H LYS* 1.3 58.6 + - + +
168H LEU 3.7 0.4 - - - +
169H CYS* 2.9 32.4 + - - +
175H VAL* 3.8 20.6 - - + +
177H VAL* 3.7 25.8 - - + -
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Residues in contact with LYS 166 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162H LYS* 2.9 43.4 + - + +
163H LYS* 3.8 10.3 - - + +
164H MET 3.3 0.2 - - - -
165H ALA* 1.3 76.2 - - + +
167H ALA* 1.3 60.8 + - - +
169H CYS* 3.3 17.8 - - - -
170H HIS* 3.2 29.3 + - + +
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Residues in contact with ALA 167 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130H TYR* 4.9 5.6 - - + -
135H LEU* 4.0 23.1 - - + +
163H LYS* 2.9 18.4 + - + +
164H MET* 3.8 5.2 - - - +
166H LYS* 1.3 78.2 - - - +
168H LEU* 1.3 61.0 + - - +
169H CYS 3.5 0.2 - - - -
170H HIS* 3.9 10.2 + - - +
171H LEU* 3.9 14.6 + - - +
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Residues in contact with LEU 168 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127H THR* 6.2 0.4 - - + -
135H LEU* 4.6 17.9 - - + +
138H LEU* 3.8 36.1 - - + -
150H VAL* 4.2 13.9 - - + -
152H VAL* 6.4 0.2 - - + -
164H MET* 2.9 30.5 + - + +
165H ALA* 3.4 2.0 + - - +
166H LYS 3.3 0.2 - - - -
167H ALA* 1.3 77.2 - - - +
169H CYS* 1.3 62.6 + - - +
170H HIS 3.3 0.9 - - - -
171H LEU* 3.3 46.8 + - + +
172H ASN 3.6 4.0 + - - -
173H VAL* 3.8 10.7 + - + +
175H VAL* 3.7 29.4 - - + +
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Residues in contact with CYS 169 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165H ALA 2.9 16.6 + - - +
166H LYS* 3.3 29.6 - - - -
168H LEU* 1.3 74.3 - - - +
170H HIS* 1.3 74.3 + - - +
171H LEU 3.2 0.4 - - - -
172H ASN* 3.2 17.5 + - - +
173H VAL 4.6 10.3 - - - +
175H VAL* 4.5 5.1 - - + +
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Residues in contact with HIS 170 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166H LYS* 3.2 24.2 + - + +
167H ALA* 4.0 10.5 - - - +
168H LEU 3.3 0.6 - - - -
169H CYS* 1.3 86.4 + - - +
171H LEU* 1.3 58.5 + - - +
172H ASN* 3.2 4.9 + - - +
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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