Contacts of the helix formed by residues 159 - 169 (chain I) in PDB entry 5A2Q
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 159 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158I ILE* 1.3 71.8 - - - +
160I SER* 1.3 67.0 + - - +
161I LEU* 4.4 10.5 - - - -
162I LEU* 2.8 35.8 + - - +
163I GLU 2.9 9.7 + - - -
191I GLU* 5.9 0.3 - - - +
192I GLY* 4.9 14.2 + - - -
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Residues in contact with SER 160 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158I ILE 3.2 6.3 + - - -
159I SER* 1.3 70.2 - - - +
161I LEU* 1.3 64.0 + - - +
163I GLU* 2.8 30.3 - - - +
164I GLU* 3.0 13.0 + - - +
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Residues in contact with LEU 161 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159I SER* 2.8 7.9 + - - -
160I SER* 1.3 79.8 - - - +
162I LEU* 1.3 63.9 + - - +
164I GLU* 3.2 9.0 + - + +
165I GLN* 3.0 27.9 + - - +
192I GLY* 4.9 5.6 - - - +
195I LEU* 3.7 18.8 - - + -
196I GLU* 4.1 33.7 - - + +
199I LEU* 4.5 15.9 - - + -
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Residues in contact with LEU 162 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67I TRP* 3.5 37.7 - - + -
69I SER* 5.0 1.1 - - - +
158I ILE* 3.4 16.8 - - + -
159I SER* 2.8 28.2 + - - +
161I LEU* 1.3 71.7 - - - +
163I GLU* 1.3 65.9 + - - +
165I GLN* 3.0 16.9 + - + +
166I PHE* 3.1 20.5 + - + -
171I LEU* 3.9 20.4 - - + -
172I LEU 6.2 0.2 - - - +
189I VAL* 4.6 2.5 - - + -
190I LEU 3.9 16.4 - - - +
191I GLU* 3.9 24.7 - - + +
195I LEU* 4.1 9.9 - - + -
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Residues in contact with GLU 163 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121I LEU* 5.0 11.9 - - + -
122I GLY* 4.6 2.2 - - - +
158I ILE* 4.1 14.8 - - + +
159I SER 2.9 11.0 + - - +
160I SER* 2.8 21.7 - - - +
162I LEU* 1.3 76.4 - - - +
164I GLU* 1.3 85.3 + - - +
166I PHE* 3.4 11.0 + - - +
167I GLN* 3.3 42.7 + - + +
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Residues in contact with GLU 164 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160I SER 3.0 10.3 + - - +
161I LEU* 3.4 11.0 - - + +
163I GLU* 1.3 86.8 + - - +
165I GLN* 1.3 71.3 + - + +
167I GLN* 2.8 27.0 + - - +
168I GLN* 3.0 25.3 + - - +
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Residues in contact with GLN 165 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103I LEU* 4.8 1.4 - - - +
161I LEU 3.0 21.5 + - - +
162I LEU* 3.0 14.9 + - + +
164I GLU* 1.3 79.3 - - + +
166I PHE* 1.3 63.5 + - - +
168I GLN* 2.8 19.7 + - - +
169I GLY 3.0 9.0 + - - -
170I LYS 2.8 37.0 + - - +
171I LEU* 3.6 14.9 - - + -
172I LEU* 3.2 50.1 + - - +
195I LEU* 3.7 17.6 - - - +
199I LEU* 4.6 8.1 - - - +
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Residues in contact with PHE 166 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67I TRP* 4.0 34.5 - + - -
106I SER* 3.1 32.0 + - - +
109I TYR* 4.0 13.5 - - + -
110I ARG* 4.0 28.3 + - + -
113I TYR* 6.0 0.9 - - + -
121I LEU* 3.8 34.8 - - + -
122I GLY* 4.0 20.1 - - - +
158I ILE* 4.7 3.1 - - + -
162I LEU* 3.1 29.4 + - + -
163I GLU* 3.6 7.2 - - - +
165I GLN* 1.3 77.2 - - - +
167I GLN* 1.3 58.7 + - - +
169I GLY* 2.8 20.5 + - - +
171I LEU* 4.2 22.0 - - + -
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Residues in contact with GLN 167 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122I GLY* 3.5 31.0 - - - +
123I ARG 3.8 20.6 + - - +
124I LYS* 4.9 5.2 - - - +
125I LYS 5.6 0.2 + - - -
163I GLU* 3.3 38.4 + - - +
164I GLU* 2.8 26.0 + - - +
166I PHE* 1.3 73.1 - - - +
168I GLN* 1.3 58.6 + - - +
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Residues in contact with GLN 168 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164I GLU* 3.0 26.4 + - - +
165I GLN* 2.8 13.8 + - - +
167I GLN* 1.3 79.5 - - - +
169I GLY* 1.3 57.6 + - - +
170I LYS* 3.3 20.8 + - + +
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Residues in contact with GLY 169 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104I ILE 3.7 1.4 - - - +
105I ASP* 3.8 2.9 - - - -
106I SER* 2.8 33.9 + - - -
107I THR* 5.9 0.7 - - - +
165I GLN 3.0 1.6 + - - -
166I PHE 2.8 16.3 + - - -
167I GLN 3.4 0.2 - - - -
168I GLN* 1.3 76.5 - - - +
170I LYS* 1.3 63.3 + - - +
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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