Contacts of the helix formed by residues 161 - 170 (chain A) in PDB entry 1I6P
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 161 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70A VAL* 6.1 0.4 - - - -
72A HIS 6.0 0.7 - - - -
78A LEU* 4.4 23.8 - - - -
157A ASN 3.2 8.9 + - - -
158A LEU* 2.7 27.6 + - - +
159A GLY 4.0 0.2 - - - +
160A HIS* 1.3 81.3 - - - +
162A THR* 1.3 63.7 + - - +
163A ILE* 3.6 10.4 + - - +
164A MET* 3.3 14.6 + - - +
165A GLN* 3.1 19.8 + - - +
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Residues in contact with THR 162 (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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160A HIS 3.6 2.4 + - - +
161A SER* 1.3 73.1 - - - +
163A ILE* 1.3 64.1 + - - +
165A GLN* 3.9 6.8 - - - +
166A SER* 3.0 33.6 + - - -
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Residues in contact with ILE 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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78A LEU* 3.4 52.7 - - + +
81A VAL* 4.1 16.4 - - + -
82A GLN* 3.8 38.1 - - + +
85A VAL* 4.4 13.6 - - + +
86A ASP* 4.7 7.2 - - - +
161A SER* 3.1 8.5 - - - +
162A THR* 1.3 83.6 + - - +
164A MET* 1.3 61.9 + - - +
166A SER* 3.0 19.1 + - - -
167A ALA* 3.2 12.1 + - - +
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Residues in contact with MET 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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81A VAL* 4.7 2.9 - - + -
85A VAL* 4.0 18.4 - - - -
93A ILE* 4.0 19.5 - - - -
158A LEU* 3.1 43.3 - - + +
159A GLY* 3.7 11.4 - - - +
161A SER* 3.3 5.5 + - - +
163A ILE* 1.3 78.1 - - - +
165A GLN* 1.3 67.2 + - - +
167A ALA* 3.7 2.9 - - + +
168A TRP* 3.0 66.9 + - + +
174A VAL* 3.8 25.4 - - + -
176A ILE* 4.0 10.8 - - + -
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Residues in contact with GLN 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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159A GLY 2.6 25.0 + - - +
160A HIS* 3.8 21.7 + - - +
161A SER 3.1 19.5 + - - +
162A THR* 3.9 7.0 - - - +
164A MET* 1.3 76.9 - - - +
166A SER* 1.3 55.9 + - - +
168A TRP* 4.3 5.5 - - - -
169A LYS 3.0 10.2 + - - -
198A ARG* 2.5 69.4 + - - +
201A LEU* 4.3 6.3 - - - +
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Residues in contact with SER 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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86A ASP* 5.4 1.9 + - - -
162A THR 3.0 19.1 + - - -
163A ILE* 3.0 9.2 + - - -
165A GLN* 1.3 75.1 - - - +
167A ALA* 1.3 67.6 + - - +
169A LYS* 3.2 10.3 + - - +
170A ARG* 3.0 40.4 + - - +
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Residues in contact with ALA 167 (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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85A VAL* 3.8 25.4 - - + -
163A ILE 3.2 15.1 + - - +
164A MET* 3.3 9.6 + - + +
166A SER* 1.3 81.7 + - - +
168A TRP* 1.3 61.1 + - + +
170A ARG* 3.3 27.1 - - - +
172A GLN* 2.9 33.3 + - + +
174A VAL* 4.8 6.1 - - + -
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Residues in contact with TRP 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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159A GLY* 3.8 23.8 - - - -
164A MET* 3.0 42.4 + - + +
165A GLN* 4.3 1.6 - - - -
167A ALA* 1.3 76.9 - - - +
169A LYS* 1.3 63.7 + - - +
171A GLY* 3.1 13.3 + - - -
172A GLN 3.9 16.6 - - - -
174A VAL* 2.9 24.8 + - + -
176A ILE* 3.8 20.9 - - + -
195A ALA* 3.8 28.5 - - + -
196A THR 3.1 18.1 + - - -
197A ASN* 3.5 27.0 - - + +
198A ARG* 3.5 35.4 - - + -
201A LEU* 4.1 9.9 - - + -
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Residues in contact with LYS 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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165A GLN 3.0 9.8 + - - +
166A SER* 3.5 10.5 - - - +
167A ALA 3.2 0.2 - - - -
168A TRP* 1.3 79.1 - - - +
170A ARG* 1.3 57.2 + - - +
171A GLY 3.0 3.3 + - - -
198A ARG* 3.0 31.8 - - - +
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Residues in contact with ARG 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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86A ASP* 2.7 36.9 + - - +
166A SER* 3.0 28.5 + - - +
167A ALA* 3.3 33.2 - - - +
169A LYS* 1.3 75.8 - - - +
171A GLY* 1.3 57.8 + - - +
172A GLN* 2.9 31.1 + - + +
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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