Contacts of the helix formed by residues 155 - 165 (chain I) in PDB entry 2ONK
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 ASP 155 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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153I SER 3.5 4.6 + - - -
154I VAL* 1.3 71.9 - - - +
156I VAL* 1.3 61.0 + - - +
157I ARG* 3.1 51.9 + - - +
158I LEU* 2.7 54.9 + - + +
159I GLU 3.7 1.0 + - - -
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Residues in contact with VAL 156 (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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78I ARG* 4.4 21.3 - - - +
154I VAL 3.0 8.7 + - - +
155I ASP* 1.3 73.6 + - - +
157I ARG* 1.3 64.1 + - + +
159I GLU* 2.8 32.7 + - - +
160I HIS* 2.9 38.2 + - + +
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Residues in contact with ARG 157 (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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42G GLU* 6.1 0.2 - - - +
74G PHE* 6.1 0.7 - - + -
76G PRO* 4.3 32.1 - - + +
77G GLN* 3.6 31.1 + - - +
78G ASP* 4.2 10.6 + - - +
80G ALA* 4.5 4.5 - - + -
155I ASP* 3.1 30.7 + - - +
156I VAL* 1.3 77.0 - - + +
158I LEU* 1.3 56.1 + - - +
160I HIS* 2.7 19.0 + - + +
161I VAL* 2.7 37.0 + - - +
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Residues in contact with LEU 158 (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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80G ALA* 3.7 33.8 - - + +
81G LEU 3.7 15.9 - - - +
82G PHE* 3.6 19.5 - - + -
83G PRO* 4.0 11.7 - - + -
154I VAL* 4.2 1.6 - - + -
155I ASP* 2.7 46.6 + - + +
157I ARG* 1.3 73.6 - - - +
159I GLU* 1.3 54.8 + - - +
161I VAL* 3.6 0.7 + - - +
162I ALA* 3.0 27.0 + - - +
176I VAL* 3.9 14.4 - - + -
180I LEU* 3.9 20.0 - - + -
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Residues in contact with GLU 159 (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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74I TYR* 3.7 10.2 + - - -
78I ARG* 2.9 46.9 + - - -
154I VAL* 3.8 12.0 - - + +
156I VAL* 2.8 16.1 + - + +
158I LEU* 1.3 77.9 - - - +
160I HIS* 1.3 69.1 + - - +
162I ALA* 3.2 4.1 + - - +
163I ARG* 3.1 28.7 + - - +
172I VAL* 3.5 27.5 - - + +
176I VAL* 4.2 9.0 - - + -
177I SER* 3.0 24.0 + - - +
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Residues in contact with HIS 160 (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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42G GLU* 3.9 21.5 + - - -
47G ILE* 3.3 39.0 - - + +
74G PHE* 5.5 4.3 - + + -
156I VAL* 2.9 36.1 + - + +
157I ARG* 2.7 31.3 + - + +
159I GLU* 1.3 72.0 - - + +
161I VAL* 1.3 64.0 + - + +
163I ARG* 3.0 14.2 + - - +
164I THR* 2.9 21.0 + - - -
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Residues in contact with VAL 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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74G PHE* 4.2 15.9 - - + +
76G PRO* 3.8 22.0 - - + -
80G ALA* 3.4 25.1 - - + -
82G PHE* 4.2 8.1 - - + -
139G ARG* 4.4 15.7 - - - +
157I ARG 2.7 21.9 + - - +
158I LEU* 3.7 4.5 - - - +
160I HIS* 1.3 71.2 - - - +
162I ALA* 1.3 53.2 + - - +
164I THR* 2.7 14.1 + - - -
165I LEU* 2.7 56.7 + - + +
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Residues in contact with ALA 162 (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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82G PHE* 4.1 11.6 - - + -
93G TYR* 3.6 15.6 + - - +
158I LEU 3.0 15.6 + - - +
159I GLU 3.2 6.5 + - - +
161I VAL* 1.3 81.6 - - - +
163I ARG* 1.3 61.1 + - - +
165I LEU 3.5 6.6 + - - -
167I SER* 2.8 24.8 + - - -
172I VAL* 4.0 9.9 - - + -
176I VAL* 3.5 26.9 - - + -
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Residues in contact with ARG 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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47G ILE* 5.8 0.2 - - + -
66G PRO* 5.1 2.0 - - - +
67G PRO* 3.8 24.4 - - + +
68G GLU* 3.3 39.6 + - - +
2H ARG* 4.7 9.3 - - - +
159I GLU* 3.1 14.7 + - - +
160I HIS* 3.0 13.7 + - - +
162I ALA* 1.3 74.0 - - - +
164I THR* 1.3 57.4 + - - +
166I GLY* 2.7 27.2 + - - -
167I SER 3.3 13.1 + - - +
168I SER 3.7 0.2 - - - -
169I PRO* 2.8 48.5 - - - +
172I VAL* 3.5 14.6 - - + -
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Residues in contact with THR 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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45G ALA* 4.9 3.5 + - - +
47G ILE* 3.5 18.7 - - - +
67G PRO* 2.8 25.0 + - - +
68G GLU* 4.1 1.7 - - - +
70G ARG 4.9 2.8 - - - +
72G ILE* 4.1 14.7 - - + +
73G GLY* 5.1 0.2 - - - -
74G PHE* 3.5 41.0 - - + +
143G ILE* 5.5 0.9 - - - +
160I HIS 2.9 13.5 + - - -
161I VAL* 2.8 16.9 - - + +
163I ARG* 1.3 71.9 - - - +
165I LEU* 1.3 67.3 + - + +
166I GLY 2.8 10.6 + - - -
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Residues in contact with LEU 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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72G ILE 5.9 0.7 - - - +
73G GLY* 6.0 2.5 - - - -
74G PHE 5.7 3.8 - - - +
82G PHE* 4.0 10.3 - - + -
93G TYR* 3.6 40.5 - - + +
94G GLY* 3.7 20.5 - - - +
139G ARG* 4.0 28.9 - - + +
140G ALA* 5.5 2.9 - - - -
143G ILE* 3.5 29.2 - - + -
161I VAL* 2.7 37.9 + - + +
162I ALA 3.8 1.1 - - - +
163I ARG 3.2 0.6 - - - -
164I THR* 1.3 80.8 - - + +
166I GLY* 1.3 64.2 + - - +
167I SER 3.7 0.9 - - - -
171I ARG* 5.4 0.2 + - - -
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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