Contacts of the helix formed by residues 160 - 167 (chain M) in PDB entry 2I5N
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 CYS 160 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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156M LEU* 2.9 33.5 + - - -
158M ILE 3.7 0.8 - - - -
159M GLY* 1.3 74.4 - - - +
161M ILE* 1.3 68.8 + - - +
163M PRO* 3.4 9.0 - - - +
164M THR* 2.7 31.0 + - - +
169M TRP* 3.6 23.2 - - + -
600M NS5 3.8 34.1 - - + -
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Residues in contact with ILE 161 (chain M).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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153M PHE* 3.6 34.8 - - + -
156M LEU* 2.9 39.8 + - + +
157M CYS* 3.9 10.5 - - - +
160M CYS* 1.3 75.7 - - - +
162M HIS* 1.3 57.4 + - - +
164M THR* 3.2 6.6 + - - -
165M LEU* 2.8 36.9 + - + +
283M LEU* 3.6 23.6 - - + -
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Residues in contact with HIS 162 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157M CYS 3.0 19.7 + - - +
158M ILE* 5.0 2.5 - - - -
161M ILE* 1.3 74.7 - - - +
163M PRO* 1.3 71.8 - - + +
165M LEU* 3.2 10.5 + - - +
166M VAL* 3.1 38.3 + - + +
171M GLU* 2.8 33.7 + - + -
187M PHE* 3.5 28.2 - + - -
191M TYR* 3.3 18.6 + + - -
282M ILE* 3.7 21.4 + - + +
283M LEU* 5.3 1.0 - - - +
285M THR 3.2 28.1 + - - -
287M THR* 5.0 2.2 + - - -
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Residues in contact with PRO 163 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102M MET* 4.2 2.2 - - - -
157M CYS 3.8 2.5 - - - +
158M ILE 4.1 5.4 - - - +
159M GLY 3.6 19.3 - - - +
160M CYS* 3.4 17.9 - - - +
161M ILE 3.8 0.2 - - - +
162M HIS* 1.3 98.4 - - + +
164M THR* 1.3 55.2 + - - +
166M VAL* 3.6 4.6 - - + +
167M GLY 2.8 24.4 + - - -
168M SER 2.8 32.6 + - - +
169M TRP* 4.1 18.4 - - + -
171M GLU* 4.3 3.8 - - + -
172M GLY 4.1 17.7 - - - +
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Residues in contact with THR 164 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102M MET* 3.5 30.8 - - + +
160M CYS* 2.7 23.8 + - - +
161M ILE* 3.2 7.4 + - - -
163M PRO* 1.3 73.8 - - - +
165M LEU* 1.3 66.2 + - + +
167M GLY* 3.2 12.1 + - - -
169M TRP* 4.3 6.2 - - - -
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Residues in contact with LEU 165 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216C ARG* 3.7 19.6 + - - -
710H UNL 4.2 31.5 - - + +
161M ILE* 2.8 29.1 + - + +
162M HIS* 3.2 7.1 + - - +
164M THR* 1.3 76.3 - - + +
166M VAL* 1.3 59.2 + - - +
167M GLY 3.7 0.2 + - - -
283M LEU* 3.7 38.1 - - + +
287M THR* 3.7 26.7 - - + +
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Residues in contact with VAL 166 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216C ARG* 3.4 13.6 - - - +
217C GLY 2.9 21.8 + - - -
220C ARG* 3.2 36.5 - - - +
162M HIS* 3.1 46.7 + - + +
163M PRO 3.6 4.5 - - - +
165M LEU* 1.3 76.2 - - - +
167M GLY* 1.3 57.7 + - - +
168M SER 4.1 2.0 - - - +
171M GLU* 4.1 14.1 - - + -
286M GLY* 3.7 31.0 - - - +
287M THR* 4.0 3.1 - - - +
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Residues in contact with GLY 167 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217C GLY* 3.2 15.9 - - - -
101M GLY* 3.1 24.3 - - - -
102M MET* 3.5 18.5 + - - +
163M PRO 2.8 10.3 + - - -
164M THR 3.2 11.9 + - - -
166M VAL* 1.3 77.0 - - - +
168M SER* 1.3 56.7 + - - -
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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