Contacts of the helix formed by residues 158 - 167 (chain B) in PDB entry 2O5F
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 158 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38B ASN* 5.5 1.3 + - - +
111B THR 4.3 2.3 - - - +
112B LEU* 3.5 22.2 - - + +
113B SER* 2.6 50.3 + - - -
116B MET* 4.2 8.6 - - + +
156B LYS* 3.6 11.3 - - - +
157B GLY* 1.3 72.8 - - - +
159B LEU* 1.3 65.5 + - - +
160B ALA 3.4 0.7 - - - -
161B GLU* 3.3 6.8 + - - +
162B LEU* 2.9 35.2 + - + +
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Residues in contact with LEU 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B PHE* 4.2 6.5 - - + -
50B ILE* 5.0 0.2 - - + -
64B LEU* 3.7 41.1 - - + +
65B ASP* 3.8 22.7 - - - +
66B VAL* 3.9 15.5 - - + +
145B LEU* 4.0 22.2 - - + -
149B ILE* 4.1 6.7 - - + -
155B ALA* 4.1 8.3 - - + -
156B LYS* 3.3 21.7 + - + +
157B GLY 3.3 2.4 - - - -
158B ASP* 1.3 75.4 - - - +
160B ALA* 1.3 65.2 + - - +
162B LEU* 3.1 8.4 + - - +
163B VAL* 3.0 40.1 + - + +
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Residues in contact with ALA 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A PHE 4.4 0.7 - - - -
109A GLN 3.6 22.9 - - - +
110A THR* 5.3 0.9 - - - -
165A ARG* 5.6 0.7 - - - +
146B LEU* 3.7 16.4 - - + +
149B ILE* 3.9 32.6 - - + +
156B LYS 4.6 0.8 + - - -
157B GLY 4.5 5.7 + - - +
158B ASP 3.4 0.6 - - - -
159B LEU* 1.3 77.7 - - - +
161B GLU* 1.3 58.5 + - - +
163B VAL 3.4 0.2 + - - -
164B ARG* 2.9 31.8 + - - +
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Residues in contact with GLU 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A PHE* 3.1 26.4 + - - +
109A GLN* 3.9 10.5 + - + +
110B THR* 3.5 1.4 - - - -
111B THR* 2.8 56.9 + - - +
112B LEU* 3.8 18.2 - - + +
157B GLY 5.1 1.4 + - - +
158B ASP* 3.3 6.6 + - - +
160B ALA* 1.3 78.2 - - - +
162B LEU* 1.3 57.7 + - - +
164B ARG* 3.3 0.3 + - - +
165B ARG* 2.7 65.1 + - - +
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Residues in contact with LEU 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B ASN* 3.8 17.5 - - + +
40B PHE* 4.1 11.7 - - + -
66B VAL* 3.6 29.4 - - + -
105B PHE* 4.4 4.5 - - + -
112B LEU* 4.1 15.9 - - + +
116B MET* 3.7 25.4 - - - -
118B VAL* 3.8 20.2 - - + -
156B LYS* 6.5 0.9 - - - -
158B ASP* 2.9 31.5 + - + +
159B LEU* 3.1 5.1 + - - +
161B GLU* 1.3 77.8 - - - +
163B VAL* 1.3 58.3 + - - +
165B ARG* 3.4 2.0 + - - -
166B CYS* 2.9 37.2 + - - +
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Residues in contact with VAL 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B PHE* 3.7 22.9 - - + -
48B LEU* 4.8 2.7 - - + -
142B PRO* 3.6 43.3 - - + +
145B LEU* 3.8 24.7 - - + -
146B LEU* 4.0 13.9 - - + -
159B LEU* 3.0 17.4 + - + +
160B ALA* 4.0 3.1 - - - +
162B LEU* 1.3 75.7 - - - +
164B ARG* 1.3 58.3 + - - +
167B TYR* 2.9 45.0 + - + +
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Residues in contact with ARG 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A GLU* 5.8 2.6 - - - +
107A PRO* 2.7 21.9 + - - +
108A PHE* 3.5 25.8 - - + +
110A THR 2.9 16.3 + - - +
111A THR* 3.7 29.5 + - - +
112A LEU 2.9 28.9 + - - -
113A SER* 4.6 3.8 + - - +
146B LEU* 4.5 10.2 - - + +
160B ALA 2.9 19.2 + - - +
161B GLU 3.5 4.5 - - - +
163B VAL* 1.3 78.5 - - - +
165B ARG* 1.3 60.1 + - + +
167B TYR 4.5 2.2 - - - -
168B ARG* 3.5 33.2 + - - +
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Residues in contact with ARG 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A GLU* 2.8 46.1 + - - +
108A PHE* 3.5 32.5 - - + +
105B PHE* 3.9 35.7 - - + -
109B GLN 4.9 0.2 + - - -
110B THR* 3.7 20.1 - - - +
111B THR* 4.2 0.4 + - - +
112B LEU* 4.6 4.0 - - - -
161B GLU* 2.7 54.6 + - + +
162B LEU 4.2 0.7 - - - +
164B ARG* 1.3 81.2 - - + +
166B CYS* 1.3 61.8 + - - +
167B TYR 3.6 0.4 - - - -
168B ARG 5.6 1.3 - - - -
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Residues in contact with CYS 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B PHE* 4.7 2.5 - - + -
102B LEU* 3.8 29.6 - - + +
103B ALA* 4.4 7.2 - - - -
105B PHE* 3.8 28.7 - - - -
118B VAL* 4.1 25.6 - - - -
162B LEU* 2.9 22.1 + - - +
165B ARG* 1.3 77.2 - - - +
167B TYR* 1.3 76.6 + - + +
168B ARG 4.2 1.0 + - - -
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Residues in contact with TYR 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B PHE* 3.3 47.4 - + - +
42B ARG* 3.9 16.8 - - - -
48B LEU* 3.7 22.6 - - + +
102B LEU* 3.7 13.4 - - + +
120B GLU* 2.8 30.3 + - - +
142B PRO* 4.1 27.0 - - + +
146B LEU* 5.4 4.2 - - - +
163B VAL* 2.9 34.8 + - + +
164B ARG* 3.9 2.0 - - - +
166B CYS* 1.3 91.3 - - + +
168B ARG* 1.3 75.1 + - + +
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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