Contacts of the helix formed by residues 85 - 90 (chain B) in PDB entry 2COJ
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 85 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81B LEU* 3.8 10.8 - - - +
82B HIS* 2.7 34.5 + - - +
83B PRO 3.4 1.2 - - - -
84B GLY* 1.3 76.1 - - - +
86B SER* 1.3 59.7 + - - +
87B ALA* 4.4 2.7 - - - -
88B LEU* 2.8 35.2 + - - +
89B HIS* 3.4 7.4 - - - -
167B ILE* 6.2 0.2 - - - -
168B GLY 3.8 3.8 - - - -
169B THR* 3.6 31.3 + - - -
170B GLU 3.2 8.0 + - - -
171B PRO* 4.6 0.2 - - - +
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Residues in contact with SER 86 (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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84B GLY 3.1 5.9 + - - -
85B SER* 1.3 70.7 - - - +
87B ALA* 1.3 57.7 + - - +
89B HIS* 3.8 2.9 - - - +
90B TYR* 2.8 45.9 + - - -
91B ALA 3.4 4.2 + - - -
92B VAL* 3.3 30.9 + - - +
168B GLY* 3.5 15.4 + - - -
170B GLU* 3.2 24.4 + - - +
172B SER 5.3 2.0 - - - -
174B GLY 5.9 1.3 - - - -
176B LYS 5.6 3.4 - - - -
178B PRO* 4.4 3.0 - - - +
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Residues in contact with ALA 87 (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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87A ALA 3.7 1.0 - - - +
88A LEU* 4.3 10.1 - - + -
93A GLU* 2.6 27.2 - - - +
81B LEU* 6.4 0.2 - - + -
85B SER* 2.9 2.8 + - - +
86B SER* 1.3 78.3 + - - +
88B LEU* 1.3 52.8 + - + +
91B ALA* 3.6 2.1 - - - -
92B VAL 3.6 23.6 - - - +
93B GLU* 3.3 18.9 - - - +
167B ILE* 3.7 20.9 - - + -
168B GLY 3.0 20.1 + - - +
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Residues in contact with LEU 88 (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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79A LEU* 3.8 29.4 - - + -
81A LEU* 4.3 16.8 - - + -
87A ALA* 4.3 11.9 - - + -
88A LEU* 3.7 28.3 - - + -
93A GLU* 2.9 32.4 - - - +
94A LEU 5.0 1.2 + - - +
165A THR* 4.1 7.3 - - + +
167A ILE* 3.8 24.8 - - + +
184A PHE* 4.8 0.9 - - + -
81B LEU* 5.0 5.6 - - + -
82B HIS 4.5 9.2 - - - +
83B PRO 4.2 10.3 - - - +
85B SER* 2.8 18.6 + - - +
87B ALA* 1.3 74.5 - - - +
89B HIS* 1.3 67.5 + - + +
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Residues in contact with HIS 89 (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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93A GLU* 3.1 6.1 - - - +
95A PHE* 3.3 21.3 - - + +
163A ARG* 2.9 43.2 + - + +
165A THR* 3.0 34.2 + - + +
184A PHE* 4.1 4.5 - + - -
186A LEU* 4.4 1.3 - - + -
224A GLY* 3.2 18.4 - - - -
83B PRO 2.8 24.5 + - - -
84B GLY* 3.5 17.3 - - - -
85B SER 3.4 16.4 - - - +
86B SER* 3.3 2.3 + - - +
88B LEU* 1.3 81.1 - - + +
90B TYR* 1.3 74.2 + + + +
173B LEU* 4.3 7.0 - - + -
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Residues in contact with TYR 90 (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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95A PHE* 3.9 14.8 - + - -
163A ARG* 3.0 28.1 + - - -
224A GLY 3.2 8.3 - - - -
227A TYR* 3.8 24.0 - + + +
228A GLY* 2.6 34.3 + - - +
231A LEU* 5.4 4.0 - - + -
420A GBN 3.4 22.4 - - + +
84B GLY 5.9 0.4 - - - -
86B SER* 2.8 28.6 + - - +
89B HIS* 1.3 88.7 - - + +
91B ALA* 1.3 60.6 + - - +
92B VAL* 3.1 9.8 + - + -
172B SER 4.9 2.7 - - - -
173B LEU* 2.4 38.0 + - - -
174B GLY 4.1 4.5 - - - -
175B VAL* 3.7 22.9 - - + -
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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