Contacts of the helix formed by residues 81 - 92 (chain B) in PDB entry 2P5V
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 81 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79B ALA 3.5 1.2 + - - -
80B LYS* 1.3 97.4 + - - +
82B ALA* 1.3 56.6 + - - +
83B ARG 3.3 3.6 - - - +
84B GLU* 3.9 14.1 - - + +
85B ASP* 2.8 53.3 + - - +
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Residues in contact with ALA 82 (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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76B ILE* 4.1 4.8 - - + +
77B ARG* 3.3 35.7 - - - +
79B ALA* 3.4 13.3 + - + +
80B LYS 3.1 4.4 + - - -
81B ASP* 1.3 76.1 - - - +
83B ARG* 1.3 59.7 + - + +
85B ASP* 3.9 4.5 - - - +
86B PHE* 2.9 31.4 + - - +
132B HIS* 5.2 2.0 - - - -
133B GLY* 4.0 25.7 - - - +
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Residues in contact with ARG 83 (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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143A LEU* 6.1 0.2 - - - +
76B ILE* 4.1 27.6 - - + +
77B ARG 5.7 0.2 - - - +
79B ALA 4.9 0.8 + - - +
81B ASP 3.3 0.6 - - - -
82B ALA* 1.3 78.7 - - + +
84B GLU* 1.3 70.6 + - + +
86B PHE* 3.4 3.2 + - - +
87B ALA* 2.9 29.1 + - - +
101B ALA* 4.1 9.1 - - - +
107B ASP* 4.2 23.4 + - - +
108B TYR* 3.1 42.3 + - - +
1015B CL 3.4 16.4 - - + +
125D LEU* 3.6 21.4 - - - +
129D LEU* 3.4 28.0 - - - +
136D ASP* 5.7 1.2 + - - -
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Residues in contact with GLU 84 (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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144A LYS* 3.8 22.6 + - - -
81B ASP* 3.4 16.9 + - + +
82B ALA 3.3 0.4 - - - -
83B ARG* 1.3 84.4 - - + +
85B ASP* 1.3 64.0 + - - +
87B ALA* 3.4 10.6 + - - +
88B ALA* 2.9 30.3 + - - +
91B ARG* 5.4 3.3 + - - -
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Residues in contact with ASP 85 (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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80B LYS 4.9 0.3 - - - +
81B ASP* 2.8 41.2 + - - +
82B ALA 3.9 2.0 - - - +
84B GLU* 1.3 78.6 - - - +
86B PHE* 1.3 61.2 + - - +
88B ALA* 3.5 6.6 + - - +
89B SER* 2.9 29.8 + - - -
131B HIS* 3.7 3.1 - - + -
132B HIS* 3.0 38.2 - - + +
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Residues in contact with PHE 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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74B VAL* 3.8 15.9 - - + -
76B ILE* 3.5 19.5 - - + -
82B ALA 2.9 19.0 + - - +
83B ARG 3.6 2.2 - - - +
85B ASP* 1.3 74.3 - - - +
87B ALA* 1.3 62.0 + - - +
89B SER* 3.3 1.4 + - - -
90B VAL* 2.9 54.6 + - + +
93B TRP* 4.0 6.3 - + - -
99B CYS* 4.2 5.4 - - - -
108B TYR* 4.0 36.8 - + + -
110B LEU* 4.1 14.6 - - + -
128B LEU* 3.9 11.2 - - + -
131B HIS* 3.6 16.3 - + + +
134B VAL* 3.4 33.2 - - + -
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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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144A LYS* 6.0 1.3 - - - +
146A ILE* 3.8 28.3 - - + -
83B ARG 2.9 17.5 + - - +
84B GLU* 3.7 14.8 - - - +
86B PHE* 1.3 78.7 - - + +
88B ALA* 1.3 62.7 + - - +
90B VAL* 3.5 2.1 + - - +
91B ARG* 3.1 49.4 + - - +
108B TYR* 5.7 0.7 - - + +
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Residues in contact with ALA 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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84B GLU 2.9 18.2 + - - +
85B ASP* 3.7 7.9 - - - +
86B PHE 3.3 0.4 - - - -
87B ALA* 1.3 76.2 - - - +
89B SER* 1.3 65.2 + - - +
91B ARG* 3.5 20.1 + - - +
92B LYS* 3.5 19.0 + - + +
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Residues in contact with SER 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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85B ASP 2.9 7.7 + - - -
86B PHE 3.7 2.7 - - - -
88B ALA* 1.3 75.5 - - - +
90B VAL* 1.3 61.5 + - - +
92B LYS* 2.9 25.5 + - - +
93B TRP* 3.2 30.0 + - - +
131B HIS* 2.7 40.3 + - - -
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Residues in contact with VAL 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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146A ILE* 4.2 4.5 - - + -
147A LYS* 2.8 36.7 + - + -
86B PHE* 2.9 53.9 + - + +
87B ALA 3.8 4.3 - - - +
88B ALA 3.5 0.2 - - - -
89B SER* 1.3 74.9 - - - +
91B ARG* 1.3 58.4 + - - +
93B TRP* 3.1 31.2 + - + +
96B VAL* 3.9 10.3 - - + +
99B CYS* 3.7 29.6 - - + -
110B LEU* 4.3 5.8 - - + -
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Residues in contact with ARG 91 (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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144A LYS* 5.2 10.7 - - - +
145A GLU 4.8 1.8 + - - -
146A ILE* 2.8 42.9 + - + +
147A LYS* 3.7 25.1 + - + -
84B GLU* 5.4 3.4 + - - -
87B ALA* 3.1 42.7 + - - +
88B ALA* 3.6 15.8 - - - +
89B SER 3.2 0.6 - - - -
90B VAL* 1.3 77.1 - - - +
92B LYS* 1.3 60.9 + - + +
93B TRP 3.5 0.2 - - - -
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Residues in contact with LYS 92 (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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88B ALA* 3.5 15.4 + - + +
89B SER* 2.9 13.4 + - - +
91B ARG* 1.3 81.4 - - + +
93B TRP* 1.3 63.4 + - + +
94B PRO* 3.3 13.4 - - - +
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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