Contacts of the helix formed by residues 84 - 94 (chain A) in PDB entry 2PO5
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 84 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A PRO* 3.7 17.3 - - + -
80A GLU* 3.6 11.8 + - - +
81A THR* 2.8 38.7 + - - +
83A GLY* 1.3 75.3 - - - +
85A VAL* 1.3 63.7 + - - +
86A HIS 3.4 0.7 - - - -
87A ASP* 3.5 9.5 + - - +
88A PHE* 3.1 21.7 + - - +
91A ARG* 5.6 0.2 + - - -
166A VAL* 4.9 5.4 - - + +
167A HIS* 5.9 2.6 - - - -
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Residues in contact with VAL 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A PRO* 3.8 24.0 - - + +
82A LEU* 3.2 26.8 + - - +
84A ASP* 1.3 77.4 - - - +
86A HIS* 1.3 64.6 + - - +
88A PHE* 3.2 5.0 + - + +
89A LEU* 3.0 41.3 + - + +
116A THR* 3.9 23.8 - - - +
119A ILE* 3.9 11.4 - - + -
120A GLN* 3.7 20.2 - - + -
123A TYR* 4.3 9.9 - - + -
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Residues in contact with HIS 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A LEU 4.7 0.2 + - - -
83A GLY 4.3 7.4 + - - +
84A ASP 3.4 0.8 - - - -
85A VAL* 1.3 79.4 - - - +
87A ASP* 1.3 74.2 + - - +
89A LEU* 3.4 3.0 + - - +
90A LEU* 3.0 42.1 + - + +
109A PRO* 4.3 10.3 + - + +
112A ALA* 3.9 3.0 - - + +
113A LYS* 4.1 25.5 + - + +
116A THR* 3.5 33.0 - - + +
120A GLN* 5.5 0.4 - - - +
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Residues in contact with ASP 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A GLY 5.2 2.9 + - - +
84A ASP* 3.5 9.5 + - - +
85A VAL 3.4 0.4 - - - -
86A HIS* 1.3 90.3 + - - +
88A PHE* 1.3 66.6 + - - +
90A LEU* 3.6 14.2 - - + +
91A ARG* 2.9 56.5 + - - +
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Residues in contact with PHE 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A MET* 4.4 11.9 - - + -
77A GLY 3.9 21.8 - - - -
78A GLY* 4.4 1.6 - - - -
79A PRO* 3.8 25.1 - - + -
84A ASP 3.1 15.4 + - - +
85A VAL* 3.3 11.9 - - - +
87A ASP* 1.3 79.3 - - - +
89A LEU* 1.3 76.6 + - + +
91A ARG* 3.5 3.2 + - - +
92A LEU* 3.1 39.0 + - + +
119A ILE* 5.3 4.9 - - + -
123A TYR* 4.4 10.5 - + - -
165A TYR* 3.6 28.0 - - + +
166A VAL* 3.6 23.1 - - + -
341A HIS* 5.2 3.1 - + - -
501A CHD 4.1 22.0 - - + -
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Residues in contact with LEU 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A VAL* 3.0 26.8 + - + +
86A HIS 3.7 4.3 - - - +
88A PHE* 1.3 98.2 - - + +
90A LEU* 1.3 63.2 + - - +
92A LEU* 3.1 6.1 + - + +
93A PHE* 2.9 43.9 + - + -
112A ALA* 3.7 18.4 - - + +
115A LEU* 3.9 13.0 - - + -
116A THR* 3.7 35.0 - - - +
119A ILE* 4.0 11.0 - - + -
501A CHD 4.3 21.8 - - + -
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Residues in contact with LEU 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A HIS* 3.0 28.4 + - + +
87A ASP* 3.2 19.3 + - - +
89A LEU* 1.3 75.5 - - - +
91A ARG* 1.3 65.4 + - + +
92A LEU 3.2 0.2 + - - -
93A PHE* 3.2 3.3 + - - +
94A LEU* 3.1 45.1 + - + +
108A ALA 3.9 2.0 - - - -
109A PRO* 3.3 47.8 - - + -
112A ALA* 3.6 9.1 - - + +
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Residues in contact with ARG 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A ASP* 2.9 50.8 + - - +
88A PHE 3.9 1.5 - - - +
90A LEU* 1.3 77.1 - - + +
92A LEU* 1.3 61.1 + - - +
94A LEU* 3.4 20.2 + - + +
95A ASP* 3.4 9.9 + - - +
164A ARG 4.7 1.1 - - - +
165A TYR* 3.1 46.6 + - + +
166A VAL* 4.1 6.8 - - - +
167A HIS* 3.3 32.8 + - - +
169A LEU* 3.7 34.0 - - - +
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Residues in contact with LEU 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A MET* 4.2 7.2 - - + -
88A PHE* 3.1 30.9 + - + +
89A LEU* 3.1 11.6 + - + +
91A ARG* 1.3 78.4 - - - +
93A PHE* 1.3 69.5 + - + +
94A LEU 3.2 1.1 + - - -
95A ASP* 3.5 15.9 + - - +
98A LEU* 3.5 26.8 - - + +
99A MET* 3.9 10.5 - - + +
165A TYR* 3.6 15.0 - - + -
501A CHD 3.5 59.0 - - + -
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Residues in contact with PHE 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A LEU* 2.9 42.7 + - + +
90A LEU 3.2 1.7 + - - +
92A LEU* 1.3 78.4 - - + +
94A LEU* 1.3 58.6 + - - +
95A ASP 3.4 0.7 - - - -
99A MET* 3.4 37.0 - - + +
101A LEU* 4.1 10.4 - - + +
104A GLN* 2.9 26.4 + - - +
108A ALA* 3.8 24.3 - - + +
111A ILE* 4.0 17.3 - - + -
112A ALA* 4.4 8.3 - - - -
115A LEU* 3.4 26.7 - - + -
501A CHD 3.4 28.9 - - + -
502A CHD 3.9 23.8 - - + -
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Residues in contact with LEU 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A LEU* 3.1 43.5 + - + +
91A ARG* 3.7 11.0 - - + +
92A LEU 3.2 0.8 - - - -
93A PHE* 1.3 78.1 - - - +
95A ASP* 1.3 59.7 + - - +
96A ARG* 3.0 21.8 + - - +
104A GLN* 3.6 6.5 - - + +
105A ASN* 3.9 30.3 - - - +
108A ALA* 3.4 23.6 - - + -
109A PRO* 4.8 2.0 - - + -
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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