Contacts of the helix formed by residues 81 - 91 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79H ALA 3.2 2.0 + - - -
80H LYS* 1.3 80.8 - - - +
82H ALA* 1.3 58.9 + - - +
83H ARG* 3.2 3.4 - - - +
84H GLU* 3.7 27.1 - - + +
85H ASP* 2.8 46.9 + - - +
132H HIS* 5.1 0.9 - - - -
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Residues in contact with ALA 82 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76H ILE* 3.7 5.3 - - + +
77H ARG* 3.3 35.0 - - + +
79H ALA* 3.3 13.8 + - + +
80H LYS 3.1 5.7 + - - -
81H ASP* 1.3 75.7 - - - +
83H ARG* 1.3 57.3 + - - +
85H ASP* 4.0 0.5 - - - +
86H PHE* 2.8 32.9 + - - +
132H HIS* 4.6 7.4 - - - -
133H GLY* 3.9 25.7 - - - -
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Residues in contact with ARG 83 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B LEU* 3.9 21.0 - - - +
129B LEU* 3.6 29.2 - - - +
136B ASP* 5.4 2.6 + - - -
143G LEU* 5.8 1.0 - - - +
76H ILE* 4.0 33.3 - - + +
77H ARG 5.4 0.9 - - - +
79H ALA 4.5 3.7 + - - +
81H ASP* 3.2 1.3 - - - +
82H ALA* 1.3 75.5 - - + +
84H GLU* 1.3 68.5 + - + +
86H PHE* 3.4 1.6 + - - +
87H ALA* 2.9 32.3 + - - +
101H ALA* 4.2 11.1 - - - +
107H ASP* 4.5 15.0 + - - +
108H TYR* 3.1 41.7 + - - +
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Residues in contact with GLU 84 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144G LYS* 5.3 6.8 + - - -
81H ASP* 3.4 33.1 + - + +
83H ARG* 1.3 84.2 - - + +
85H ASP* 1.3 62.3 + - - +
87H ALA* 3.5 6.4 - - - +
88H ALA* 2.9 30.0 + - - +
91H ARG* 5.2 0.9 + - - -
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Residues in contact with ASP 85 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81H ASP* 2.8 35.7 + - - +
82H ALA 4.0 0.7 - - - +
84H GLU* 1.3 73.7 - - - +
86H PHE* 1.3 63.3 + - - +
88H ALA* 3.4 7.1 + - - +
89H SER* 3.0 27.7 + - - -
131H HIS* 3.8 4.3 - - + +
132H HIS* 3.0 39.3 + - + +
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Residues in contact with PHE 86 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74H VAL* 3.8 14.8 - - + -
76H ILE* 3.6 20.4 - - + -
82H ALA 2.8 23.6 + - - +
83H ARG 3.9 1.3 - - - +
85H ASP* 1.3 71.1 - - - +
87H ALA* 1.3 58.5 + - - +
89H SER* 3.2 2.9 + - - -
90H VAL* 2.9 57.1 + - + +
93H TRP* 4.1 9.0 - + - -
99H CYS* 4.1 7.4 - - - -
108H TYR* 3.9 37.5 - + + -
110H LEU* 3.8 18.2 - - + -
128H LEU* 3.9 13.2 - - + -
131H HIS* 3.6 14.5 - - + +
134H VAL* 3.6 28.9 - - + -
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Residues in contact with ALA 87 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146G ILE* 3.6 33.9 - - + +
83H ARG 2.9 19.1 + - - +
84H GLU* 3.5 7.9 - - - +
86H PHE* 1.3 79.0 - - - +
88H ALA* 1.3 62.2 + - - +
90H VAL* 3.4 4.1 + - - +
91H ARG* 3.2 44.5 + - - +
108H TYR* 5.7 1.6 - - + +
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Residues in contact with ALA 88 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84H GLU 2.9 16.8 + - - +
85H ASP* 3.8 6.7 - - - +
86H PHE 3.3 0.2 - - - -
87H ALA* 1.3 77.1 - - - +
89H SER* 1.3 62.6 + - - +
91H ARG* 3.7 22.0 + - - +
92H LYS* 3.7 18.2 - - - +
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Residues in contact with SER 89 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85H ASP 3.0 8.8 + - - -
86H PHE 3.6 2.7 - - - -
88H ALA* 1.3 74.4 - - - +
90H VAL* 1.3 59.4 + - - +
92H LYS* 2.9 21.6 + - - +
93H TRP* 3.4 35.0 + - - +
131H HIS* 2.8 39.3 + - - -
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Residues in contact with VAL 90 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146G ILE* 4.7 1.3 - - + -
147G LYS* 3.0 28.3 + - + -
86H PHE* 2.9 59.6 + - + +
87H ALA* 3.4 7.4 + - - +
89H SER* 1.3 74.3 - - - +
91H ARG* 1.3 59.2 + - - +
92H LYS 3.1 1.2 + - - -
93H TRP* 3.1 23.8 + - + +
96H VAL* 3.8 20.0 - - + -
99H CYS* 3.7 30.3 - - + -
110H LEU* 4.4 1.8 - - + -
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Residues in contact with ARG 91 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144G LYS* 5.2 6.9 - - - +
145G GLU 4.9 2.2 + - - -
146G ILE* 3.0 46.6 + - + +
147G LYS* 3.8 25.3 + - + -
84H GLU 5.2 0.4 + - - -
87H ALA* 3.2 36.9 + - - +
88H ALA* 3.7 16.0 - - - +
90H VAL* 1.3 75.9 - - - +
92H LYS* 1.3 61.1 + - + +
93H TRP 3.5 0.4 - - - -
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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