Contacts of the helix formed by residues 75 - 89 (chain B) in PDB entry 1P7D
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 THR 75 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B MET* 1.3 76.4 - - - +
76B LEU* 1.3 66.1 + - - +
78B SER* 4.0 16.2 - - - -
79B TRP* 2.9 21.2 + - - +
113B ASP* 2.7 35.7 - - - -
114B ALA 3.6 3.1 - - - -
115B PRO* 4.2 1.8 - - - -
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Residues in contact with LEU 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B MET 3.8 0.8 + - - -
75B THR* 1.3 69.6 - - - +
77B HIS* 1.3 59.7 + - + +
79B TRP* 2.9 14.1 + - + +
80B LEU* 2.8 54.7 + - + +
107B ILE* 4.5 10.3 - - + +
111B LEU* 3.5 42.0 - - + +
112B PRO* 3.6 15.5 - - + +
113B ASP 3.3 2.0 + - - -
114B ALA 2.9 18.1 + - - +
115B PRO 4.8 2.9 + - - +
151B PHE* 4.6 21.3 - - + -
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Residues in contact with HIS 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B THR 3.4 0.4 - - - -
76B LEU* 1.3 87.2 - - + +
78B SER* 1.3 63.2 + - - +
80B LEU* 3.3 13.1 + - + +
81B ASP* 3.1 18.9 + - - +
108B ARG* 3.5 49.2 + - + +
111B LEU 2.6 28.0 + - - -
112B PRO* 2.7 23.1 + - + -
113B ASP* 3.6 24.3 + - + +
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Residues in contact with SER 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B MET* 5.3 2.7 - - - -
75B THR* 3.3 25.2 + - - -
76B LEU 3.2 0.6 - - - -
77B HIS* 1.3 78.8 - - - +
79B TRP* 1.3 61.3 + - - +
81B ASP* 3.2 23.9 + - - +
82B ARG* 3.5 5.9 + - - +
113B ASP* 4.1 1.8 + - - -
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Residues in contact with TRP 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B MET* 4.1 15.8 - - + +
75B THR 2.9 12.5 + - - +
76B LEU* 2.9 16.7 + - + +
78B SER* 1.3 73.4 - - - +
80B LEU* 1.3 73.2 + - + +
81B ASP 3.0 2.0 - - - -
82B ARG* 3.0 36.9 + - + +
83B TYR* 2.8 38.8 + + + +
86B ILE* 4.3 6.5 - - + -
150B ALA* 3.3 22.4 + - + +
151B PHE* 6.2 2.9 - + - -
153B GLU* 3.6 18.8 - - + -
154B ALA* 3.2 40.8 - - + +
157B GLU* 4.3 8.3 - - + -
159B HIS* 3.8 32.3 - + + -
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Residues in contact with LEU 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B LEU* 2.8 39.3 + - + +
77B HIS* 3.6 9.0 - - - +
78B SER 3.3 0.4 - - - -
79B TRP* 1.3 85.4 - - + +
81B ASP* 1.3 58.3 + - - +
83B TYR* 3.2 8.9 + - + +
84B GLU* 2.9 32.2 + - - +
104B ILE* 4.0 22.9 - - + +
107B ILE* 4.1 24.9 - - + -
108B ARG* 3.7 42.2 - - + +
150B ALA* 4.7 15.3 - - + -
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Residues in contact with ASP 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B HIS 3.1 15.4 + - - +
78B SER* 3.2 13.7 + - - +
79B TRP 3.0 0.4 - - - -
80B LEU* 1.3 76.3 - - - +
82B ARG* 1.3 66.6 + - - +
84B GLU* 3.1 28.0 - - - +
85B LYS* 3.4 8.8 + - - +
108B ARG* 3.0 18.9 + - - -
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Residues in contact with ARG 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B SER 3.5 4.6 + - - +
79B TRP* 3.0 45.0 + - + +
81B ASP* 1.3 78.2 - - - +
83B TYR* 1.3 63.1 + - - +
85B LYS* 2.9 28.1 + - - +
86B ILE* 3.0 40.0 + - - +
157B GLU* 6.0 3.6 - - - +
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Residues in contact with TYR 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B TRP* 2.8 22.1 + + - +
80B LEU* 3.4 12.3 - - + +
82B ARG* 1.3 78.3 - - - +
84B GLU* 1.3 56.6 + - - +
86B ILE* 3.1 16.6 - - + +
87B LEU* 2.9 58.7 + - + +
90B ARG* 5.0 0.2 - - - -
104B ILE* 3.4 25.6 - - + -
146B THR* 4.0 14.9 + - + +
149B ASP* 2.5 31.5 + - - +
150B ALA* 3.4 38.8 + - + -
153B GLU* 3.7 30.3 - - + -
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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
----------------------------------------------------------
80B LEU 2.9 11.6 + - - +
81B ASP* 3.1 35.7 - - - +
83B TYR* 1.3 74.9 - - - +
85B LYS* 1.3 60.5 + - - +
87B LEU* 3.2 11.6 + - - +
88B ALA* 2.8 29.8 + - - +
97B LEU* 5.2 2.3 - - - +
101B MET* 3.2 41.8 - - - +
104B ILE* 3.8 16.0 - - + +
108B ARG* 3.6 15.6 + - - -
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Residues in contact with LYS 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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81B ASP 3.4 11.0 + - - +
82B ARG* 2.9 22.2 + - - +
84B GLU* 1.3 77.8 - - - +
86B ILE* 1.3 66.1 - - - +
88B ALA* 3.1 21.1 - - - +
89B SER* 3.6 6.6 + - - -
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Residues in contact with ILE 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B TRP* 4.3 14.1 - - + -
82B ARG* 3.0 52.0 + - - +
83B TYR* 3.1 21.8 - - + +
85B LYS* 1.3 75.7 - - - +
87B LEU* 1.3 68.6 + - + +
89B SER* 2.8 28.3 + - - -
90B ARG* 4.2 10.8 + - + +
153B GLU* 3.7 35.9 - - + +
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Residues in contact with LEU 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B TYR* 2.9 55.1 + - + +
84B GLU* 3.5 8.3 - - - +
86B ILE* 1.3 80.5 - - + +
88B ALA* 1.3 55.5 + - - +
89B SER 2.7 23.2 + - - +
90B ARG* 3.7 41.4 - - - +
92B ILE* 4.0 8.6 - - + +
97B LEU* 4.8 12.8 - - + +
100B TYR* 4.0 32.1 - - + -
101B MET* 5.5 0.7 - - - +
104B ILE* 3.5 20.2 - - + -
146B THR* 5.4 1.3 - - + -
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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 2.8 16.3 + - - +
85B LYS* 3.1 19.5 - - - +
87B LEU* 1.3 71.3 - - - +
89B SER* 1.3 61.7 + - - +
92B ILE* 5.7 1.3 - - - +
97B LEU* 4.5 24.7 - - + +
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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
----------------------------------------------------------
85B LYS 3.6 7.1 + - - -
86B ILE* 2.8 16.1 + - - -
87B LEU 2.7 6.5 + - - +
88B ALA* 1.3 84.2 - - - +
90B ARG* 1.3 58.7 + - - +
91B GLY* 2.4 22.7 + - - -
92B ILE* 3.5 6.1 + - - +
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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
------------------------------------------------------------
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