Contacts of the helix formed by residues 72 - 79 (chain B) in PDB entry 3ORH
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 ALA 72 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B PHE* 3.0 51.2 + - + -
70B GLY 3.4 1.4 + - - -
71B MET* 1.4 78.9 - - - +
73B ILE* 1.3 56.8 + - - +
74B ALA 3.6 1.6 - - - -
75B ALA* 3.9 5.2 - - - -
76B SER* 2.8 36.5 + - - +
102B TRP* 4.1 17.5 - - + +
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Residues in contact with ILE 73 (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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42B MET* 3.8 18.2 - - + -
44B ARG* 3.9 35.9 - - + +
47B THR* 3.7 37.0 - - + +
50B MET* 3.7 18.4 - - + -
51B HIS* 4.2 9.3 + - - +
71B MET* 3.2 30.0 - - + +
72B ALA* 1.3 76.5 - - - +
74B ALA* 1.3 66.1 + - - +
76B SER* 3.5 4.3 + - - -
77B LYS* 3.4 18.5 + - - +
4001B SAH 3.3 9.7 + - - +
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Residues in contact with ALA 74 (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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50B MET* 3.9 26.2 - - + +
53B LEU* 5.5 0.2 - - + -
54B ALA* 3.4 4.0 - - - +
66B GLU* 3.6 15.7 - - - +
73B ILE* 1.3 72.9 - - - +
75B ALA* 1.4 58.4 + - - +
77B LYS 3.2 2.4 + - - -
78B VAL* 2.9 30.9 + - - +
133B LEU* 3.8 22.2 - - + -
4001B SAH 2.8 25.5 + - - +
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Residues in contact with ALA 75 (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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66B GLU* 3.2 27.1 + - - +
69B PHE* 3.8 22.2 - - + -
72B ALA* 3.6 7.3 + - - +
73B ILE 3.3 0.6 - - - -
74B ALA* 1.4 79.4 - - - +
76B SER* 1.3 61.3 + - - +
78B VAL* 3.3 1.1 + - - -
79B GLN* 3.2 27.2 + - - +
86B HIS* 3.5 7.3 - - + -
88B ILE* 4.4 0.9 - - + -
102B TRP* 3.8 22.9 - - + -
4001B SAH 5.4 0.2 - - - -
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Residues in contact with SER 76 (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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72B ALA* 2.8 23.9 + - - +
73B ILE* 3.9 5.2 - - - -
75B ALA* 1.3 74.6 - - - +
77B LYS* 1.3 60.6 + - - +
79B GLN* 3.5 17.0 + - - +
80B GLU* 3.5 16.8 + - - +
102B TRP* 3.4 25.0 + - - -
106B GLN* 5.3 1.3 - - - -
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Residues in contact with LYS 77 (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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51B HIS* 3.7 54.4 + - + +
54B ALA* 3.5 24.0 - - + -
55B ALA* 4.8 8.1 - - - +
58B SER* 5.0 1.2 + - - -
73B ILE 3.4 3.3 + - - +
74B ALA* 3.2 4.1 + - - +
76B SER* 1.3 77.2 - - - +
78B VAL* 1.4 64.5 + - - +
80B GLU* 3.1 45.6 + - - +
81B ALA* 3.9 3.8 + - - +
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Residues in contact with VAL 78 (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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54B ALA* 3.8 24.0 - - + +
57B ALA* 5.0 0.7 - - + -
58B SER* 4.4 12.8 - - - -
64B VAL* 4.0 20.0 - - + -
66B GLU* 4.1 11.7 - - - +
74B ALA 2.9 18.0 + - - +
75B ALA 3.3 7.6 + - - +
77B LYS* 1.4 73.9 - - - +
79B GLN* 1.3 57.0 + - - +
81B ALA* 3.1 28.2 + - - +
83B ILE* 3.8 21.0 - - + +
86B HIS* 3.6 26.0 - - + +
133B LEU* 4.4 8.3 - - + -
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Residues in contact with GLN 79 (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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75B ALA 3.2 16.9 + - - +
76B SER* 3.5 11.9 - - - +
77B LYS 3.2 0.2 - - - -
78B VAL* 1.3 75.4 - - - +
80B GLU* 1.4 58.4 + - - +
81B ALA 3.3 0.4 - - - -
83B ILE* 4.3 1.4 - - - +
86B HIS* 3.0 34.5 + - - +
102B TRP* 3.7 5.8 - - + -
106B GLN* 3.5 33.2 - - - +
107B THR* 3.5 8.1 + - - +
108B HIS* 2.9 77.5 + - - +
110B VAL* 3.6 6.5 - - - +
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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