Contacts of the helix formed by residues 72 - 84 (chain B) in PDB entry 1OE5
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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68B PRO* 2.7 23.3 + - + +
71B TYR* 1.3 88.8 - - + +
73B TRP* 1.3 65.7 + - - +
74B ALA 3.2 3.4 + - - -
75B PRO* 3.3 9.1 - - - +
76B HIS* 3.1 22.2 + - - +
104B GLN 4.6 1.1 - - - +
105B THR 4.1 0.4 - - - -
106B GLY* 3.7 25.7 - - - +
124B PRO 4.7 0.4 - - - -
125B VAL* 4.1 17.0 - - + -
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Residues in contact with TRP 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B LEU* 3.4 37.7 - - + -
46B GLU* 4.7 8.3 - - + -
47B LEU* 3.7 46.2 - - + -
50B ASN* 4.8 2.9 - - - -
68B PRO 3.4 1.0 + - - -
69B LEU* 3.1 44.2 - - + +
70B VAL* 3.3 12.1 + - - +
71B TYR 3.4 0.8 - - - -
72B ALA* 1.3 78.6 - - - +
74B ALA* 1.3 57.2 + - + +
76B HIS* 3.2 22.1 + + - +
77B GLU* 2.6 61.5 + - + +
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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
----------------------------------------------------------
72B ALA 3.3 0.2 - - - -
73B TRP* 1.3 82.5 - - + +
75B PRO* 1.4 60.2 - - + +
77B GLU* 3.2 5.5 + - - +
78B ASN* 2.7 36.9 + - - +
123B GLY* 4.5 2.0 - - - -
124B PRO* 3.9 31.3 + - + +
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Residues in contact with PRO 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B ALA 3.3 14.6 - - - +
74B ALA* 1.4 88.5 - - + +
76B HIS* 1.3 50.4 + - - -
78B ASN* 4.0 1.3 - - + -
79B TYR* 2.7 36.2 + - - +
105B THR 3.4 22.9 - - - +
107B VAL* 4.6 1.1 - - - -
121B ILE* 3.5 13.0 - - + +
122B GLU 3.9 20.9 - - - +
123B GLY* 3.8 5.6 - - - +
124B PRO 3.4 18.2 - - - +
125B VAL* 3.8 20.6 - - + -
140B PHE* 4.0 15.0 - - + -
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Residues in contact with HIS 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B PHE* 5.0 2.5 - + - -
43B LEU* 4.0 5.6 - - + -
46B GLU* 2.5 36.8 + - - -
69B LEU* 3.3 30.1 - - + +
72B ALA 3.1 14.9 + - - +
73B TRP* 3.4 25.1 - + - +
75B PRO* 1.3 76.9 - - - +
77B GLU* 1.3 64.9 + - - +
79B TYR* 2.9 27.8 + + - +
80B VAL* 2.9 28.2 + - + +
102B MET* 4.2 7.1 - - + +
106B GLY 2.8 29.0 + - - +
108B PRO* 5.0 4.0 - - + -
173B HIS* 5.9 1.6 - - - -
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Residues in contact with GLU 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B LEU* 3.8 20.2 - - + +
73B TRP* 2.6 51.0 + - + +
74B ALA* 3.8 4.8 - - - +
76B HIS* 1.3 74.1 - - - +
78B ASN* 1.4 64.1 + - - +
80B VAL* 3.5 0.7 + - - +
81B GLN* 2.9 53.5 + - + +
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Residues in contact with ASN 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B ALA 2.7 21.2 + - - +
75B PRO* 3.5 8.7 - - + +
76B HIS 3.1 0.2 - - - -
77B GLU* 1.4 75.0 - - + +
79B TYR* 1.3 61.3 + - - +
81B GLN* 4.0 4.4 - - - +
82B THR* 2.8 36.3 + - - -
120B GLN 5.0 1.2 - - - +
121B ILE* 3.7 11.6 - - + +
122B GLU* 3.2 31.4 + - - +
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Residues in contact with TYR 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B PHE* 5.8 0.4 - + - -
75B PRO 2.7 16.9 + - - +
76B HIS* 2.9 14.6 + + - +
78B ASN* 1.3 74.7 - - - +
80B VAL* 1.3 77.9 + - + +
83B TYR* 2.9 41.1 + + - +
107B VAL* 4.0 30.1 - - + -
108B PRO* 3.5 26.0 - - + +
119B LEU* 4.7 6.7 - - + -
121B ILE* 3.8 14.6 - - + +
153B TRP* 4.9 2.2 - + - -
167B PHE* 3.7 25.7 - + - -
171B PHE* 3.6 24.3 - + - -
172B VAL* 2.7 40.9 + - - +
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Residues in contact with VAL 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B ALA* 3.7 26.6 - - + +
42B PHE* 3.9 24.9 - - + -
43B LEU* 4.0 16.2 - - + -
76B HIS* 2.9 37.3 + - + +
77B GLU 4.1 0.2 - - - +
79B TYR* 1.3 88.9 - - + +
81B GLN* 1.3 54.9 + - - +
84B CYS* 2.6 52.6 + - + +
171B PHE* 4.1 8.5 - - + -
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Residues in contact with GLN 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B ALA* 3.7 19.7 - - - +
40B ASP* 4.9 10.1 + - - +
43B LEU* 3.6 14.3 - - + +
77B GLU* 2.9 44.9 + - + +
78B ASN* 4.0 5.6 - - - +
80B VAL* 1.3 72.7 - - - +
82B THR* 1.3 66.7 + - - +
85B LYS* 3.4 26.0 + - - +
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Residues in contact with THR 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B ASN* 2.8 38.9 + - - -
81B GLN* 1.3 78.7 - - - +
83B TYR* 1.3 98.7 + - + +
84B CYS 3.7 0.2 - - - -
85B LYS* 3.9 23.8 + - - +
121B ILE* 3.8 5.4 - - + +
164B GLU* 5.7 2.2 - - - +
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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 TYR* 2.9 28.6 + + + +
80B VAL 3.6 0.2 - - - -
82B THR* 1.3 103.8 - - + +
84B CYS* 1.3 59.4 + - - +
85B LYS* 3.6 2.9 - - - -
88B LYS* 3.0 22.3 + - - -
119B LEU* 2.6 38.8 + - + -
120B GLN* 5.1 0.3 - - - +
121B ILE* 4.0 11.9 - - + -
163B PRO* 3.5 38.0 - - + +
164B GLU* 4.4 15.4 + - + -
167B PHE* 3.1 48.2 - + + +
171B PHE* 3.7 8.0 - - + -
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Residues in contact with CYS 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B PRO* 3.6 14.2 - - - +
39B ALA* 3.0 33.0 + - - +
42B PHE* 4.7 2.0 - - - -
80B VAL* 2.6 32.8 + - + +
82B THR 3.7 0.2 - - - -
83B TYR* 1.3 75.1 - - - +
85B LYS* 1.3 60.0 + - - +
86B SER 3.3 3.4 - - - -
88B LYS* 4.0 9.6 - - - +
171B PHE* 3.6 22.0 - - + -
216B LEU* 3.6 31.4 - - - -
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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