Contacts of the helix formed by residues 72 - 84 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68A PRO* 2.8 25.4 + - + +
71A TYR* 1.4 80.8 - - + +
73A TRP* 1.3 62.5 + - - +
74A ALA 3.2 2.9 - - - +
75A PRO* 3.3 8.5 - - + +
76A HIS* 3.2 22.2 + - - +
104A GLN 4.4 1.6 - - - +
105A THR 4.2 0.9 - - - -
106A GLY* 3.8 23.2 - - - +
124A PRO 4.7 0.9 - - - -
125A VAL* 4.1 24.0 - - + -
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Residues in contact with TRP 73 (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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43A LEU* 3.6 40.4 - - + -
46A GLU* 4.5 11.4 - - + -
47A LEU* 3.7 45.2 - - + +
50A ASN* 4.6 0.9 - - - -
68A PRO 3.4 1.6 + - - -
69A LEU* 3.2 33.4 - - + +
70A VAL* 3.3 16.7 + - - +
71A TYR 3.6 1.0 - - - -
72A ALA* 1.3 77.3 - - - +
74A ALA* 1.3 61.6 + - - +
76A HIS* 3.2 23.0 + + - +
77A GLU* 2.7 54.3 + - + +
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Residues in contact with ALA 74 (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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73A TRP* 1.3 86.3 - - - +
75A PRO* 1.3 66.7 - - + +
77A GLU* 3.2 4.0 + - - +
78A ASN* 2.9 27.2 + - - -
123A GLY* 4.8 1.6 - - - -
124A PRO* 3.8 32.0 + - + +
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Residues in contact with PRO 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A ALA 3.3 12.1 - - - +
74A ALA* 1.3 91.4 - - + +
76A HIS* 1.3 62.7 + - - -
78A ASN* 3.4 7.6 + - - -
79A TYR* 3.0 20.4 + - - +
105A THR 3.3 26.5 - - - +
107A VAL* 4.2 0.8 - - - +
121A ILE* 3.4 13.1 - - + +
122A GLU 4.0 14.6 - - - +
123A GLY* 4.1 3.5 - - - +
124A PRO 3.4 13.7 - - - +
125A VAL* 3.8 20.4 - - + -
140A PHE* 3.8 21.3 - - + -
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Residues in contact with HIS 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A PHE* 5.0 1.8 - + - -
43A LEU* 4.0 1.8 - - + -
46A GLU* 2.4 41.7 + - - -
69A LEU* 3.3 24.9 - - + +
72A ALA 3.2 18.5 + - - +
73A TRP* 3.5 22.2 - + - +
74A ALA 3.2 0.8 - - - -
75A PRO* 1.3 77.6 - - - +
77A GLU* 1.3 57.8 + - - +
79A TYR* 3.2 18.0 + + - +
80A VAL* 2.9 44.6 + - + +
102A MET* 4.4 2.9 - - + +
106A GLY 2.7 30.3 + - - +
108A PRO* 4.5 10.8 - - + -
173A HIS* 5.6 2.0 - + - -
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Residues in contact with GLU 77 (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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40A ASP* 5.2 0.2 - - - +
43A LEU* 3.8 25.9 - - + +
73A TRP* 2.7 50.8 + - + +
74A ALA* 3.9 4.5 - - - +
76A HIS* 1.3 73.8 - - - +
78A ASN* 1.3 58.1 + - - +
80A VAL* 3.9 0.5 - - - +
81A GLN* 2.9 52.7 + - + +
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Residues in contact with ASN 78 (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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74A ALA 2.9 17.1 + - - -
75A PRO* 3.5 7.4 - - - -
77A GLU* 1.3 76.5 - - - +
79A TYR* 1.3 58.2 + - - +
81A GLN* 4.1 3.3 - - + -
82A THR* 2.6 49.9 + - - +
120A GLN 4.7 2.6 + - - -
121A ILE* 3.6 11.3 - - - +
122A GLU 3.1 32.8 + - - +
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Residues in contact with TYR 79 (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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75A PRO 3.0 13.2 + - - +
76A HIS* 3.2 15.0 + + - +
78A ASN* 1.3 75.0 + - - +
80A VAL* 1.3 71.7 + - + +
83A TYR* 2.9 43.7 + + - +
107A VAL* 3.9 30.3 - - + -
108A PRO* 3.7 26.8 - - + +
119A LEU* 4.7 4.3 - - + -
121A ILE* 3.7 13.6 - - + +
153A TRP* 4.5 3.5 - + - -
167A PHE* 3.7 28.1 - + - -
171A PHE* 3.5 23.7 - + - -
172A VAL* 2.9 41.7 + - - +
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Residues in contact with VAL 80 (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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39A ALA* 4.0 13.9 - - + +
42A PHE* 3.9 21.5 - - + -
43A LEU* 3.6 32.8 - - + -
46A GLU* 4.1 2.7 - - - +
76A HIS* 2.9 42.3 + - + +
77A GLU 4.0 0.7 - - - +
79A TYR* 1.3 86.8 - - + +
81A GLN* 1.4 57.7 + - - +
84A CYS* 2.7 49.1 + - + +
171A PHE* 4.2 7.0 - - + -
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Residues in contact with GLN 81 (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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39A ALA* 3.7 19.2 - - - +
40A ASP* 2.9 26.1 + - - +
43A LEU* 3.7 6.6 - - + +
77A GLU* 2.9 45.4 + - + +
78A ASN* 4.1 4.5 - - + +
80A VAL* 1.4 76.4 - - - +
82A THR* 1.3 62.9 + - - +
84A CYS 4.5 0.3 + - - -
85A LYS* 3.8 20.1 + - - +
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Residues in contact with THR 82 (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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78A ASN* 2.6 36.2 + - - +
81A GLN* 1.3 78.2 - - - +
83A TYR* 1.3 99.4 + - + +
84A CYS 3.6 0.4 - - - -
85A LYS* 3.3 27.4 + - - +
121A ILE* 3.9 5.0 - - + +
164A GLU* 6.1 0.2 - - - +
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Residues in contact with TYR 83 (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 TYR* 2.9 35.5 + + + +
82A THR* 1.3 104.9 - - + +
84A CYS* 1.3 56.1 + - - +
85A LYS* 3.7 2.7 - - - -
88A LYS* 2.7 28.6 + - - -
119A LEU* 2.5 43.9 + - + -
120A GLN* 4.9 0.7 - - - +
121A ILE* 3.9 13.0 - - + -
163A PRO* 3.5 33.5 - - + +
164A GLU* 4.5 13.3 + - + -
167A PHE* 3.2 45.3 - + + +
171A PHE* 3.6 9.0 - - + -
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Residues in contact with CYS 84 (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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38A PRO* 4.0 7.4 - - - +
39A ALA* 3.5 27.2 + - - +
42A PHE* 4.8 2.2 - - - -
80A VAL* 2.7 26.7 + - + +
81A GLN 5.1 0.2 - - - -
82A THR 3.6 0.2 - - - -
83A TYR* 1.3 81.0 - - - +
85A LYS* 1.3 60.1 + - - +
86A SER 3.4 6.4 + - - -
88A LYS* 3.8 13.2 - - - +
171A PHE* 3.6 23.6 - - + -
216A LEU* 3.5 31.9 - - - -
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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