Contacts of the helix formed by residues 68 - 83 (chain A) in PDB entry 1OPT
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 TYR 68 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56A ILE* 5.2 1.6 - - + -
57A ASN* 3.5 36.0 + - - -
66A ASP* 3.1 61.0 + - + +
67A ILE* 1.3 68.3 - - - +
69A LEU* 1.3 59.8 + - - +
70A LEU 3.6 1.3 - - - -
71A ASN* 3.8 22.7 - - + +
72A LEU* 3.0 32.5 + - + +
146A VAL* 4.1 31.7 + - + +
147A VAL* 5.4 6.1 - - + -
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Residues in contact with LEU 69 (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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67A ILE* 3.0 24.3 + - + -
68A TYR* 1.3 76.5 - - - +
70A LEU* 1.3 63.6 + - + +
72A LEU* 3.6 11.4 - - + +
73A ALA* 2.9 29.7 + - - +
119A ILE* 3.7 24.9 - - + +
122A LEU* 3.8 31.6 - - + -
123A THR* 3.9 31.9 - - + +
126A ARG* 3.6 22.4 - - - +
145A GLY 4.9 4.5 - - - +
146A VAL 5.9 2.0 - - - +
150A VAL* 5.7 4.0 - - + -
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Residues in contact with LEU 70 (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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52A ILE* 5.9 1.8 - - + -
56A ILE* 3.9 16.4 - - + -
67A ILE 4.2 3.2 + - - +
69A LEU* 1.3 79.7 - - + +
71A ASN* 1.3 57.2 + - - +
73A ALA* 4.3 7.2 - - + -
74A ILE* 2.9 47.8 + - + +
239A THR* 5.0 6.5 - - + +
243A VAL* 5.8 5.6 - - + -
293A ASN* 3.4 37.9 - - + +
294A PRO* 4.3 6.5 - - + -
297A TYR* 3.7 43.5 - - + -
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Residues in contact with ASN 71 (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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53A LEU* 3.2 37.5 - - - +
56A ILE* 3.4 18.4 - - + +
57A ASN* 3.2 37.2 + - - +
68A TYR* 3.4 28.6 + - + +
70A LEU* 1.3 73.8 - - - +
72A LEU* 1.3 58.1 + - - +
75A SER* 3.0 29.3 + - - -
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Residues in contact with LEU 72 (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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68A TYR 3.0 18.7 + - - +
69A LEU* 3.6 20.0 - - + +
71A ASN* 1.3 74.0 - - - +
73A ALA* 1.3 59.9 + - - +
75A SER* 3.5 8.6 + - - -
76A ASP* 3.0 27.8 + - + +
119A ILE* 3.9 14.6 - - + -
122A LEU* 5.2 0.7 - - + -
150A VAL* 5.4 3.1 - - + -
153A TRP* 3.1 54.3 - - + -
154A VAL* 5.2 0.7 - - + -
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Residues in contact with ALA 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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69A LEU 2.9 22.0 + - - +
70A LEU* 4.1 13.7 - - + +
72A LEU* 1.3 71.7 - - - +
74A ILE* 1.3 58.4 + - - +
76A ASP* 3.2 7.1 + - - +
77A LEU* 2.9 36.5 + - + +
116A ILE* 4.4 17.5 - - + -
119A ILE* 3.8 22.7 - - + -
293A ASN* 5.6 3.8 - - + +
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Residues in contact with ILE 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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49A MET* 3.5 50.3 - - + +
52A ILE* 4.1 9.6 - - + -
53A LEU* 3.8 36.1 - - + +
56A ILE* 5.5 0.7 - - + -
70A LEU* 2.9 42.3 + - + +
73A ALA* 1.3 69.1 - - + +
75A SER* 1.3 55.2 + - - +
77A LEU* 3.4 9.3 + - + +
78A PHE* 2.9 33.1 + - + -
293A ASN* 5.8 0.7 - - + -
294A PRO* 4.0 24.2 - - + -
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Residues in contact with SER 75 (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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53A LEU* 3.9 6.7 - - - +
71A ASN* 3.0 24.1 + - - -
72A LEU* 3.6 8.7 - - - -
73A ALA 3.5 0.2 - - - -
74A ILE* 1.3 70.9 - - - +
76A ASP* 1.3 59.2 + - - +
78A PHE* 3.5 14.0 + - - +
79A PHE* 3.3 39.4 + - - -
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Residues in contact with ASP 76 (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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72A LEU* 3.0 16.6 + - + +
73A ALA* 3.4 11.4 - - - +
75A SER* 1.3 70.1 - - - +
77A LEU* 1.3 61.6 + - - +
79A PHE* 3.5 9.0 + - - -
80A LEU 3.2 16.1 + - - -
112A PHE* 3.5 55.2 - - - +
115A GLY* 3.9 15.2 - - - -
116A ILE* 3.6 11.9 - - + +
119A ILE* 5.3 3.8 - - + -
157A VAL* 6.1 0.2 - - - +
158A PHE* 5.6 5.5 - - - -
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Residues in contact with LEU 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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49A MET* 3.8 18.8 - - + -
73A ALA* 2.9 38.6 + - + +
74A ILE* 3.8 7.6 - - + +
76A ASP* 1.3 68.7 - - - +
78A PHE* 1.3 58.9 + - - +
80A LEU* 3.4 22.9 + - + +
81A LEU* 2.9 29.9 + - - +
112A PHE* 5.6 0.2 - - + -
116A ILE* 3.9 30.7 - - + -
289A HIS* 5.1 0.4 - - - +
290A CYS* 3.6 48.7 - - + +
293A ASN* 4.2 17.0 - - + +
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Residues in contact with PHE 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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46A VAL* 4.6 16.4 - - + -
49A MET* 3.6 22.4 - - + -
50A LEU* 3.7 41.5 - - + -
53A LEU* 4.2 13.2 - - + -
74A ILE* 2.9 36.6 + - + -
75A SER* 3.5 12.7 + - - +
77A LEU* 1.3 71.0 - - - +
79A PHE* 1.3 57.2 + - + +
81A LEU* 3.4 17.4 + - + +
82A THR* 2.9 35.0 + - - +
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Residues in contact with PHE 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 SER* 3.3 34.9 + - - -
76A ASP* 3.5 6.5 + - - +
78A PHE* 1.3 73.3 - - + +
80A LEU* 1.4 59.8 + - - +
82A THR* 4.5 6.5 - - + +
83A VAL* 3.1 36.2 + - + +
84A PRO* 3.5 6.4 - - - +
112A PHE* 3.6 25.6 - + + -
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Residues in contact with LEU 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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76A ASP 3.2 10.1 + - - +
77A LEU* 3.4 31.2 + - + +
79A PHE* 1.4 73.2 - - - +
81A LEU* 1.3 60.8 + - - +
84A PRO* 3.3 34.1 - - + +
85A PHE* 3.5 44.0 + - + -
108A TYR 5.3 0.4 - - - +
112A PHE* 3.7 39.0 - - + -
113A PHE* 4.9 16.4 - - + -
287A MET* 5.5 6.7 - - + +
290A CYS* 4.8 7.6 - - + +
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Residues in contact with LEU 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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41A PHE 4.6 0.4 - - - +
42A ILE* 4.0 32.3 - - + +
45A PHE* 3.8 29.4 - - + -
46A VAL* 3.8 34.5 - - + +
49A MET* 5.2 2.7 - - + -
77A LEU 2.9 19.6 + - - +
78A PHE* 3.4 20.4 + - + +
80A LEU* 1.3 73.1 - - - +
82A THR* 1.3 61.6 + - - +
85A PHE* 3.6 26.5 - - + +
86A TRP* 3.4 19.7 - - - +
290A CYS* 5.9 0.7 - - - -
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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 PHE* 2.9 21.0 + - - +
79A PHE* 4.2 8.1 - - + -
80A LEU 3.5 0.2 - - - -
81A LEU* 1.3 76.0 - - - +
83A VAL* 1.3 72.3 + - + +
86A TRP* 3.5 30.7 - - + +
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Residues in contact with VAL 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 PHE* 3.1 22.3 + - + +
82A THR* 1.3 87.9 - - + +
84A PRO* 1.4 69.2 - - + +
86A TRP* 4.5 0.2 - - - +
87A ALA* 3.3 26.5 + - + +
104A LEU* 5.6 3.6 - - + -
108A TYR* 3.7 44.4 - - + -
112A PHE* 5.6 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