Contacts of the helix formed by residues 63 - 73 (chain A) in PDB entry 1O9H
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 GLY 63 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60A CYS* 2.9 20.5 + - - -
61A GLY 3.2 2.0 + - - -
62A SER* 1.3 75.6 - - - +
64A TYR* 1.3 57.8 + - - +
65A LEU 3.4 2.5 - - - -
66A LEU* 3.4 9.0 + - - +
67A THR* 2.8 40.0 + - - -
93A ALA* 3.5 15.9 - - - +
96A ASN* 3.8 1.6 - - - -
97A LEU* 5.4 3.1 - - - -
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Residues in contact with TYR 64 (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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16A LEU 2.6 24.0 + - - -
17A ALA* 4.1 1.2 - - - -
18A CYS* 3.8 33.4 + - + -
22A LEU* 3.3 38.3 - - + +
23A HIS 4.7 3.4 - - - +
29A PRO 5.4 4.7 - - - +
30A ALA* 4.3 5.8 - - + +
31A PHE* 3.4 42.4 + - + -
33A VAL* 3.8 15.0 - - + +
60A CYS 4.6 0.2 + - - -
62A SER* 3.2 17.4 + - - +
63A GLY* 1.3 76.3 - - - +
65A LEU* 1.3 62.9 + - - +
67A THR* 3.9 1.5 - - - -
68A VAL* 2.9 43.1 + - + +
96A ASN* 3.7 9.6 - - - +
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Residues in contact with LEU 65 (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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31A PHE* 3.9 35.7 - - + -
36A ALA* 3.6 31.0 - - + -
57A ASP* 4.1 18.6 - - - +
60A CYS 5.6 2.4 + - - +
63A GLY 3.4 0.2 - - - -
64A TYR* 1.3 81.2 - - - +
66A LEU* 1.3 67.5 + - - +
68A VAL* 3.7 5.0 - - + +
69A LEU* 3.2 32.5 + - + +
173A LEU* 3.7 26.7 - - + -
175A ASP* 4.2 19.3 - - + +
213A THR* 5.7 0.2 - - - +
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Residues in contact with LEU 66 (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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55A LEU* 3.4 38.5 - - + +
57A ASP* 4.0 25.9 + - + +
60A CYS* 4.9 2.0 + - + -
63A GLY* 3.4 11.0 + - - +
64A TYR 3.4 0.2 - - - -
65A LEU* 1.3 80.8 - - - +
67A THR* 1.3 58.7 + - - +
69A LEU* 3.2 7.0 + - + +
70A GLY* 2.9 25.5 + - - -
80A VAL* 4.1 22.7 - - + +
81A ILE 3.3 27.6 - - - +
82A ALA* 3.5 23.6 - - + -
97A LEU* 4.5 8.7 - - + -
100A LEU* 5.2 1.0 - - - +
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Residues in contact with THR 67 (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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22A LEU* 4.4 15.3 - - + -
63A GLY 2.8 23.3 + - - -
64A TYR 3.9 2.2 - - - -
66A LEU* 1.3 76.2 - - - +
68A VAL* 1.3 64.6 + - - +
70A GLY* 3.0 2.4 + - - -
71A LEU* 3.0 39.9 + - + +
96A ASN* 3.2 41.9 - - + +
97A LEU* 3.6 9.9 + - - +
99A LEU* 4.5 3.4 - - + -
100A LEU* 3.8 18.1 - - + +
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Residues in contact with VAL 68 (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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16A LEU* 4.1 25.7 - - + +
22A LEU* 3.7 24.2 - - + +
33A VAL* 4.4 16.6 - - + -
36A ALA* 4.3 16.6 - - + -
64A TYR* 2.9 38.0 + - + +
65A LEU* 3.7 8.7 - - + +
67A THR* 1.3 77.0 - - - +
69A LEU* 1.3 72.1 + - + +
71A LEU* 3.5 2.0 + - - +
72A LEU* 3.1 28.8 + - + +
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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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36A ALA* 3.8 31.9 - - + +
37A THR* 4.1 2.0 - - - +
40A PHE* 4.1 9.9 - - + -
55A LEU* 4.2 23.8 - - + -
65A LEU* 3.2 24.2 + - + +
66A LEU* 3.2 9.0 + - + +
68A VAL* 1.3 78.7 - - + +
70A GLY* 1.3 60.9 + - - +
72A LEU* 4.6 2.2 - - + -
73A HIS* 2.9 56.2 + - + +
77A LEU* 3.8 3.7 - - + +
173A LEU* 3.7 30.1 - - + -
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Residues in contact with GLY 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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55A LEU* 5.4 0.2 - - - +
66A LEU 2.9 14.3 + - - -
67A THR 3.0 3.8 + - - -
69A LEU* 1.3 77.6 - - - +
71A LEU* 1.3 58.6 + - - +
74A ARG* 3.3 26.7 + - - +
77A LEU* 3.6 16.5 - - - +
80A VAL* 5.0 1.8 - - - -
100A LEU* 3.8 12.7 - - - +
138A LEU* 4.8 0.5 - - - +
145A LEU* 3.7 15.2 - - - +
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Residues in contact with LEU 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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16A LEU* 4.2 17.7 - - + -
22A LEU* 4.1 25.8 - - + -
67A THR* 3.0 28.6 + - + +
68A VAL 4.1 2.9 - - - +
70A GLY* 1.3 76.2 - - - +
72A LEU* 1.3 63.0 + - - +
74A ARG* 4.0 10.1 + - - +
99A LEU* 3.6 27.6 - - + +
100A LEU* 3.9 10.3 - - + -
105A LEU* 4.3 11.4 - - + -
134A LEU* 4.5 21.1 - - + +
137A ARG* 4.5 15.5 + - - +
138A LEU* 4.2 23.7 - - + +
141A GLU* 4.6 1.7 - - - +
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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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11A ILE* 4.7 21.8 - - + -
12A ASP 5.5 3.1 - - - +
16A LEU* 3.7 22.7 - - + -
33A VAL* 4.3 20.4 - - + +
37A THR* 3.8 30.7 - - + +
68A VAL* 3.1 22.4 + - + +
69A LEU* 5.4 1.1 - - + -
71A LEU* 1.3 77.6 - - - +
73A HIS* 1.3 74.5 + - + +
74A ARG 3.5 1.1 + - - -
75A ARG* 4.5 5.7 + - - -
137A ARG* 5.3 11.5 - - - +
141A GLU* 4.0 9.9 - - - +
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Residues in contact with HIS 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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37A THR* 2.8 35.3 + - - -
40A PHE* 3.5 37.1 - + + -
41A GLN* 3.9 25.5 - - + +
44A LEU* 5.8 0.8 - - - +
69A LEU* 2.9 32.8 + - + +
70A GLY 4.1 0.2 - - - -
72A LEU* 1.3 91.2 + - + +
74A ARG* 1.3 63.4 + - - +
75A ARG* 3.0 8.1 + - - +
76A SER* 3.0 19.7 + - - +
77A LEU* 3.2 12.1 - - + +
141A GLU* 4.7 0.7 - - - -
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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