Contacts of the helix formed by residues 86 - 98 (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 ASP 86 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28A TYR* 5.6 0.7 + - - -
84A ASP* 4.1 3.8 + - - +
85A VAL* 1.3 90.6 - - + +
87A PRO* 1.3 69.2 - - + +
88A ALA* 3.2 7.6 - - - +
89A PRO* 3.4 27.7 - - + +
90A LEU* 3.4 20.9 - - - +
151A THR* 4.8 0.4 - - - -
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Residues in contact with PRO 87 (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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85A VAL 3.6 6.0 - - - +
86A ASP* 1.3 90.9 - - + +
88A ALA* 1.3 66.0 + - + +
89A PRO 3.6 0.2 - - - -
90A LEU* 3.7 14.1 + - + +
91A GLU* 3.5 26.2 + - - +
151A THR* 4.9 9.6 - - + +
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Residues in contact with ALA 88 (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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28A TYR* 3.9 11.3 - - - +
86A ASP* 4.4 9.4 - - + -
87A PRO* 1.3 81.2 - - + +
89A PRO* 1.3 73.9 - - + +
91A GLU* 3.4 20.8 + - - +
92A LEU* 4.3 2.1 + - - +
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Residues in contact with PRO 89 (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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28A TYR* 3.5 35.9 - - + +
61A GLY* 3.2 29.3 - - - +
62A SER 4.2 0.2 - - - +
84A ASP* 4.3 17.0 - - + +
86A ASP* 3.4 26.2 - - + +
88A ALA* 1.3 96.5 - - + +
90A LEU* 1.3 55.2 + - - +
92A LEU* 2.8 31.0 + - + +
93A ALA 3.0 9.2 + - - -
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Residues in contact with LEU 90 (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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60A CYS* 3.4 32.8 - - - -
61A GLY 4.5 1.1 - - - +
83A SER 4.5 0.2 - - - -
84A ASP* 3.8 16.8 - - + +
86A ASP 3.4 19.5 - - - +
87A PRO* 3.8 10.5 - - + +
88A ALA 3.2 0.4 - - - -
89A PRO* 1.3 78.3 - - - +
91A GLU* 1.3 61.6 + - + +
93A ALA* 3.7 4.8 - - - +
94A ALA* 3.0 24.4 + - - +
149A ILE* 3.8 20.6 - - + +
150A ARG 4.0 15.7 - - - +
151A THR* 3.4 29.2 - - - +
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Residues in contact with GLU 91 (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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87A PRO* 3.5 17.2 - - - +
88A ALA* 3.8 12.2 - - - +
89A PRO 3.1 1.2 + - - -
90A LEU* 1.3 76.9 - - - +
92A LEU* 1.3 60.5 + - - +
94A ALA* 3.8 13.5 - - - +
95A LYS* 3.8 13.9 + - - +
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Residues in contact with LEU 92 (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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23A HIS* 4.0 26.2 - - + +
24A SER 4.2 10.1 - - - +
25A ALA* 3.3 32.3 - - + +
28A TYR* 4.3 9.6 - - + -
62A SER* 3.5 30.9 - - - +
88A ALA 4.3 1.3 + - - +
89A PRO* 2.8 15.2 + - + +
91A GLU* 1.3 77.1 - - - +
93A ALA* 1.3 61.8 + - - +
94A ALA 3.1 1.6 - - - -
95A LYS* 3.0 32.4 + - + +
96A ASN* 3.2 6.8 + - - +
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Residues in contact with ALA 93 (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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60A CYS* 4.3 6.3 - - - -
61A GLY 3.7 9.9 - - - +
62A SER 3.1 13.1 + - - -
63A GLY* 3.5 24.9 - - - +
82A ALA* 5.6 0.2 - - + -
89A PRO 3.0 6.3 + - - +
90A LEU* 3.4 4.7 + - - +
92A LEU* 1.3 75.3 - - - +
94A ALA* 1.3 57.4 + - - +
96A ASN* 3.3 1.3 + - - +
97A LEU* 2.8 37.3 + - + +
149A ILE* 3.8 20.2 - - + -
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Residues in contact with ALA 94 (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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90A LEU 3.0 17.5 + - - +
91A GLU* 3.8 9.2 - - - +
92A LEU 3.1 0.4 - - - -
93A ALA* 1.3 77.6 - - - +
95A LYS* 1.3 61.6 + - - +
97A LEU* 3.7 4.9 + - - +
98A ALA* 3.2 22.7 + - - +
149A ILE* 4.2 16.3 - - + +
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Residues in contact with LYS 95 (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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23A HIS* 3.5 51.3 + - + -
91A GLU 3.8 10.4 + - - +
92A LEU* 3.0 32.7 + - + +
94A ALA* 1.3 80.2 - - - +
96A ASN* 1.3 60.6 + - - +
98A ALA* 3.7 15.2 - - - +
99A LEU* 3.8 6.2 - - - +
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Residues in contact with ASN 96 (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* 3.6 9.8 - - - +
23A HIS* 2.9 48.9 + - - +
62A SER* 2.9 25.8 + - - +
63A GLY 4.2 1.3 - - - +
64A TYR* 3.5 20.0 - - - +
67A THR* 3.2 33.3 - - - +
92A LEU* 3.2 8.8 + - - +
93A ALA 3.6 6.7 - - - +
94A ALA 3.2 0.4 - - - -
95A LYS* 1.3 75.4 - - - +
97A LEU* 1.3 59.8 + - - +
98A ALA 3.2 0.4 - - - -
99A LEU* 3.1 21.6 + - - +
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Residues in contact with LEU 97 (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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63A GLY* 5.0 2.9 - - - +
66A LEU* 4.5 22.0 - - + -
67A THR* 3.8 13.5 - - - +
80A VAL* 4.5 4.7 - - + -
82A ALA* 3.8 24.9 - - + -
93A ALA* 2.8 22.8 + - + +
94A ALA* 4.2 4.5 - - - +
96A ASN* 1.3 71.6 - - - +
98A ALA* 1.3 56.8 + - - +
99A LEU 3.0 5.6 - - - -
100A LEU* 3.0 48.7 + - + +
147A CYS* 4.2 22.7 - - + -
148A ALA 4.9 1.8 - - - +
149A ILE* 4.0 24.9 - - + +
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Residues in contact with ALA 98 (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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94A ALA 3.2 17.3 + - - +
95A LYS* 3.7 12.3 - - - +
96A ASN 3.2 0.6 - - - -
97A LEU* 1.3 75.7 - - - +
99A LEU* 1.3 57.9 + - + +
100A LEU 3.2 1.3 - - - -
101A SER* 3.2 16.1 + - - -
104A GLY* 3.2 25.2 - - - -
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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