Contacts of the strand formed by residues 77 - 84 (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 LEU 77 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40A PHE* 3.5 32.3 - - + -
52A PRO* 4.2 4.6 - - - +
53A VAL* 3.6 11.9 - - + +
55A LEU* 4.3 16.6 - - + -
69A LEU 3.8 6.7 - - - +
70A GLY* 3.6 32.8 - - - +
73A HIS* 3.2 16.6 - - + +
74A ARG* 3.0 34.7 + - - +
75A ARG 3.2 2.5 + - - +
76A SER* 1.3 81.5 - - - +
78A ARG* 1.3 61.3 + - - +
79A GLN 4.6 1.8 - - - +
80A VAL* 3.9 11.4 - - + -
145A LEU* 3.8 19.7 - - + +
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Residues in contact with ARG 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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52A PRO* 3.8 42.9 + - + +
53A VAL 3.1 10.7 + - - +
54A THR* 3.6 19.3 + - - +
74A ARG* 5.4 0.9 + - - -
77A LEU* 1.3 73.6 - - - +
79A GLN* 1.3 76.0 + - + +
145A LEU* 3.7 1.5 - - - +
146A PRO* 3.5 21.1 - - - +
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Residues in contact with GLN 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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53A VAL 3.7 2.5 + - - +
54A THR* 3.4 21.3 + - + +
55A LEU 3.1 22.3 + - - -
77A LEU 3.6 0.8 - - - -
78A ARG* 1.3 93.1 - - + +
80A VAL* 1.3 69.7 + - - +
81A ILE* 3.8 17.0 - - + +
145A LEU* 3.7 5.8 - - - -
146A PRO* 3.2 29.3 - - + +
147A CYS* 4.8 3.3 - - - -
148A ALA* 5.3 2.1 - - - +
167A SER* 3.2 28.6 + - - -
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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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55A LEU* 3.3 19.7 - - + +
66A LEU* 4.1 22.2 - - + +
70A GLY* 5.0 3.6 - - - -
77A LEU* 3.9 16.8 - - + -
79A GLN* 1.3 80.6 - - - +
81A ILE* 1.3 64.4 + - - +
97A LEU* 4.5 2.0 - - + -
100A LEU* 3.8 18.2 - - + -
145A LEU* 3.8 20.0 - - + -
146A PRO 2.9 8.7 + - - +
147A CYS* 3.1 39.0 - - + +
148A ALA 3.1 5.2 + - - +
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Residues in contact with ILE 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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54A THR* 4.4 12.6 - - + -
55A LEU 2.7 13.6 + - - +
56A TRP* 3.3 27.9 - - + -
57A ASP 2.9 26.7 + - - -
66A LEU* 3.3 7.6 - - - +
79A GLN* 3.8 26.7 - - - +
80A VAL* 1.3 75.3 - - - +
82A ALA* 1.3 63.4 + - - +
148A ALA* 3.5 19.5 - - + +
150A ARG* 6.0 0.2 - - - +
163A VAL* 3.8 29.2 - - + +
164A LEU* 4.5 14.8 - - + +
167A SER* 4.4 13.5 - - - +
169A PRO* 4.8 1.8 - - + -
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Residues in contact with ALA 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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57A ASP 3.6 3.6 - - - -
60A CYS* 3.9 17.3 - - + -
63A GLY* 6.1 0.9 - - - -
66A LEU* 3.5 18.2 - - + -
80A VAL 4.3 0.2 + - - -
81A ILE* 1.3 78.1 - - - +
83A SER* 1.3 66.1 + - - +
93A ALA* 5.6 0.4 - - + -
97A LEU* 3.8 25.8 - - + -
148A ALA 2.8 9.0 + - - +
149A ILE* 3.3 7.3 - - + -
150A ARG 3.2 21.1 + - - -
163A VAL* 4.6 0.5 - - - +
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Residues in contact with SER 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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56A TRP* 3.1 21.8 + - - -
57A ASP 2.9 6.3 + - - -
58A PRO* 2.9 25.4 + - - +
60A CYS* 2.9 28.5 + - - -
82A ALA* 1.3 77.9 - - - +
84A ASP* 1.3 61.8 + - - +
90A LEU* 4.8 0.9 - - - -
150A ARG 3.2 14.6 - - - -
152A ALA* 4.9 5.8 + - - +
163A VAL* 3.7 24.2 - - - +
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Residues in contact with ASP 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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58A PRO 3.8 6.9 - - - +
59A CYS* 3.4 22.3 - - - +
60A CYS* 4.1 1.6 - - - +
61A GLY* 3.0 27.8 + - - +
83A SER* 1.3 75.1 - - - +
85A VAL* 1.3 80.9 + - - +
86A ASP* 3.7 10.4 - - - +
89A PRO* 4.3 7.9 - - + +
90A LEU* 3.8 21.5 - - + +
150A ARG 3.6 2.6 + - - -
151A THR* 3.3 10.2 - - - +
152A ALA 2.9 24.2 + - - -
177A PRO* 6.0 2.8 - - - +
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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