Contacts of the strand formed by residues 79 - 85 (chain A) in PDB entry 1O7F
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 ASN 79 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77A GLY 3.9 0.2 - - - -
78A THR* 1.3 109.1 + - - +
80A TRP* 1.3 62.0 + - - +
81A TYR* 3.5 32.3 + - + +
114A GLY* 3.6 6.9 - - - +
117A ILE* 3.5 7.3 - - - +
123A ARG* 2.8 27.1 + - - +
137A ARG* 3.1 38.0 + - + +
138A ILE 3.4 7.3 - - - +
139A GLU* 3.4 19.1 + - - +
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Residues in contact with TRP 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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44A PHE* 3.8 34.5 - + - -
47A PHE* 4.8 5.4 - + - -
55A ILE* 5.0 3.8 - - + -
79A ASN* 1.3 75.2 - - - +
81A TYR* 1.3 72.8 + - - +
82A ALA* 4.8 0.9 - - + -
112A ALA* 3.3 24.1 - - + +
113A PHE 3.2 28.0 + - - +
114A GLY 4.3 0.7 - - - -
115A GLU* 3.6 24.5 + - - +
117A ILE* 3.9 4.7 - - + -
136A LEU* 3.7 2.9 - - + +
137A ARG* 3.2 6.1 - - - +
138A ILE* 2.9 56.9 + - + +
143A PHE* 3.3 56.1 - + + -
154A MET* 5.6 2.0 - - + -
157A LEU* 4.2 16.8 - - + -
158A LEU* 4.3 4.9 - - + +
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Residues in contact with TYR 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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62A GLU* 5.2 3.6 - - + -
70A LEU* 3.4 42.8 + - + +
71A PHE* 4.2 12.8 - + - -
78A THR* 5.0 1.4 + - - -
79A ASN* 3.5 39.7 + - + +
80A TRP* 1.3 81.4 - - - +
82A ALA* 1.3 63.7 + - - +
112A ALA* 3.1 8.5 - - - +
113A PHE* 2.9 67.4 + + + +
123A ARG* 4.3 2.2 + - - -
135A LEU* 3.9 17.0 - - + -
136A LEU 3.2 7.0 - - - +
137A ARG* 3.6 31.7 - - + -
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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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41A VAL* 4.9 8.7 - - + -
44A PHE* 3.7 33.7 - - + -
80A TRP* 4.8 3.4 - - + -
81A TYR* 1.3 76.1 - - - +
83A VAL* 1.3 65.8 + - - +
84A LEU* 3.3 3.4 + - + +
111A THR 3.6 6.7 - - - +
112A ALA* 4.1 5.6 - - + +
135A LEU* 3.4 4.8 - - - -
136A LEU* 2.9 41.1 + - + +
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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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41A VAL* 5.0 3.5 - - - +
82A ALA* 1.3 72.3 - - - +
84A LEU* 1.3 63.6 + - - +
85A ALA 3.7 19.5 - - - +
86A GLY 3.8 11.0 - - - +
88A LEU* 3.7 25.8 - - + -
107A LEU* 4.9 5.2 - - + -
108A GLY* 3.4 33.4 - - - +
109A ILE* 3.8 3.8 - - - +
110A GLY* 3.1 22.5 + - - -
111A THR 2.9 20.3 + - - +
113A PHE* 3.9 11.9 - - + -
134A GLU 4.5 0.2 - - - +
135A LEU* 3.8 12.1 - - + -
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Residues in contact with LEU 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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15A TRP* 3.8 31.0 - - + -
19A LEU* 5.4 0.2 - - + -
37A ARG* 4.0 31.5 + - - +
38A LEU* 4.0 16.2 - - + -
41A VAL* 3.7 29.2 - - + -
61A TYR* 4.6 4.3 - - + -
82A ALA* 3.3 2.7 + - + +
83A VAL* 1.3 76.9 - - - +
85A ALA* 1.3 63.0 + - - +
109A ILE* 3.7 15.3 - - - +
134A GLU* 2.8 18.1 + - + +
135A LEU 4.1 9.9 - - - +
136A LEU* 3.9 33.9 - - + +
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Residues in contact with ALA 85 (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 ARG* 5.4 2.7 - - - +
83A VAL* 3.5 5.8 - - - +
84A LEU* 1.3 79.5 - - - +
86A GLY* 1.3 63.7 + - - +
109A ILE* 3.2 11.0 - - + -
132A SER 5.5 0.9 - - - +
133A SER* 3.2 7.0 - - - -
134A GLU* 2.9 55.3 + - + +
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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