Contacts of the strand formed by residues 126 - 133 (chain B) in PDB entry 1I09
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 VAL 126 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88B LEU* 3.6 3.7 - - - +
89B GLN* 2.7 46.7 + - + +
91B LYS* 4.8 14.8 - - + +
117B TYR* 4.8 15.3 - - + -
118B SER 3.5 11.4 - - - +
119B SER* 5.4 2.5 - - - +
120B GLY 4.0 0.7 - - - +
123B LYS 5.4 1.6 - - - +
124B ASP* 4.0 8.9 + - - +
125B GLU* 1.3 83.6 - - - +
127B TYR* 1.3 69.1 + - - +
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Residues in contact with TYR 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B PHE 5.8 1.6 - - - -
86B LYS* 3.2 48.2 - - + -
87B VAL* 3.1 10.8 - - - +
88B LEU* 3.1 49.5 - - + +
89B GLN* 4.4 0.7 - - - -
117B TYR* 3.1 33.2 - - - +
118B SER* 3.0 16.1 + - - +
119B SER 4.3 1.1 - - - -
120B GLY* 3.1 33.9 - - - -
121B GLU* 3.8 9.3 + - + +
125B GLU* 3.3 18.1 + - - -
126B VAL* 1.3 74.6 - - - +
128B LEU* 1.3 59.7 + - - +
129B ASN* 4.0 0.4 - - - -
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Residues in contact with LEU 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85B LYS 3.5 2.8 - - - +
86B LYS* 3.4 2.5 - - - -
87B VAL* 2.8 34.3 + - + +
89B GLN* 3.8 16.7 - - + +
95B ASN* 3.4 42.6 - - + +
98B LEU* 3.9 19.1 - - + -
115B PHE* 4.2 10.5 - - + -
116B PHE 3.7 5.6 - - - +
117B TYR* 3.6 30.5 - - + +
127B TYR* 1.3 73.1 - - - +
129B ASN* 1.3 64.2 + - - +
130B LEU* 3.3 27.1 - - + +
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Residues in contact with ASN 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84B ILE* 4.1 11.6 - - + +
85B LYS 3.7 3.6 - - - -
86B LYS* 3.8 24.3 - - - +
115B PHE* 2.8 31.4 - - - +
116B PHE* 2.6 68.9 + - + +
118B SER* 3.2 28.6 + - - +
127B TYR* 3.7 3.2 + - - +
128B LEU* 1.3 77.4 - - - +
130B LEU* 1.3 61.2 + - - +
131B VAL 3.7 0.4 + - - -
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Residues in contact with LEU 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B ALA 3.2 6.1 - - - +
84B ILE* 3.2 1.2 - - - -
85B LYS* 2.8 57.4 + - + +
87B VAL* 5.5 4.0 - - + -
95B ASN* 6.2 0.2 - - - +
97B GLU* 3.7 39.5 - - + +
98B LEU* 5.0 7.9 - - + +
101B MET* 4.9 10.3 - - + -
112B LEU* 4.2 12.8 - - + -
114B TYR 4.0 3.8 - - - -
115B PHE* 4.9 1.8 - - + -
128B LEU* 3.3 40.8 - - + +
129B ASN* 1.3 72.3 - - - +
131B VAL* 1.3 60.8 + - - +
132B LEU* 3.3 15.1 + - + +
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Residues in contact with VAL 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B VAL* 6.4 0.7 - - + -
56B TYR* 5.8 2.5 - - + -
75B LEU* 5.0 3.1 - - + -
82B VAL* 3.9 27.6 - - + -
83B ALA 3.4 3.8 - - - -
84B ILE* 4.2 16.4 - - + +
112B LEU* 3.6 1.3 - - - -
113B ARG* 2.7 47.2 + - + -
114B TYR* 3.0 38.9 + - + +
115B PHE 4.8 0.2 - - - +
116B PHE* 3.8 29.8 - - + -
129B ASN 4.9 0.4 - - - +
130B LEU* 1.3 69.0 - - - +
132B LEU* 1.3 55.7 + - - +
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Residues in contact with LEU 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82B VAL* 3.2 8.3 - - - +
83B ALA* 2.7 45.6 + - + +
85B LYS* 4.2 18.4 - - + +
97B GLU* 5.8 0.7 - - - +
101B MET* 3.9 24.2 - - - -
110B VAL* 3.9 17.0 - - + -
111B ARG 3.3 17.3 - - - +
112B LEU* 3.8 17.7 - - + -
113B ARG* 4.0 4.3 - - - -
130B LEU* 3.8 28.3 - - + +
131B VAL* 1.3 76.3 - - - +
133B ASP* 1.3 63.9 + - - +
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Residues in contact with ASP 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80B GLU* 5.3 0.2 - - - +
81B LEU 4.6 4.1 - - - +
82B VAL* 4.6 0.2 - - - +
83B ALA* 4.0 5.4 - - - +
110B VAL* 3.7 23.8 - - + +
111B ARG* 3.2 39.7 + - - +
113B ARG* 2.4 39.4 + - - +
132B LEU* 1.3 79.4 - - - +
134B TYR* 1.3 63.8 + - - +
135B VAL* 4.0 7.7 + - + +
188B LEU* 4.9 2.9 - - - +
197B LYS* 4.9 11.3 - - + -
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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