Contacts of the strand formed by residues 89 - 96 (chain B) in PDB entry 1X1O
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 GLU 89 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46B VAL* 3.5 19.8 - - + +
47B ILE 3.8 3.8 - - - -
48B LEU* 3.7 12.7 - - + +
77B LEU* 3.4 30.7 - - + +
78B VAL* 3.6 4.2 - - - +
87B GLY 3.7 2.8 + - - +
88B THR* 1.3 81.3 - - - +
90B VAL* 1.3 63.3 + - - +
92B ARG* 2.7 43.4 + - - -
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Residues in contact with VAL 90 (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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47B ILE* 2.8 26.2 + - + +
48B LEU 4.4 1.8 - - - -
49B ALA* 4.0 17.0 - - + +
55B LEU* 3.6 38.8 - - + -
58B LEU* 3.6 25.1 - - + -
76B PRO* 3.7 2.3 - - - +
77B LEU 2.8 20.1 + - - -
78B VAL* 3.6 13.6 - - + +
84B VAL* 5.0 3.6 - - + -
88B THR 4.0 9.9 - - - +
89B GLU* 1.3 73.6 - - - +
91B ALA* 1.3 64.3 + - + +
111B LEU* 5.6 1.3 - - + -
279B LEU* 4.4 5.4 - - + -
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Residues in contact with ALA 91 (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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46B VAL* 3.5 8.8 - - - +
47B ILE* 2.9 32.3 + - + +
58B LEU* 4.7 0.4 - - + -
74B PHE* 3.5 35.9 - - + -
75B THR 3.2 14.8 - - - +
76B PRO* 3.9 4.0 - - + -
77B LEU* 4.0 6.5 - - - +
89B GLU 3.6 1.2 - - - -
90B VAL* 1.3 87.3 - - + +
92B ARG* 1.3 63.2 + - - +
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Residues in contact with ARG 92 (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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44B GLU* 2.9 39.2 + - - +
45B ALA 3.3 10.8 - - - +
46B VAL* 3.6 17.5 - - + +
47B ILE* 6.1 0.2 - - - -
73B ALA 3.8 0.9 - - - +
74B PHE* 3.7 3.5 - - - -
75B THR* 2.8 43.0 + - - +
77B LEU* 3.8 18.5 - - + +
89B GLU* 2.7 35.9 + - - -
91B ALA* 1.3 77.9 - - - +
93B VAL* 1.3 60.4 + - - +
94B ARG* 5.7 0.4 - - + -
284B VAL* 4.5 7.3 - - - +
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Residues in contact with VAL 93 (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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44B GLU* 3.2 5.4 - - - +
45B ALA* 2.9 60.0 + - + +
47B ILE* 5.7 3.8 - - + +
65B PHE* 4.1 30.3 - - + -
72B THR* 4.6 3.8 - - - -
73B ALA 3.3 11.2 - - - +
74B PHE* 4.5 9.6 - - + -
92B ARG* 1.3 74.6 - - - +
94B ARG* 1.3 65.6 + - - +
100B ILE* 3.6 29.8 - - + +
281B LEU* 4.3 9.6 - - + -
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Residues in contact with ARG 94 (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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42B GLU* 3.7 23.6 - - - +
43B GLY 3.4 11.7 - - - +
44B GLU* 4.3 19.2 + - + -
71B ARG 4.1 0.3 - - - +
72B THR* 3.2 4.1 - - - -
73B ALA* 2.7 64.5 + - - +
75B THR* 4.3 14.1 + - - -
92B ARG* 5.7 0.7 - - + -
93B VAL* 1.3 76.5 - - - +
95B GLY* 1.3 62.2 + - - +
100B ILE* 4.1 5.2 - - - -
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Residues in contact with GLY 95 (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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42B GLU* 3.8 14.6 - - - +
43B GLY 2.9 24.3 + - - +
71B ARG 4.3 5.6 - - - -
72B THR* 4.4 1.1 - - - -
94B ARG* 1.3 84.0 - - - +
96B PRO* 1.3 79.3 - - - +
97B LEU 3.0 0.3 + - - -
100B ILE* 3.9 3.8 - - - +
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Residues in contact with PRO 96 (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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39B GLU 5.0 8.5 - - - +
40B ASP 6.0 0.9 - - - -
41B LEU 3.7 9.2 - - - +
42B GLU* 4.4 2.6 - - + -
69B ASP* 3.6 14.6 - - - +
71B ARG* 3.6 58.6 - - + +
72B THR* 4.3 7.1 - - + +
95B GLY* 1.3 79.8 - - - +
97B LEU* 1.3 67.2 + - - +
98B ARG* 3.3 4.0 - - + +
99B GLY* 3.1 14.0 + - - +
100B ILE* 3.2 11.6 + - - +
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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