Contacts of the strand formed by residues 93 - 98 (chain B) in PDB entry 1MOX
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 TYR 93 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B TYR* 3.6 5.2 - - - +
88B TYR* 3.6 5.7 - - - -
89B TYR* 3.0 43.9 + + + +
90B GLU* 4.2 13.9 - - + -
92B SER* 1.3 94.0 - - - +
94B ALA* 1.3 60.9 + - - +
95B LEU 3.7 14.6 - - - +
96B ALA* 4.6 6.5 - - + -
123B ALA* 2.9 24.5 - - + +
124B VAL 3.4 18.2 - - - -
125B ARG* 3.3 51.3 - - + -
151B ASN* 4.1 10.8 + - - -
153B SER* 4.3 7.5 - - - -
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Residues in contact with ALA 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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64B TYR* 3.1 10.3 - - - -
65B VAL* 2.6 33.2 + - - -
83B ILE* 3.5 16.6 - - + +
85B GLY* 4.0 11.0 - - - -
88B TYR* 4.8 1.3 - - + -
93B TYR* 1.3 74.3 - - - +
95B LEU* 1.3 54.5 + - - +
96B ALA 4.3 0.2 - - - -
119B ILE* 3.5 18.4 - - + -
121B HIS 3.2 27.1 - - - +
122B GLY* 4.2 2.0 - - - -
123B ALA 2.8 6.8 + - - +
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Residues in contact with LEU 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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65B VAL* 3.4 35.2 - - + +
67B ILE* 4.8 2.7 - - + -
83B ILE* 4.0 12.6 - - + -
93B TYR* 3.7 4.6 - - - +
94B ALA* 1.3 80.4 - - - +
96B ALA* 1.3 63.2 + - - +
97B VAL* 4.5 11.0 - - + -
113B MET* 4.0 18.8 - - + -
116B LEU* 4.4 4.9 - - + -
119B ILE* 4.1 8.1 - - + -
123B ALA 3.5 2.2 + - - -
124B VAL* 3.4 27.3 - - + -
125B ARG 2.9 25.1 + - - -
126B PHE* 3.8 17.5 - - + -
140B TRP* 3.8 17.0 - - + -
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Residues in contact with ALA 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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65B VAL 2.8 10.7 + - - +
66B LEU* 3.5 12.2 - - + +
67B ILE 2.8 32.1 + - - +
89B TYR* 3.9 31.9 - - + -
93B TYR* 4.6 8.1 - - + -
95B LEU* 1.3 74.9 - - - +
97B VAL* 1.3 58.2 + - - +
98B LEU* 3.8 8.1 - - + -
125B ARG* 3.4 11.9 - - + +
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Residues in contact with VAL 97 (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 ILE* 3.1 21.3 - - + +
95B LEU* 4.3 8.0 - - + -
96B ALA* 1.3 73.7 - - - +
98B LEU* 1.3 59.8 - - - +
100B ASN* 3.1 22.0 - - - +
108B LEU* 4.5 1.6 - - + -
111B LEU* 3.9 15.5 - - + -
125B ARG 3.1 6.3 + - - -
126B PHE* 3.5 41.7 - - + -
127B SER 3.1 24.3 + - - -
129B ASN* 3.2 17.7 + - - +
132B LEU* 4.4 6.7 - - + -
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Residues in contact with LEU 98 (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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14B LEU* 5.7 0.7 - - + -
66B LEU* 4.6 3.8 - - + -
67B ILE 2.6 11.3 + - - -
68B ALA* 3.0 17.7 - - + +
69B LEU* 2.9 19.1 + - - +
89B TYR* 4.0 29.4 - - + +
96B ALA* 4.2 7.4 - - + +
97B VAL* 1.3 89.0 - - - +
99B SER* 1.3 71.4 + - - +
100B ASN* 3.1 3.7 - - - +
125B ARG* 3.1 50.0 - - + +
127B SER* 3.5 13.2 - - - +
27D GLU* 3.7 26.2 - - + +
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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