Contacts of the helix formed by residues 86 - 95 (chain B) in PDB entry 1XR2
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 GLY 86 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84B TYR* 3.7 23.8 + - - -
85B ARG* 1.3 81.7 - - - +
87B LEU* 1.3 67.2 + - - -
88B SER* 3.2 2.9 - - - -
89B THR* 2.9 3.9 + - - -
90B TYR* 2.8 20.1 + - - +
126B GLU* 5.8 0.4 - - - -
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Residues in contact with LEU 87 (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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24B PHE* 4.3 19.3 - - + -
31B GLU* 4.6 13.9 - - + +
34B PHE* 3.9 23.3 - - + -
35B GLU* 5.5 5.4 - - + +
63B TYR* 3.9 24.9 - - + -
86B GLY* 1.3 70.1 - - - -
88B SER* 1.3 57.7 + - - +
90B TYR* 3.1 11.1 + - + +
91B PHE* 2.8 72.5 + - + +
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Residues in contact with SER 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B PHE* 6.0 1.1 - - - -
85B ARG* 3.9 16.3 - - - +
86B GLY* 4.3 1.4 + - - -
87B LEU* 1.3 76.2 - - - +
89B THR* 1.3 65.3 + - - +
91B PHE* 3.7 5.2 + - - +
92B ASP* 2.7 37.6 + - - +
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Residues in contact with THR 89 (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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77B VAL* 4.8 1.3 - - + -
81B PHE* 4.2 28.3 - - + +
83B GLU 4.0 4.8 + - - +
84B TYR* 3.5 30.5 - - + -
85B ARG* 2.7 35.6 + - - +
86B GLY 2.9 6.6 + - - -
88B SER* 1.3 73.9 + - - +
90B TYR* 1.3 67.3 + - - +
92B ASP* 3.1 9.9 + - - +
93B MET* 3.1 29.6 + - - +
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Residues in contact with TYR 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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62B SER* 3.3 3.8 + - - -
63B TYR* 4.0 14.9 + + + -
64B TYR* 3.4 28.0 + - + -
65B ASP 3.2 24.1 + - - -
68B LEU* 3.6 26.4 - - + +
69B ASP* 2.5 33.9 + - - -
72B VAL* 4.1 10.5 - - + -
84B TYR* 3.4 28.8 - - - +
86B GLY 2.8 7.3 + - - +
87B LEU* 3.4 15.5 - - + +
89B THR* 1.3 78.1 - - - +
91B PHE* 1.3 76.2 + + - +
93B MET* 3.2 9.0 + - - +
94B ALA* 3.1 17.8 + - - +
128B LYS* 5.4 6.3 - - - -
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Residues in contact with PHE 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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21B LEU* 3.5 25.4 - - + -
24B PHE* 3.7 28.9 - + - -
25B TRP* 3.5 29.4 - + + +
34B PHE* 4.2 5.6 - + - -
63B TYR* 3.5 21.5 - - + -
64B TYR* 4.2 15.9 - + - -
87B LEU* 2.8 47.7 + - + +
88B SER* 4.3 4.0 - - - +
90B TYR* 1.3 85.7 - + - +
92B ASP* 1.3 61.9 + - - +
94B ALA* 3.5 1.8 - - + -
95B ARG* 2.8 34.1 + - + +
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Residues in contact with ASP 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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81B PHE* 3.5 23.6 - - + -
88B SER* 2.7 25.2 + - - +
89B THR* 3.1 13.0 + - + +
91B PHE* 1.3 78.4 - - - +
93B MET* 1.3 60.3 + - - +
95B ARG 3.3 15.1 - - - +
96B GLY* 5.1 0.2 - - - -
98B LYS* 4.1 3.1 + - + +
99B ALA* 3.5 11.4 + - - -
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Residues in contact with MET 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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68B LEU* 3.6 30.3 - - + -
71B ALA* 5.4 0.7 - - + -
72B VAL* 4.5 5.4 - - + -
76B ALA 3.9 11.7 - - - +
77B VAL* 4.1 19.7 - - + -
78B PRO* 3.9 25.4 - - + -
81B PHE* 3.7 30.3 - - + -
84B TYR* 4.3 18.6 - - - -
89B THR* 3.1 17.9 + - - +
90B TYR* 3.5 8.3 - - - +
92B ASP* 1.3 79.6 - - - +
94B ALA* 1.3 56.4 + - - +
99B ALA* 3.4 0.5 - - - -
100B LEU* 2.8 43.0 + - + +
113B LEU* 4.3 2.6 - - - +
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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* 3.5 52.9 + - + -
68B LEU* 4.2 1.3 - - + -
90B TYR 3.1 14.6 + - - +
91B PHE* 3.2 8.3 + - + +
93B MET* 1.3 79.5 - - - +
95B ARG* 1.3 60.3 + - - +
99B ALA* 3.6 8.3 - - - +
100B LEU 5.0 0.5 - - - +
102B MET* 5.1 1.7 - - - +
113B LEU* 3.7 24.1 - - + +
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Residues in contact with ARG 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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25B TRP* 5.5 8.5 - - + -
64B TYR* 4.6 13.7 - - + +
91B PHE* 2.8 25.4 + - + +
92B ASP* 3.3 16.3 - - - +
93B MET 3.7 0.2 - - - -
94B ALA* 1.3 76.7 - - + +
96B GLY* 1.3 61.8 + - - +
99B ALA* 3.7 4.9 - - - -
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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