Contacts of the helix formed by residues 85 - 98 (chain B) in PDB entry 2XGZ
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 ASP 85 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82B ASP* 2.9 24.4 + - + +
83B VAL 4.0 1.6 - - - -
84B LYS* 1.3 74.2 - - - +
86B GLN* 1.3 64.0 + - - +
87B LYS* 3.5 11.8 + - - +
88B ALA* 3.0 37.8 + - + +
89B VAL* 3.1 14.4 + - - +
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Residues in contact with GLN 86 (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 VAL 4.2 7.5 - - - +
84B LYS 3.2 5.4 + - - +
85B ASP* 1.3 73.1 + - - +
87B LYS* 1.3 63.3 + - - +
89B VAL* 3.3 11.5 + - - +
90B ASP* 2.9 46.7 + - - +
114B SER* 3.1 29.9 + - - +
117B ALA* 4.3 1.6 - - - +
118B SER* 3.4 28.8 + - - -
132B HIS* 4.9 0.2 + - - -
136B LEU* 3.7 35.4 - - + +
352B LEU* 3.8 18.5 - - + +
353B SER* 3.2 13.0 + - - +
356B ILE* 5.7 0.4 - - + -
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Residues in contact with LYS 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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85B ASP* 3.2 9.8 - - - +
86B GLN* 1.3 78.9 - - - +
88B ALA* 1.3 51.8 + - - +
90B ASP* 3.4 0.9 + - - +
91B ASP* 2.8 47.5 + - - +
353B SER* 3.5 14.9 + - - +
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Residues in contact with ALA 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B ILE* 4.2 13.7 - - + +
85B ASP* 3.0 32.4 + - + +
87B LYS* 1.3 78.4 - - - +
89B VAL* 1.3 65.5 + - - +
91B ASP* 3.9 6.9 - - - +
92B PHE* 3.0 25.6 + - - +
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Residues in contact with VAL 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B PHE* 4.0 22.2 - - + -
81B ILE* 3.9 19.9 - - + +
83B VAL* 4.0 24.7 - - - +
85B ASP 3.1 13.7 + - - +
86B GLN* 3.5 13.9 - - - +
88B ALA* 1.3 76.8 - - - +
90B ASP* 1.3 69.1 + - - +
92B PHE* 3.4 5.7 + - - +
93B LEU* 3.1 35.0 + - + +
113B VAL 4.8 0.4 - - - +
114B SER* 4.4 1.8 - - - -
117B ALA* 3.9 24.9 - - + -
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Residues in contact with ASP 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B GLN* 2.9 28.3 + - - +
87B LYS 4.0 0.9 - - - +
89B VAL* 1.3 73.7 - - - +
91B ASP* 1.3 61.0 + - - +
93B LEU* 3.2 7.7 + - - +
94B ILE* 2.8 38.8 + - + +
114B SER* 2.6 32.8 + - - -
351B THR* 3.5 20.1 - - + +
353B SER* 2.6 44.8 + - - +
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Residues in contact with ASP 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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87B LYS* 2.8 31.4 + - - +
88B ALA* 3.9 6.4 - - - +
90B ASP* 1.3 73.3 - - - +
92B PHE* 1.3 57.4 + - - +
94B ILE* 3.9 12.0 - - - +
95B SER* 3.0 34.7 + - - +
353B SER* 6.2 0.2 - - - -
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Residues in contact with PHE 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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72B ILE 4.6 0.2 - - - -
75B ALA* 3.4 35.4 - - + -
76B PHE* 3.7 37.0 - + + -
79B ALA* 3.7 20.0 - - + -
81B ILE* 3.6 15.7 - - + -
88B ALA 3.0 18.6 + - - +
89B VAL 3.5 3.8 - - - +
91B ASP* 1.3 78.0 - - - +
93B LEU* 1.3 69.1 + - + +
95B SER* 3.4 6.1 + - - -
96B LEU* 3.1 41.1 + - + +
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Residues in contact with LEU 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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72B ILE* 3.5 37.7 - - + -
76B PHE* 4.2 8.5 - - + -
89B VAL* 3.1 20.5 + - + +
90B ASP* 3.2 20.2 + - - +
92B PHE* 1.3 80.6 - - + +
94B ILE* 1.3 65.3 + - - +
96B LEU* 3.3 6.2 + - + +
97B ASP* 3.2 22.5 + - - +
105B LEU* 4.5 2.1 - - + +
110B ILE* 3.8 32.6 - - + +
113B VAL* 3.8 17.0 - - + -
114B SER* 3.7 28.5 - - - +
351B THR* 5.1 0.2 - - + -
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Residues in contact with ILE 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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90B ASP* 2.8 28.2 + - + +
91B ASP* 3.9 11.7 - - - +
93B LEU* 1.3 75.4 - - - +
95B SER* 1.3 59.8 + - - +
97B ASP* 3.4 6.0 + - - +
98B GLY* 2.9 27.1 + - - -
99B THR 4.6 6.8 + - - +
102B LYS* 4.3 13.5 - - + +
110B ILE* 5.4 2.0 - - - -
351B THR* 4.2 17.0 - - + +
353B SER* 6.3 0.2 - - - -
354B GLU* 3.7 33.4 - - + +
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Residues in contact with SER 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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91B ASP* 3.0 20.8 + - - +
92B PHE* 3.7 6.7 - - - -
94B ILE* 1.3 76.4 - - - +
96B LEU* 1.3 65.6 + - - +
97B ASP 3.5 0.2 + - - -
98B GLY* 3.6 11.7 + - - +
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Residues in contact with LEU 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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71B VAL* 4.1 16.3 - - + +
72B ILE* 3.6 43.7 - - + +
75B ALA* 4.4 15.5 - - + -
92B PHE* 3.1 35.3 + - + +
93B LEU* 3.3 6.7 + - - +
95B SER* 1.3 77.3 - - - +
97B ASP* 1.3 64.4 + - - +
104B LYS* 4.9 8.0 + - - +
105B LEU* 4.0 11.4 - - + +
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Residues in contact with ASP 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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93B LEU 3.2 4.7 + - - +
94B ILE* 3.7 7.4 - - - +
96B LEU* 1.3 81.6 - - - +
98B GLY* 1.3 59.9 + - - +
99B THR* 2.6 46.5 + - - +
102B LYS* 3.2 18.2 - - + +
104B LYS* 3.1 28.1 + - - +
105B LEU* 2.9 40.6 + - + +
110B ILE* 3.7 21.2 - - + +
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Residues in contact with GLY 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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94B ILE 2.9 19.1 + - - -
95B SER* 3.6 10.5 + - - -
96B LEU 3.5 0.4 - - - -
97B ASP* 1.3 73.1 - - - +
99B THR* 1.3 62.2 + - - +
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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