Contacts of the helix formed by residues 81 - 92 (chain B) in PDB entry 1IXR
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 81 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75B LEU* 3.2 9.3 - - - +
79B GLY 3.5 3.8 + - - -
80B VAL* 1.3 74.4 - - - +
82B PRO* 1.3 70.2 - - - +
83B LYS* 3.3 2.9 - - - -
84B VAL* 4.1 9.3 - - - +
85B ALA* 2.9 30.5 + - - +
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Residues in contact with PRO 82 (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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51B LEU* 3.9 18.4 - - + -
60B TYR* 3.1 46.9 - - + +
71B PHE* 3.7 15.3 - - + -
75B LEU* 3.8 11.4 - - + -
81B GLY* 1.3 80.1 - - - +
83B LYS* 1.3 57.6 + - - +
86B LEU* 2.7 41.7 + - - +
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Residues in contact with LYS 83 (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 GLY* 3.3 1.3 - - - -
82B PRO* 1.3 82.8 - - + +
84B VAL* 1.3 58.0 + - + +
86B LEU* 2.9 9.7 + - - +
87B ALA* 2.7 34.5 + - + +
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Residues in contact with VAL 84 (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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79B GLY 5.4 1.6 - - - +
80B VAL* 3.9 11.7 - - + -
81B GLY* 3.5 13.5 + - - +
83B LYS* 1.3 80.0 - - + +
85B ALA* 1.3 71.0 + - - +
87B ALA* 2.7 20.5 + - + +
88B LEU* 2.9 35.4 + - + +
114B GLY* 5.1 13.7 - - - +
119B LEU* 3.9 31.2 - - + -
123B ILE* 4.2 1.8 - - + -
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Residues in contact with ALA 85 (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 PHE* 3.9 23.3 - - + +
74B LEU* 3.6 29.6 - - + +
75B LEU* 4.4 2.5 - - + -
80B VAL* 3.8 4.9 - - + +
81B GLY 2.9 23.7 + - - +
82B PRO 3.9 2.0 - - - +
84B VAL* 1.3 73.3 - - - +
86B LEU* 1.3 64.2 + - - +
88B LEU* 3.4 14.1 + - - +
89B LEU* 2.8 24.0 + - - +
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Residues in contact with LEU 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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15B GLY 5.7 0.4 - - - +
29B GLN* 4.2 16.4 - - + +
30B ALA* 3.4 35.7 - - - +
31B PRO* 3.6 18.4 - - + -
60B TYR* 3.9 26.7 - - + -
62B PHE* 4.3 8.7 - - + -
71B PHE* 3.9 10.5 - - + -
82B PRO 2.7 27.5 + - - +
83B LYS* 3.0 10.8 - - - +
85B ALA* 1.3 73.2 - - - +
87B ALA* 1.3 49.6 + - - +
89B LEU* 2.8 8.0 + - - +
90B SER* 2.6 39.6 + - - +
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Residues in contact with ALA 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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83B LYS* 2.7 16.4 + - + +
84B VAL* 2.7 15.3 + - + +
86B LEU* 1.3 68.2 - - - +
88B LEU* 1.3 58.7 + - + +
90B SER* 2.5 31.3 + - - -
91B ALA* 2.6 15.7 + - - +
113B SER* 3.4 33.5 - - - +
114B GLY* 4.4 7.2 - - - +
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Residues in contact with LEU 88 (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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74B LEU* 3.7 28.7 - - + -
84B VAL* 2.9 42.8 + - + +
85B ALA 3.4 4.3 - - - +
87B ALA* 1.3 78.5 - - + +
89B LEU* 1.3 64.0 + - - +
91B ALA* 3.1 12.8 + - - +
92B LEU* 3.6 21.3 + - + +
97B LEU* 4.0 19.7 - - + +
101B LEU* 5.7 0.2 - - + -
109B LEU* 3.6 48.2 - - + +
112B ALA* 5.2 3.6 - - + -
113B SER 4.6 2.2 + - - +
114B GLY 6.1 0.9 - - - +
120B ALA* 6.3 0.2 - - - -
123B ILE* 4.1 10.8 - - + -
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Residues in contact with LEU 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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31B PRO* 4.1 14.8 - - + +
33B PRO* 4.2 7.8 - - - +
62B PHE* 3.9 17.0 - - + -
67B ASN* 3.3 50.8 - - + +
70B LEU* 3.9 20.6 - - + -
71B PHE* 4.6 6.1 - - - +
74B LEU* 5.9 1.3 - - + -
85B ALA 2.8 13.2 + - - +
86B LEU* 2.8 14.7 + - - +
88B LEU* 1.3 73.7 - - - +
90B SER* 1.3 62.1 + - - +
91B ALA 3.5 0.3 + - - -
92B LEU 3.7 11.1 - - - +
93B PRO* 5.6 0.3 - - - +
94B PRO* 4.9 9.2 - - + +
97B LEU* 3.2 28.3 - - + -
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Residues in contact with SER 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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30B ALA 4.4 0.5 + - - -
31B PRO* 2.9 12.4 - - - +
32B THR* 2.8 43.0 + - - +
33B PRO* 3.3 21.9 - - - +
86B LEU* 2.6 12.6 + - - +
87B ALA* 2.5 20.9 + - - -
89B LEU* 1.3 72.6 - - - +
91B ALA* 1.3 61.6 + - - +
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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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33B PRO* 5.7 0.5 - - - +
87B ALA 2.6 17.7 + - - +
88B LEU 3.1 5.2 + - - +
89B LEU 4.6 0.2 - - - +
90B SER* 1.3 78.3 - - - +
92B LEU* 1.3 64.9 + - + +
93B PRO* 3.9 3.3 - - - +
112B ALA* 3.3 35.9 - - + -
113B SER* 4.4 8.7 - - - +
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Residues in contact with LEU 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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88B LEU* 3.6 14.2 + - + +
89B LEU* 3.7 13.5 - - - +
91B ALA* 1.3 83.4 - - + +
93B PRO* 1.3 75.1 - - + +
94B PRO* 3.7 1.0 - - - +
96B LEU* 3.6 15.3 - - + +
97B LEU* 3.5 48.2 - - + +
108B LEU* 3.3 33.9 - - + +
109B LEU* 5.0 2.9 - - - +
111B SER 4.3 2.7 - - - +
112B ALA* 3.7 27.6 - - + -
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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