Contacts of the helix formed by residues 81 - 96 (chain B) in PDB entry 2A8L
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 LEU 81 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76B LEU* 4.9 0.2 - - - -
79B GLY 5.9 0.7 - - - +
80B ALA* 1.3 77.5 - - - +
82B ALA* 1.3 65.5 + - - +
83B THR* 4.0 14.4 - - - +
84B ASP* 2.9 36.4 + - - +
85B ALA* 3.0 12.1 + - - +
123B LYS* 6.3 4.5 - - + -
148B CYS* 5.7 6.5 - - - -
151B GLN* 5.8 4.5 - - - +
241B ASP* 5.6 0.9 - - - -
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Residues in contact with ALA 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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76B LEU* 4.4 12.3 - - - +
80B ALA 3.8 1.6 + - - -
81B LEU* 1.3 72.2 - - - +
83B THR* 1.3 57.4 + - - +
85B ALA* 3.4 2.6 + - - +
86B VAL* 3.0 29.6 + - - +
121B ASP* 5.1 3.8 - - - +
239B VAL* 4.2 10.6 - - + +
241B ASP* 4.2 15.5 + - + +
245B ASN* 3.8 25.6 - - + +
246B VAL 4.4 4.3 - - - +
247B ALA* 3.7 17.6 - - + +
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Residues in contact with THR 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B LEU* 4.0 15.6 - - - +
82B ALA* 1.3 74.4 - - - +
84B ASP* 1.3 60.7 + - - +
86B VAL* 3.1 9.2 - - - +
87B THR* 2.7 37.7 + - - -
119B ILE* 4.0 11.7 - - + -
120B MET 4.4 0.2 - - - +
121B ASP* 3.3 42.1 + - + +
144B ASN* 4.0 10.0 + - - -
147B LEU* 4.3 17.6 - - + +
148B CYS* 5.2 3.1 - - - -
151B GLN* 5.3 2.1 + - - +
247B ALA* 4.0 10.1 - - + -
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Residues in contact with ASP 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B LYS* 4.3 11.6 - - + +
80B ALA* 4.4 8.5 - - + +
81B LEU* 2.9 46.7 + - - +
83B THR* 1.3 79.5 + - - +
85B ALA* 1.3 58.3 + - - +
87B THR* 3.3 6.6 + - - +
88B ALA* 2.9 27.8 + - - +
144B ASN* 3.7 18.4 + - - +
148B CYS* 4.7 6.9 - - - -
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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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72B ALA* 3.5 34.8 - - - +
75B LYS* 3.6 19.9 - - + +
76B LEU* 3.7 23.6 - - + -
81B LEU 3.0 6.6 + - - +
82B ALA 3.7 6.5 - - - +
84B ASP* 1.3 75.8 - - - +
86B VAL* 1.3 63.5 + - - +
88B ALA* 3.3 3.1 + - - +
89B ALA 3.1 17.3 + - - -
239B VAL* 4.4 5.6 - - + -
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Residues in contact with VAL 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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82B ALA 3.0 15.8 + - - +
83B THR* 3.1 16.4 - - - +
85B ALA* 1.3 77.4 - - - +
87B THR* 1.3 65.1 + - - +
89B ALA* 3.3 3.8 + - - +
90B LEU* 3.0 31.3 + - - +
119B ILE* 3.6 22.2 - - + -
237B ALA* 3.3 40.8 - - + +
238B VAL* 4.1 2.2 - - - +
239B VAL* 3.9 15.8 - - + +
247B ALA* 4.1 9.0 - - + -
248B ALA* 4.1 4.9 - - - +
249B ALA* 3.8 12.3 - - + +
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Residues in contact with THR 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 THR 2.7 22.0 + - - -
84B ASP* 3.4 6.7 - - - +
86B VAL* 1.3 77.0 - - - +
88B ALA* 1.3 66.0 + - - +
90B LEU* 3.2 7.5 + - - +
91B VAL* 2.9 34.1 + - + +
119B ILE* 3.4 7.3 - - - +
140B VAL* 4.5 8.8 - - + +
141B SER* 4.4 14.4 - - - +
144B ASN* 3.1 41.6 - - + +
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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
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71B LYS* 4.2 19.2 - - + +
75B LYS* 3.5 33.4 - - + -
84B ASP 2.9 17.4 + - - +
85B ALA 3.3 6.5 + - - +
87B THR* 1.3 77.8 - - - +
89B ALA* 1.3 62.1 + - - +
91B VAL* 3.3 9.9 + - - +
92B GLU* 3.3 20.6 + - - +
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Residues in contact with ALA 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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44B VAL* 4.8 0.4 - - + -
46B VAL* 4.2 9.6 - - + -
68B ALA* 3.5 29.4 + - - +
71B LYS* 4.7 0.2 - - - +
72B ALA* 4.0 8.1 - - + -
85B ALA 3.1 12.9 + - - +
86B VAL* 3.5 9.6 - - - +
88B ALA* 1.3 77.0 - - - +
90B LEU* 1.3 61.9 - - - +
92B GLU 3.3 2.1 + - - -
93B LEU* 3.0 26.9 + - - +
237B ALA* 4.0 19.5 - - + -
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Residues in contact with LEU 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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86B VAL* 3.0 24.8 + - + +
87B THR 3.7 7.2 - - - +
89B ALA* 1.3 73.6 - - - +
91B VAL* 1.3 58.1 + - - +
93B LEU* 3.7 3.9 - - + +
94B GLU* 2.8 41.2 + - - +
140B VAL* 3.7 19.7 - - + -
235B VAL* 3.6 40.8 - - + +
236B GLY* 3.9 5.8 - - - +
237B ALA* 3.4 31.9 - - + +
249B ALA* 3.8 22.7 - - + -
250B VAL 4.3 0.7 - - - -
251B SER* 4.1 14.6 - - - +
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Residues in contact with VAL 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B THR* 2.9 25.7 + - + +
88B ALA* 3.5 11.2 - - - +
89B ALA 3.3 0.2 - - - -
90B LEU* 1.3 76.5 - - - +
92B GLU* 1.3 59.2 + - - +
94B GLU* 3.4 1.7 + - - -
95B ASP* 2.9 46.0 + - - +
138B ASN* 3.5 26.2 + - - +
140B VAL* 4.0 7.6 - - + -
141B SER* 3.8 22.7 - - - +
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Residues in contact with GLU 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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64B VAL* 3.6 5.7 - - - +
67B ARG* 3.0 56.3 + - + +
68B ALA* 3.6 18.2 - - + +
71B LYS* 3.3 27.3 - - + +
88B ALA 3.3 7.2 + - - +
89B ALA 3.3 9.1 + - - +
90B LEU 3.2 0.4 - - - -
91B VAL* 1.3 81.7 - - - +
93B LEU* 1.3 62.3 + - - +
95B ASP* 3.2 20.3 + - - +
96B SER 3.4 8.8 + - - -
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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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46B VAL* 3.9 12.1 - - + -
47B HIS 4.1 14.6 - - - +
48B ALA* 4.4 12.6 - - + -
64B VAL* 3.6 20.0 - - + +
65B CYS* 4.2 11.7 - - - -
68B ALA* 3.6 15.7 - - + -
89B ALA 3.0 25.8 + - - +
90B LEU* 3.7 7.9 - - + +
92B GLU* 1.3 76.0 - - - +
94B GLU* 1.3 55.8 + - - +
96B SER* 3.4 6.2 + - - -
99B THR* 2.6 32.1 + - - +
235B VAL* 3.8 15.5 - - + -
236B GLY 3.6 31.9 - - - +
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Residues in contact with GLU 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 LEU 2.8 25.8 + - - +
91B VAL 3.7 2.2 - - - +
93B LEU* 1.3 71.9 - - - +
95B ASP* 1.3 63.4 + - - +
96B SER 3.2 2.4 + - - +
99B THR* 4.0 0.9 - - - -
101B ALA* 3.0 32.3 - - + +
102B GLY* 4.1 5.6 - - - -
103B MET 3.3 14.8 + - - +
137B LYS 5.0 0.2 - - - +
138B ASN* 3.0 34.4 + - - +
139B PRO* 3.4 12.5 - - - +
140B VAL* 3.0 36.9 + - - +
235B VAL* 4.5 1.8 - - + +
251B SER* 2.6 35.7 + - - +
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Residues in contact with ASP 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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67B ARG* 5.5 0.9 - - - -
91B VAL* 2.9 31.1 + - - +
92B GLU* 3.2 14.5 + - - +
94B GLU* 1.3 75.1 - - - +
96B SER* 1.3 63.8 + - - +
97B PRO* 3.3 8.3 - - - +
103B MET* 3.6 28.8 - - + +
137B LYS* 3.6 26.6 + - - +
138B ASN* 3.0 21.1 + - - +
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Residues in contact with SER 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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60B GLU 5.2 0.9 + - - -
64B VAL* 3.6 36.0 - - - +
67B ARG* 4.1 10.9 + - - +
92B GLU 3.4 4.9 + - - -
93B LEU 3.7 5.8 - - - -
94B GLU 3.1 1.8 - - - +
95B ASP* 1.3 75.6 - - - +
97B PRO* 1.3 69.1 - - - +
98B PHE* 3.0 26.6 + - - +
99B THR* 3.0 23.5 + - - +
103B MET 3.3 10.0 - - - +
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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