Contacts of the helix formed by residues 77 - 88 (chain B) in PDB entry 2AY6
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 PRO 77 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72B GLY* 6.2 0.2 - - - -
75B GLY 4.1 3.6 - - - +
76B GLU* 1.3 87.9 - - + +
78B GLU* 1.3 70.6 + - + +
80B GLN* 3.3 16.0 + - - +
81B LYS* 2.9 31.6 + - - +
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Residues in contact with GLU 78 (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 GLU* 3.5 23.8 - - - +
77B PRO* 1.3 98.3 - - + +
79B PHE* 1.3 56.5 + - - +
81B LYS* 3.2 6.1 + - - +
82B ALA* 2.8 32.1 + - - +
300B PHE* 5.7 0.5 - - - -
304B LYS* 5.0 12.1 - - - +
307B SER* 3.1 22.3 + - - +
311B THR* 5.2 8.5 - - + +
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Residues in contact with PHE 79 (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 GLU* 3.1 18.8 + - + +
78B GLU* 1.3 80.1 - - - +
80B GLN* 1.3 64.9 + - + +
82B ALA* 3.9 1.7 - - - +
83B MET* 2.9 57.5 + - + +
104B ALA* 3.9 21.1 - - + -
256B CYS* 4.5 1.1 - - - -
267B THR* 4.2 9.9 - - - -
268B GLY* 3.7 24.2 - - - -
269B CYS* 3.7 23.1 - - + -
303B ALA* 3.4 45.5 - - + +
306B VAL* 4.1 18.4 - - + -
307B SER* 3.9 9.5 + - - -
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Residues in contact with GLN 80 (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 SER* 3.2 29.8 + - - +
75B GLY 4.3 6.6 + - - +
76B GLU 2.9 13.7 + - - +
77B PRO* 3.5 22.5 - - - +
79B PHE* 1.3 82.9 - - + +
81B LYS* 1.3 62.0 + - - +
83B MET* 4.0 1.7 - - - +
84B GLY* 3.2 19.8 + - - -
95B LEU* 5.5 0.5 - - - +
102B THR* 3.0 62.7 + - + +
284B GLN* 4.7 4.6 + - - -
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Residues in contact with LYS 81 (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 PRO 2.9 17.4 + - - +
78B GLU* 3.6 5.4 - - - +
80B GLN* 1.3 73.4 - - - +
82B ALA* 1.3 66.9 + - - +
83B MET 3.2 0.5 + - - -
84B GLY* 3.2 2.1 + - - -
85B GLU* 2.7 59.0 + - + +
95B LEU* 4.4 8.4 - - + +
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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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78B GLU 2.8 21.6 + - - +
79B PHE* 3.9 4.9 - - - +
81B LYS* 1.3 72.6 - - - +
83B MET* 1.3 58.2 + - + +
85B GLU* 3.9 7.2 - - - +
86B LEU* 2.9 28.4 + - - +
306B VAL* 5.6 0.4 - - + -
307B SER* 4.7 6.3 - - - -
310B LEU* 3.8 35.4 - - + +
311B THR* 4.4 13.9 - - + +
316B ARG* 5.3 1.4 + - - -
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Residues in contact with MET 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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79B PHE* 2.9 44.6 + - + +
80B GLN 4.0 3.4 - - - +
82B ALA* 1.3 74.6 - - - +
84B GLY* 1.3 65.9 + - - +
86B LEU* 3.2 23.6 + - + +
87B ILE* 3.0 38.4 + - + +
254B ALA* 4.0 27.1 - - + -
255B SER 5.5 0.9 - - - +
256B CYS* 3.6 31.2 - - - -
269B CYS* 3.9 22.0 - - - +
271B LEU* 5.1 0.7 - - + -
306B VAL* 4.1 12.6 - - + -
310B LEU* 4.6 1.1 - - - -
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Residues in contact with GLY 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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80B GLN 3.2 12.9 + - - -
81B LYS 3.2 2.6 + - - -
83B MET* 1.3 78.4 - - - +
85B GLU* 1.3 56.7 + - - +
88B LEU* 2.9 34.7 + - - +
95B LEU* 3.7 26.5 - - - +
102B THR* 5.9 0.2 - - - -
271B LEU* 4.6 17.2 - - - +
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Residues in contact with GLU 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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81B LYS* 2.7 52.9 + - - +
82B ALA* 3.9 6.2 - - - +
84B GLY* 1.3 73.2 - - - +
86B LEU* 1.3 67.0 + - - +
89B GLY* 2.9 35.4 + - - +
95B LEU* 3.8 14.6 - - + +
241B ARG* 4.1 0.7 + - - -
316B ARG* 5.5 7.0 + - - +
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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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82B ALA 2.9 19.5 + - - +
83B MET* 3.2 31.2 + - + +
85B GLU* 1.3 75.4 - - - +
87B ILE* 1.3 58.6 + - + +
226B GLN* 3.4 31.5 + - - +
233B LEU* 4.5 9.2 - - + -
234B GLU* 4.9 2.6 - - - +
241B ARG* 2.9 21.7 + - - -
259B ASN* 4.6 9.4 - - - +
260B PHE* 4.3 15.7 - - + -
310B LEU* 4.2 16.2 - - + -
316B ARG* 4.8 18.6 - - - +
319B TRP* 4.3 21.8 - - + -
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Residues in contact with ILE 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 MET* 3.0 25.8 + - + +
84B GLY 4.2 0.2 - - - +
86B LEU* 1.3 80.0 - - + +
88B LEU* 1.3 65.4 - - + +
223B LEU* 3.7 26.7 - - + -
226B GLN* 4.0 11.0 - - - +
237B ALA* 3.4 10.0 - - - +
240B THR* 4.4 5.6 - - + -
241B ARG* 2.7 27.9 + - - +
252B ILE* 4.2 13.0 - - + -
254B ALA* 3.5 29.8 - - + -
269B CYS* 5.0 0.2 - - - -
271B LEU* 3.3 33.0 - - + -
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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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84B GLY 2.9 15.0 + - - +
87B ILE* 1.3 81.4 - - + +
89B GLY* 1.3 64.5 + - - +
90B ASP 3.3 0.3 + - - -
91B GLY* 3.0 19.1 + - - +
95B LEU* 3.6 38.1 - - + +
100B THR* 5.1 1.8 - - + +
240B THR* 4.7 6.3 - - + +
241B ARG* 3.3 24.0 + - - +
244B ALA* 3.7 29.2 - - + -
252B ILE* 3.8 16.8 - - + -
271B LEU* 4.4 14.4 - - + -
273B LEU* 4.0 22.7 - - + -
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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