Contacts of the helix formed by residues 80 - 91 (chain B) in PDB entry 3AP3
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 80 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B A3P 2.5 36.6 + - - -
78B ARG 3.5 1.4 - - - -
79B SER* 1.3 73.7 - - - +
81B THR* 1.3 57.6 + - - -
82B THR 3.2 3.1 - - - -
83B LEU* 3.2 7.6 + - - +
84B MET* 2.9 27.0 + - - +
181B MET* 3.8 5.5 - - - +
238B TYR* 3.8 16.7 - - - -
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Residues in contact with THR 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B A3P 2.5 36.4 + - - +
73B VAL* 4.1 2.1 - - + +
74B GLY* 3.5 33.9 - - - +
75B GLY* 4.3 10.8 - - - +
76B VAL 4.8 1.1 - - - +
77B PRO* 5.0 1.6 - - - +
79B SER* 3.3 4.0 - - - -
80B GLY* 1.3 72.6 - - - +
82B THR* 1.3 53.3 + - - -
84B MET* 3.3 2.4 + - - +
85B ARG* 2.9 31.2 + - - +
158B LYS* 3.8 28.4 + - - +
160B PRO* 4.7 8.5 - - + +
181B MET* 3.6 22.2 - - + -
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Residues in contact with THR 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B A3P 2.2 31.9 + - - -
78B ARG* 5.8 0.2 + - - -
81B THR* 1.3 71.8 + - - +
83B LEU* 1.3 58.3 + - - +
85B ARG* 3.4 21.3 - - - +
86B ALA* 2.7 38.8 + - - +
158B LYS* 3.6 12.6 + - - +
279B LEU* 5.2 2.2 - - + -
283B GLU* 4.5 15.1 + - + +
289B VAL* 3.2 33.7 - - + -
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Residues in contact with LEU 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B A3P 3.9 39.2 - - + +
80B GLY* 3.2 11.7 + - - +
82B THR* 1.3 78.2 - - - +
84B MET* 1.3 65.6 + - - +
86B ALA* 2.9 7.2 + - - +
87B MET* 2.9 40.8 + - + +
238B TYR* 4.4 9.2 - - + -
241B LEU* 4.0 19.3 - - + -
242B VAL* 3.8 29.8 - - + -
267B HIS* 4.0 24.7 - - + +
289B VAL* 3.8 6.6 - - - +
293B VAL* 4.7 7.0 - - + -
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Residues in contact with MET 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B VAL* 4.1 13.5 - - + -
80B GLY 2.9 9.7 + - - +
81B THR* 3.4 9.4 - - - +
83B LEU* 1.3 78.2 - - - +
85B ARG* 1.3 63.1 + - - +
87B MET* 3.3 12.4 + - + +
88B LEU* 3.2 37.1 + - + +
179B LEU* 4.1 19.1 - - + -
181B MET* 3.3 37.2 - - + +
236B VAL* 4.0 11.2 - - - -
241B LEU* 3.9 15.5 - - + +
249B LEU* 4.5 13.2 - - + -
252B ILE* 4.4 14.8 - - + -
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Residues in contact with ARG 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B VAL* 4.4 3.4 - - + -
81B THR 2.9 15.6 + - - +
82B THR* 3.4 19.9 + - - +
84B MET* 1.3 74.1 - - - +
86B ALA* 1.3 63.3 + - - +
88B LEU* 2.8 13.6 + - - +
89B ASP* 2.8 51.2 + - - +
96B CYS* 4.0 16.4 - - - -
97B GLY 2.9 27.1 + - - -
98B GLU* 3.7 10.1 - - - +
158B LYS* 4.0 27.0 - - + +
277B VAL* 3.6 15.8 - - - +
278B SER 2.7 30.3 + - - -
279B LEU* 3.7 20.1 - - - +
280B SER 4.8 0.2 - - - +
283B GLU* 4.6 9.1 + - - -
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Residues in contact with ALA 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 THR* 2.7 24.3 + - + +
83B LEU* 3.3 5.4 - - - +
85B ARG* 1.3 77.7 - - - +
87B MET* 1.3 63.2 + - - +
89B ASP 3.4 0.3 + - - -
90B ALA* 3.3 5.4 + - - +
267B HIS* 4.1 13.6 - - + +
277B VAL* 3.1 44.2 - - + +
279B LEU* 5.0 0.9 - - + -
289B VAL* 3.8 24.5 - - + -
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Residues in contact with MET 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 LEU* 2.9 33.2 + - + +
84B MET* 3.7 8.7 - - + +
86B ALA* 1.3 73.8 - - - +
88B LEU* 1.3 65.0 + - - +
90B ALA* 3.5 14.0 - - - +
91B HIS 3.8 0.5 + - - -
241B LEU* 3.3 36.3 - - + -
245B PRO* 5.3 2.0 - - - -
249B LEU* 3.8 26.0 - - + -
264B VAL* 3.5 38.7 - - - +
265B LEU* 5.3 1.8 - - - -
267B HIS* 3.5 25.4 - - + +
293B VAL* 4.1 23.6 - - + -
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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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71B ILE* 4.5 11.2 - - + -
73B VAL* 3.8 29.4 - - + -
84B MET* 3.2 31.1 + - + +
85B ARG* 2.8 8.6 + - - +
87B MET* 1.3 77.1 - - - +
89B ASP* 1.3 64.9 + - - +
91B HIS* 3.1 24.6 + - - +
94B VAL* 3.3 19.5 - - + +
96B CYS* 3.9 15.7 - - - -
179B LEU* 3.9 16.4 - - + -
249B LEU* 4.9 9.2 - - + -
252B ILE* 5.0 3.8 - - + -
253B LEU* 5.6 7.4 - - + -
256B LEU* 4.7 16.6 - - + -
258B ILE* 6.0 0.4 - - + -
264B VAL* 5.2 2.0 - - + -
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Residues in contact with ASP 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B ARG* 2.8 26.1 + - - +
86B ALA 3.7 8.7 - - - +
88B LEU* 1.3 75.5 - - - +
90B ALA* 1.3 57.6 + - - +
91B HIS 2.9 16.1 - - - +
94B VAL 3.2 8.5 - - - +
95B ARG* 3.2 27.8 - - - +
96B CYS* 3.4 11.8 + - - +
97B GLY* 2.8 24.1 + - - -
275B GLY 3.0 13.2 - - - +
276B GLY* 2.9 29.8 - - - +
277B VAL* 3.7 11.2 - - + -
278B SER* 4.3 1.9 + - - -
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Residues in contact with ALA 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 ALA 3.3 10.4 + - - +
87B MET 3.5 13.9 - - - +
89B ASP* 1.3 76.3 - - - +
91B HIS* 1.3 65.9 + - - +
92B PRO* 3.3 5.4 - - - +
263B ALA* 3.8 25.4 - - - +
267B HIS* 4.1 10.3 - - + -
270B LEU* 3.6 28.0 - - + +
275B GLY 4.0 4.0 - - - +
276B GLY* 4.0 3.2 - - - -
277B VAL* 3.7 12.3 - - + +
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Residues in contact with HIS 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B MET 3.8 4.2 + - - +
88B LEU* 3.1 18.4 + - + +
89B ASP 2.9 14.7 - - - +
90B ALA* 1.3 76.4 - - - +
92B PRO* 1.3 67.5 - - + +
93B GLU* 3.2 51.9 + - + +
94B VAL* 3.1 25.6 - - + +
253B LEU* 4.0 17.9 - - + -
258B ILE* 3.8 7.9 - - + +
259B ALA 2.8 23.8 + - - -
261B SER* 3.5 27.8 - - - -
263B ALA* 4.8 3.1 - - - +
264B VAL* 4.4 13.8 - - + +
275B GLY 3.0 4.5 - - - +
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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
------------------------------------------------------------
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