Contacts of the helix formed by residues 75 - 89 (chain B) in PDB entry 2O07
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 75 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211A TRP* 3.5 28.2 - - + -
59B TYR* 4.0 2.9 - - + -
71B CYS* 5.4 0.5 - - - -
72B THR* 2.9 21.9 + - - +
74B ARG* 1.3 81.4 - - + +
76B GLU* 1.4 69.6 + - - +
77B PHE* 3.0 5.7 + - - -
78B SER* 3.0 21.5 + - - -
238B ILE* 3.6 13.4 - - - +
239B PRO* 3.4 11.1 - - + +
240B THR* 2.8 46.3 + - - +
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Residues in contact with GLU 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B CYS* 4.1 8.3 - - + -
72B THR 3.0 22.1 + - - +
73B GLU* 3.9 15.5 - - - +
74B ARG 3.8 0.4 - - - -
75B ASP* 1.4 79.6 + - - +
77B PHE* 1.3 75.3 + - - +
78B SER 3.1 0.9 + - - -
79B TYR* 3.4 3.1 + - - +
80B GLN* 2.8 43.9 + - - +
109B ARG* 2.9 43.8 + - - -
139B GLY* 4.7 1.7 - - - +
140B MET* 3.6 30.3 - - + +
238B ILE* 4.6 5.8 - - - -
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Residues in contact with PHE 77 (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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211A TRP* 3.4 33.0 - + - -
293A PHE* 3.7 18.4 - + + -
73B GLU 5.2 2.2 - - - -
74B ARG 3.2 27.8 - - - -
75B ASP* 3.0 2.6 + - - -
76B GLU* 1.3 94.8 + - - +
78B SER* 1.3 71.3 + - - +
81B GLU* 3.0 39.3 + - - +
109B ARG* 4.4 8.5 - - - +
277B LYS* 3.4 60.1 - - + +
278B TYR* 3.8 9.6 - - + -
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Residues in contact with SER 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A TRP* 3.9 7.3 - - - -
75B ASP 3.0 14.9 + - - -
77B PHE* 1.3 81.1 - - - +
79B TYR* 1.3 61.6 + - - +
81B GLU* 4.0 0.7 - - - +
82B MET* 3.0 36.3 + - - +
236B CYS* 4.3 2.2 - - - -
237B THR 3.2 21.0 + - - -
238B ILE* 3.3 10.4 - - - +
278B TYR* 3.2 39.5 - - - -
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Residues in contact with TYR 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B GLU 3.4 3.7 + - - +
78B SER* 1.3 79.4 + - - +
80B GLN* 1.3 80.2 + - - +
82B MET* 3.3 0.3 + - - +
83B ILE* 2.9 57.1 + - + +
173B ASP* 2.8 32.2 + - - -
206B GLN* 3.4 29.6 - - + +
236B CYS* 4.0 10.5 - - - -
238B ILE* 3.6 21.8 - - + -
241B TYR* 3.6 23.6 - + + +
246B ILE* 3.7 16.4 - - + -
248B PHE* 3.7 21.7 - + - -
601B SPD 3.5 14.5 + - - -
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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
----------------------------------------------------------
71B CYS* 5.0 0.8 - - - +
76B GLU* 2.8 57.0 + - - +
77B PHE 4.3 0.4 - - - +
79B TYR* 1.3 91.9 - - - +
81B GLU* 1.3 64.0 + - - +
83B ILE* 3.7 6.0 - - - +
84B ALA* 3.3 25.3 + - - +
104B ASP* 3.9 1.4 - - - +
106B GLY* 3.3 32.1 - - - -
107B VAL* 3.5 10.1 - - - +
109B ARG* 3.6 16.6 - - - +
110B GLU* 3.5 8.0 - - + +
140B MET* 3.5 10.1 - - - +
241B TYR* 5.5 0.4 + - - -
601B SPD 2.9 29.5 + - - -
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Residues in contact with GLU 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B PHE* 3.0 34.6 + - - +
78B SER 4.0 1.8 - - - +
80B GLN* 1.3 77.9 - - - +
82B MET* 1.3 58.5 + - - +
85B ASN* 2.9 38.6 + - - +
110B GLU* 3.6 31.9 - - - +
113B LYS* 5.3 0.7 + - - -
275B GLN 4.2 2.8 - - - +
276B LEU* 3.5 16.2 - - + +
277B LYS* 2.8 24.2 + - - +
278B TYR* 2.8 23.9 + - + -
279B TYR* 2.9 21.6 + - + +
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Residues in contact with MET 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B SER 3.0 26.0 + - - +
79B TYR 3.9 0.9 - - - +
81B GLU* 1.3 75.5 - - - +
83B ILE* 1.3 66.3 + - - +
86B LEU* 2.9 50.5 + - + +
235B TYR 4.0 11.4 - - - +
236B CYS* 3.7 5.8 - - + -
248B PHE* 3.8 17.5 - - + -
278B TYR* 3.4 36.1 - - + -
279B TYR* 3.6 25.1 - - + -
283B VAL* 4.0 10.5 - - + +
287B ALA* 3.6 30.5 - - + -
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Residues in contact with ILE 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B TYR* 2.9 48.1 + - + +
80B GLN* 3.7 2.0 - - - +
82B MET* 1.3 77.7 - - - +
84B ALA* 1.3 61.0 + - - +
87B PRO* 3.0 23.7 - - - +
107B VAL* 3.4 31.9 - - + -
171B ILE* 3.7 20.8 - - + +
172B THR 3.6 20.9 - - - +
173B ASP* 4.0 4.0 - - - -
204B CYS* 3.8 21.1 - - - +
206B GLN 4.1 8.3 - - - +
248B PHE* 3.6 16.9 - - + -
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Residues in contact with ALA 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 3.3 16.4 + - - +
81B GLU 4.1 0.7 - - - +
82B MET 3.1 0.6 - - - -
83B ILE* 1.3 81.9 - - - +
85B ASN* 1.3 63.2 + - - +
86B LEU 3.5 0.2 - - - -
87B PRO* 3.3 5.0 - - - +
88B LEU* 3.2 34.9 + - + +
107B VAL* 4.3 5.2 - - + +
110B GLU* 3.6 23.3 - - + -
111B VAL* 3.9 19.7 - - + +
171B ILE* 4.0 9.1 - - - +
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Residues in contact with ASN 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B GLU* 2.9 30.7 + - - +
84B ALA* 1.3 79.0 - - - +
86B LEU* 1.3 66.4 + - - +
88B LEU* 4.4 1.8 - - - +
89B CYS* 2.9 36.2 + - - +
110B GLU* 4.5 5.9 - - - +
114B HIS* 2.7 40.3 + - - -
266B LEU* 4.5 2.4 - - - +
274B MET* 3.9 9.7 - - - +
276B LEU* 4.3 13.3 - - - +
279B TYR* 3.6 31.2 + - + -
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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
----------------------------------------------------------
82B MET* 2.9 51.9 + - + +
85B ASN* 1.3 78.6 - - - +
87B PRO* 1.4 64.2 - - + +
90B SER* 2.9 26.3 + - - -
204B CYS* 5.0 0.4 - - - -
234B ALA* 4.1 11.0 - - + -
248B PHE* 3.6 36.3 - - + -
250B LEU* 4.1 14.4 - - + -
279B TYR* 4.1 1.9 - - + -
284B HIS* 3.6 29.6 + - + +
287B ALA* 4.5 1.3 - - + -
288B PHE* 3.9 23.3 - - + -
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Residues in contact with PRO 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 ILE 3.0 29.2 - - - +
84B ALA 3.3 11.0 - - - +
86B LEU* 1.4 91.2 - - + +
88B LEU* 1.3 63.3 + - - +
90B SER* 3.0 15.5 + - - -
91B HIS* 3.4 8.5 + - - +
169B VAL* 3.9 16.4 - - + -
171B ILE* 3.8 12.6 - - + -
202B VAL* 3.7 22.7 - - + +
204B CYS* 3.4 29.6 - - + +
250B LEU* 4.0 8.0 - - + -
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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 ALA 3.2 25.7 + - - +
85B ASN 4.4 0.2 - - - +
87B PRO* 1.3 76.4 - - + +
89B CYS* 1.3 58.1 + - - +
91B HIS 3.2 12.5 + - - +
94B PRO* 3.6 31.2 - - + +
97B VAL* 3.8 23.3 - - + -
111B VAL* 3.8 32.8 - - + -
114B HIS* 3.6 42.4 - - + +
117B VAL* 4.1 5.4 - - + -
169B VAL* 4.0 12.6 - - + -
171B ILE* 5.1 0.4 - - + -
264B GLN* 3.0 21.0 + - - -
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Residues in contact with CYS 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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85B ASN* 2.9 26.2 + - - +
88B LEU* 1.3 76.8 - - - +
90B SER* 1.3 58.4 + - - +
91B HIS 3.4 2.0 - - - -
114B HIS* 3.9 20.4 - - - -
262B PRO* 3.6 3.8 - - + +
263B VAL 3.2 6.2 + - - -
264B GLN* 2.9 54.0 + - - +
266B LEU* 4.0 17.9 - - - -
279B TYR* 3.2 24.0 - - - +
284B HIS* 4.3 4.0 - - + -
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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