Contacts of the helix formed by residues 85 - 93 (chain M) in PDB entry 2X86
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 85 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83M GLU* 2.9 21.7 + - - +
84M TRP* 1.3 75.3 - - - +
86M GLY* 1.3 56.6 - - - +
87M LYS* 2.9 12.6 + - - +
88M TYR* 2.7 34.2 + - + +
89M MET* 2.9 28.1 + - - +
139M VAL* 5.1 0.4 - - - -
34N LYS* 3.2 37.8 + - - +
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Residues in contact with GLY 86 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84M TRP 3.0 8.1 + - - -
85M ASP* 1.3 70.4 - - - +
87M LYS* 1.3 61.1 + - - +
89M MET* 4.1 1.6 - - - -
90M MET* 2.8 36.2 + - - +
139M VAL* 4.1 15.5 - - - -
33N LEU* 2.9 25.7 + - - -
34N LYS 3.2 1.0 + - - -
36N GLY* 4.0 10.1 - - - -
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Residues in contact with LYS 87 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85M ASP* 2.9 8.9 + - - +
86M GLY* 1.3 76.5 - - - +
88M TYR* 1.3 63.8 + - - +
90M MET* 3.9 2.5 - - - +
91M ASP* 3.0 44.8 + - - +
32N ASN* 4.3 10.8 - - - +
33N LEU* 3.2 10.6 + - - +
34N LYS* 3.8 24.2 - - + +
52N ASP* 3.6 35.2 + - + +
54N GLU* 5.4 4.7 - - - +
55N ASP* 5.7 0.4 + - - -
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Residues in contact with TYR 88 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53M LYS* 3.0 25.9 + - - -
78M CYS* 3.6 30.1 - - + -
83M GLU* 4.6 14.6 - - + -
85M ASP* 2.7 29.7 + - - +
87M LYS* 1.3 74.1 - - - +
89M MET* 1.3 65.2 + - - +
91M ASP* 3.1 7.1 + - + +
92M ASN* 2.8 52.1 + - + +
400M NAP 3.2 17.2 + - - -
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Residues in contact with MET 89 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78M CYS* 3.9 15.9 - - - +
80M SER 3.9 10.1 - - - +
83M GLU* 3.4 49.1 - - + +
85M ASP 2.9 14.7 + - - +
86M GLY* 3.3 8.7 + - - +
88M TYR* 1.3 80.8 - - - +
90M MET* 1.3 58.4 + - + +
92M ASN* 5.0 0.4 - - - -
93M ASN* 2.9 60.9 + - - +
139M VAL* 3.8 14.1 - - + +
140M PHE* 3.9 15.7 - - - +
143M SER* 3.6 20.0 - - - +
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Residues in contact with MET 90 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86M GLY* 2.8 24.1 + - - +
87M LYS* 4.1 3.1 - - - +
89M MET* 1.3 73.0 - - + +
91M ASP* 1.3 57.3 + - - +
94M TYR* 3.2 29.0 + - + +
95M GLN* 2.8 29.2 + - - +
139M VAL* 5.0 4.7 - - + -
142M TYR* 4.1 20.4 - - + -
143M SER* 3.9 22.9 - - - -
146M LEU* 3.7 33.0 - - + -
33N LEU* 3.6 20.4 - - + -
50N TYR* 4.1 28.7 - - + -
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Residues in contact with ASP 91 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87M LYS* 3.0 41.7 + - - +
88M TYR* 3.7 6.5 - - + +
90M MET* 1.3 78.4 - - - +
92M ASN* 1.3 58.9 + - + +
95M GLN* 3.3 18.0 - - - +
96M TYR* 2.9 32.2 + - - +
52N ASP* 5.1 4.9 - - - +
55N ASP* 4.1 15.9 - - - +
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Residues in contact with ASN 92 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53M LYS* 2.8 30.0 + - - +
74M HIS* 5.7 0.5 + - - -
76M GLY 5.1 0.5 - - - +
77M ALA* 4.9 0.9 - - - -
78M CYS* 3.2 8.1 - - - +
88M TYR* 2.8 47.1 + - + +
89M MET 4.4 0.4 - - - +
91M ASP* 1.3 76.5 - - + +
93M ASN* 1.3 71.7 + - - +
96M TYR* 3.0 22.9 - - - +
400M NAP 2.8 37.3 + - - -
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Residues in contact with ASN 93 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74M HIS* 6.2 0.2 - - - -
77M ALA* 3.4 12.3 - - + +
78M CYS* 2.8 46.6 + - - +
89M MET* 2.9 28.5 + - - +
92M ASN* 1.3 84.3 + - - +
94M TYR* 1.3 63.2 + - - +
97M SER* 2.8 33.3 + - - -
140M PHE* 4.0 8.3 - - - -
143M SER* 3.2 28.4 + - - +
144M LYS* 4.6 7.6 - - + +
147M PHE* 6.0 0.4 - - - -
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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