Contacts of the helix formed by residues 85 - 93 (chain O) 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 O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34K LYS* 3.3 37.0 + - + +
83O GLU* 2.9 21.9 + - - +
84O TRP* 1.3 73.5 - - - +
86O GLY* 1.3 59.3 + - - +
87O LYS* 2.9 12.3 + - - +
88O TYR* 2.7 33.9 + - + +
89O MET* 2.9 28.0 + - - +
139O VAL* 5.1 0.7 - - - -
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Residues in contact with GLY 86 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33K LEU* 2.9 25.8 + - - -
34K LYS 3.3 0.8 + - - -
36K GLY* 4.1 1.6 - - - -
84O TRP 3.0 8.9 + - - -
85O ASP* 1.3 70.0 + - - +
87O LYS* 1.3 60.5 + - - +
89O MET* 4.1 0.9 - - - -
90O MET* 2.8 36.4 + - - +
139O VAL* 4.1 24.7 - - - -
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Residues in contact with LYS 87 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32K ASN* 4.3 9.4 - - - +
33K LEU* 3.3 9.8 + - - +
34K LYS* 3.9 23.3 - - + +
50K TYR* 6.5 0.2 - - - -
52K ASP* 3.6 37.3 + - + +
54K GLU* 5.4 4.7 - - - +
55K ASP* 5.6 0.6 + - - -
85O ASP* 2.9 8.8 + - - +
86O GLY* 1.3 78.4 - - - +
88O TYR* 1.3 62.9 + - - +
90O MET* 3.5 2.5 + - - +
91O ASP* 3.0 44.8 + - - +
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Residues in contact with TYR 88 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53O LYS* 3.0 26.3 + - - -
78O CYS* 3.6 29.6 - - + -
83O GLU* 4.6 14.6 - - + -
85O ASP* 2.7 29.1 + - - +
87O LYS* 1.3 74.1 - - - +
89O MET* 1.3 66.7 + - - +
91O ASP* 3.1 6.3 + - + +
92O ASN* 2.8 52.7 + - + +
400O NAP 3.4 15.1 + - - -
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Residues in contact with MET 89 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78O CYS* 3.9 16.2 - - - +
80O SER 3.9 11.0 - - - +
83O GLU* 3.4 48.0 - - + +
85O ASP 2.9 14.7 + - - +
86O GLY* 3.3 9.4 + - - +
88O TYR* 1.3 80.6 - - - +
90O MET* 1.3 57.5 + - - +
92O ASN* 5.0 0.4 - - - -
93O ASN* 2.9 60.7 + - - +
139O VAL* 3.8 14.4 - - + +
140O PHE* 3.9 15.9 - - - +
143O SER* 3.6 20.9 - - - +
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Residues in contact with MET 90 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33K LEU* 3.7 19.3 - - + -
50K TYR* 4.0 29.2 - - + -
86O GLY* 2.8 24.9 + - - +
87O LYS* 4.1 2.9 - - - +
89O MET* 1.3 73.6 - - + +
91O ASP* 1.3 57.8 + - - +
94O TYR* 3.2 28.7 + - + +
95O GLN* 2.8 29.2 + - - +
139O VAL* 5.0 3.8 - - - -
142O TYR* 4.1 21.3 - - + -
143O SER* 3.9 23.6 - - - -
146O LEU* 3.7 31.6 - - + -
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Residues in contact with ASP 91 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52K ASP* 5.1 4.5 - - - +
55K ASP* 4.0 16.4 - - - +
87O LYS* 3.0 40.7 + - - +
88O TYR* 3.7 6.5 - - + +
90O MET* 1.3 77.2 - - - +
92O ASN* 1.3 60.5 + - + +
95O GLN* 3.3 17.4 - - - +
96O TYR* 2.9 31.7 + - - +
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Residues in contact with ASN 92 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53O LYS* 2.8 30.3 + - - +
74O HIS* 5.7 0.7 + - - -
76O GLY 5.0 0.9 - - - +
77O ALA* 3.8 1.4 - - - -
78O CYS* 3.2 8.5 - - - +
88O TYR* 2.8 47.3 + - + +
89O MET* 4.9 0.4 - - - -
91O ASP* 1.3 76.3 - - + +
93O ASN* 1.3 71.8 + - - +
96O TYR* 3.1 23.8 - - - +
400O NAP 3.0 32.6 + - - -
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Residues in contact with ASN 93 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74O HIS* 4.9 0.2 + - - -
77O ALA* 3.4 13.0 - - + +
78O CYS* 2.8 46.9 + - - +
89O MET* 2.9 28.8 + - - +
92O ASN* 1.3 82.7 + - - +
94O TYR* 1.3 63.5 + - - +
97O SER* 2.8 33.2 + - - -
140O PHE* 4.0 7.9 - - - -
143O SER* 3.2 28.8 + - - +
144O LYS* 4.6 7.4 - - + +
147O 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