Contacts of the helix formed by residues 85 - 93 (chain E) in PDB entry 6K71
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 85 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83E ASP 2.8 14.1 + - - -
84E MET* 1.3 70.9 - - - +
86E THR* 1.3 56.3 + - - -
87E ALA 3.1 2.9 - - - -
88E ASP* 3.0 17.7 + - - +
89E SER* 2.7 35.3 + - - -
222E THR* 4.2 13.7 - - - -
223E SER* 5.1 3.1 - - - -
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Residues in contact with THR 86 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8E MET* 3.8 17.8 - - + +
84E MET* 3.4 32.5 + - + +
85E GLY* 1.3 70.8 - - - -
87E ALA* 1.3 55.3 + - - +
89E SER* 3.1 6.1 + - - -
90E LEU* 3.0 29.1 + - - +
203E HIS* 6.0 3.4 - - - +
223E SER* 3.3 6.3 - - - +
224E ILE* 2.4 52.3 + - + +
225E ARG* 5.2 3.4 - - + +
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Residues in contact with ALA 87 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85E GLY 3.1 0.6 - - - -
86E THR* 1.3 82.8 + - - +
88E ASP* 1.3 57.2 + - - +
90E LEU* 3.3 18.5 - - + +
91E ARG* 2.8 51.7 + - - +
216E MET* 6.5 0.4 - - - -
221E ILE 4.1 6.7 - - - +
222E THR* 3.7 26.9 - - + -
223E SER 4.2 1.9 - - - +
224E ILE* 4.8 7.6 - - + +
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Residues in contact with ASP 88 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80E ASP* 4.9 1.0 - - - -
83E ASP* 4.3 11.8 - - - +
85E GLY* 3.0 24.0 + - - +
87E ALA* 1.3 77.1 - - - +
89E SER* 1.3 59.0 + - - +
91E ARG* 3.0 31.0 + - - +
92E TYR* 3.0 30.7 + - - +
222E THR* 4.5 7.2 - - - +
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Residues in contact with SER 89 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8E MET* 3.6 25.6 - - - +
54E VAL* 5.4 3.9 - - - +
80E ASP* 3.3 32.9 + - - +
84E MET* 3.5 22.3 - - - +
85E GLY 2.7 18.7 + - - -
86E THR 3.4 9.4 - - - -
88E ASP* 1.3 74.8 - - - +
90E LEU* 1.3 59.6 + - - +
92E TYR 4.0 3.1 + - - -
93E ILE* 4.2 11.8 + - - +
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Residues in contact with LEU 90 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8E MET* 4.7 6.0 - - + +
86E THR 3.0 16.9 + - - +
87E ALA* 3.3 24.0 - - + +
89E SER* 1.3 75.8 - - - +
91E ARG* 1.3 59.1 + - + +
92E TYR 3.2 1.8 - - - -
93E ILE 3.6 1.8 - - - +
94E TYR* 2.8 36.6 + - + +
97E LEU* 4.7 11.4 - - + +
101E VAL* 6.5 0.7 - - + -
207E LEU* 5.2 7.4 - - + -
212E VAL* 5.1 18.8 - - + -
216E MET* 4.0 34.1 - - + -
224E ILE* 4.2 24.5 - - + -
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Residues in contact with ARG 91 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87E ALA* 2.8 46.2 + - - +
88E ASP* 3.0 32.8 + - - +
90E LEU* 1.3 76.1 - - - +
92E TYR* 1.3 62.1 + - - +
94E TYR* 4.0 7.2 + - - +
95E PRO* 4.9 2.3 - - - +
216E MET* 3.2 59.5 + - + +
217E GLU* 5.8 0.8 + - - -
219E GLY* 3.3 30.1 + - - -
221E ILE 4.4 9.3 + - - -
222E THR* 4.3 6.3 + - - +
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Residues in contact with TYR 92 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78E ILE* 3.6 25.0 - - + +
79E PRO* 3.9 10.6 + - - +
80E ASP* 3.2 29.6 - - - +
88E ASP 3.0 13.0 + - - +
89E SER 4.3 0.4 - - - +
90E LEU 3.2 0.8 - - - -
91E ARG* 1.3 80.7 - - - +
93E ILE* 1.3 71.6 + - + +
94E TYR 3.5 0.4 + - - -
95E PRO* 4.4 6.9 - - - +
96E LYS* 6.0 0.2 + - - -
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Residues in contact with ILE 93 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52E ILE* 4.4 11.0 - - + -
54E VAL* 3.7 30.5 - - + -
76E VAL* 6.1 0.2 - - + -
78E ILE* 3.7 31.2 - - + -
80E ASP* 5.0 2.7 - - - +
89E SER 4.2 6.8 + - - +
90E LEU* 3.5 6.1 + - - -
91E ARG 3.5 0.2 - - - -
92E TYR* 1.3 96.1 - - + +
94E TYR* 1.3 63.2 + - - +
95E PRO* 3.4 4.7 - - - -
96E LYS* 3.6 37.2 + - + +
97E LEU* 3.3 23.2 + - + +
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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