Contacts of the helix formed by residues 81 - 91 (chain A) in PDB entry 6AH0
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 PHE 81 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78A ASN* 3.4 18.3 + - - +
80A LYS* 1.3 71.2 - - - +
82A ARG* 1.3 58.8 + - - -
83A HIS 3.5 2.5 - - - -
84A ASP* 3.5 8.1 + - - +
85A LYS* 3.3 16.1 + - - -
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Residues in contact with ARG 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A ASN 4.5 2.5 - - - -
79A ARG 3.6 13.2 + - - -
80A LYS 2.3 23.9 + - - -
81A PHE* 1.3 64.2 - - - +
83A HIS* 1.3 55.7 + - - +
84A ASP 3.3 4.5 - - - -
85A LYS* 3.3 14.7 + - - +
86A ARG 3.9 4.2 + - - -
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Residues in contact with HIS 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A LYS 4.2 2.2 + - - -
82A ARG* 1.3 72.9 - - - +
84A ASP* 1.3 59.9 + - - +
85A LYS 3.2 0.9 - - - -
86A ARG 4.8 1.6 - - - +
87A VAL* 3.3 21.5 + - - -
108N LEU* 4.4 22.0 - - - +
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Residues in contact with ASP 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A PHE* 3.5 11.5 + - - +
82A ARG 3.3 0.6 - - - -
83A HIS* 1.3 76.7 - - - +
85A LYS* 1.3 55.6 + - - +
87A VAL* 4.7 0.2 - - - +
88A TYR* 2.2 42.4 + - - +
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Residues in contact with LYS 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A PHE 3.3 9.2 + - - -
82A ARG* 3.3 10.6 + - - +
83A HIS 3.2 1.0 - - - -
84A ASP* 1.3 79.4 - - - +
86A ARG* 1.3 62.6 - - - +
89A LEU* 3.2 14.6 + - - -
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Residues in contact with ARG 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A ARG 3.9 8.3 + - - -
83A HIS* 4.2 1.4 + - - +
85A LYS* 1.3 75.9 - - - +
87A VAL* 1.3 62.9 + - - +
89A LEU* 3.5 1.2 + - - -
90A GLY* 3.3 15.4 + - - -
108N LEU 4.9 9.9 - - - -
109N ASP* 5.8 2.7 - - - +
112N MET* 4.9 4.7 - - - -
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Residues in contact with VAL 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A HIS 3.3 18.2 + - - -
84A ASP* 4.8 0.2 - - - -
85A LYS 3.2 0.4 - - - -
86A ARG* 1.3 74.8 - - - +
88A TYR* 1.3 64.4 + - - +
90A GLY* 3.1 3.5 + - - +
91A ALA* 3.0 19.4 + - - -
108N LEU 4.5 5.9 + - - -
111N ARG 5.6 0.2 - - - -
112N MET* 4.6 15.2 - - - +
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Residues in contact with TYR 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A ASP* 2.2 32.8 + - - +
87A VAL* 1.3 68.0 - - - +
89A LEU* 1.3 61.8 + - - +
91A ALA* 3.4 19.5 + - - +
92A LEU* 3.7 2.8 + - - -
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Residues in contact with LEU 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A LYS 3.2 13.3 + - - -
86A ARG 4.1 2.2 - - - -
88A TYR* 1.3 75.7 - - - +
90A GLY* 1.3 63.5 + - - +
92A LEU* 3.2 14.8 + - - +
652A LEU 5.6 0.2 - - - +
653A GLY* 5.0 11.8 - - - +
656A LEU* 5.3 14.5 - - - +
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Residues in contact with GLY 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A ARG 3.3 9.4 + - - -
87A VAL* 3.1 8.7 + - - -
89A LEU* 1.3 76.8 - - - +
91A ALA* 1.3 55.3 + - - +
92A LEU 3.2 4.3 + - - -
93A LYS 4.5 2.3 + - - -
112N MET* 5.3 11.7 - - - -
115N ARG* 6.0 3.3 - - - -
116N ARG* 5.9 3.0 + - - -
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Residues in contact with ALA 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A VAL 3.0 12.9 + - - -
88A TYR* 3.5 9.9 - - - +
89A LEU 3.2 0.2 - - - -
90A GLY* 1.3 73.3 - - - +
92A LEU* 1.3 58.2 + - - +
93A LYS 3.5 2.5 - - - +
94A TYR* 4.6 5.4 + - - -
95A MET 5.4 0.7 + - - -
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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