Contacts of the helix formed by residues 77 - 109 (chain P) in PDB entry 5KHU
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 THR 77 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76P ILE* 3.8 29.2 - - - +
78P GLU* 3.7 29.8 - - - +
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Residues in contact with GLU 78 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77P THR* 3.7 29.6 - - - +
79P GLU* 3.8 25.1 - - - +
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Residues in contact with GLU 79 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78P GLU* 3.8 26.7 - - - +
80P ASP* 3.8 29.8 - - - +
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Residues in contact with ASP 80 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79P GLU* 3.8 30.1 - - - +
81P ALA* 3.8 26.2 - - - +
83P ASP* 4.5 16.2 - - - +
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Residues in contact with ALA 81 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80P ASP* 3.8 26.7 - - - +
82P GLN* 3.8 29.2 - - - +
84P MET* 4.6 14.6 - - - +
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Residues in contact with GLN 82 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81P ALA* 3.8 28.5 - - - +
83P ASP* 3.8 25.1 - - - +
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Residues in contact with ASP 83 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80P ASP* 4.5 15.0 - - - +
82P GLN* 3.8 26.9 - - - +
84P MET* 3.8 29.6 - - - +
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Residues in contact with MET 84 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81P ALA* 4.6 16.4 - - - +
83P ASP* 3.8 30.3 - - - +
85P ASP* 3.8 28.5 - - - +
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Residues in contact with ASP 85 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84P MET* 3.8 27.6 - - - +
86P ALA* 3.8 29.4 - - - +
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Residues in contact with ALA 86 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85P ASP* 3.8 30.1 - - - +
87P TYR* 3.8 27.6 - - - +
89P LEU* 4.7 14.1 - - - +
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Residues in contact with TYR 87 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86P ALA* 3.8 25.8 - - - +
88P THR* 3.7 29.4 - - - +
90P ALA* 4.4 14.1 - - - +
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Residues in contact with THR 88 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87P TYR* 3.7 29.6 - - - +
89P LEU* 3.8 26.2 - - - +
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Residues in contact with LEU 89 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86P ALA* 4.7 12.8 - - - +
88P THR* 3.8 24.7 - - - +
90P ALA* 3.8 28.9 - - - +
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Residues in contact with ALA 90 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87P TYR* 4.4 15.9 - - - +
89P LEU* 3.8 28.9 - - - +
91P LYS* 3.8 28.0 - - - +
93P TYR* 4.7 11.4 - - - +
102P ALA* 4.3 24.0 - - - +
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Residues in contact with LYS 91 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90P ALA* 3.8 25.1 - - - +
92P ALA* 3.8 29.8 - - - +
94P PHE* 4.2 17.3 - - - +
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Residues in contact with ALA 92 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91P LYS* 3.8 26.5 - - - +
93P TYR* 3.7 29.8 - - - +
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Residues in contact with TYR 93 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90P ALA* 4.7 12.6 - - - +
92P ALA* 3.7 25.6 - - - +
94P PHE* 3.7 29.4 - - - +
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Residues in contact with PHE 94 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91P LYS* 4.2 19.5 - - - +
93P TYR* 3.7 26.0 - - - +
95P ASP* 3.7 29.8 - - - +
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Residues in contact with ASP 95 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94P PHE* 3.7 30.1 - - - +
96P VAL* 3.7 26.9 - - - +
97P LYS* 4.6 3.8 - - - +
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Residues in contact with VAL 96 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95P ASP* 3.7 22.9 - - - +
97P LYS* 2.9 39.3 - - - +
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Residues in contact with LYS 97 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95P ASP* 4.6 8.3 - - - +
96P VAL* 2.9 39.0 - - - +
98P GLU* 3.8 26.5 - - - +
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Residues in contact with GLU 98 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97P LYS* 3.8 28.3 - - - +
99P TYR* 3.7 30.5 - - - +
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Residues in contact with TYR 99 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98P GLU* 3.7 29.8 - - - +
100P ASP* 3.7 29.6 - - - +
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Residues in contact with ASP 100 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99P TYR* 3.7 29.2 - - - +
101P ARG* 3.7 25.8 - - - +
103P ALA* 4.4 16.8 - - - +
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Residues in contact with ARG 101 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100P ASP* 3.7 27.8 - - - +
102P ALA* 3.7 29.6 - - - +
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Residues in contact with ALA 102 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90P ALA* 4.3 23.6 - - - +
101P ARG* 3.7 29.6 - - - +
103P ALA* 3.8 25.1 - - - +
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Residues in contact with ALA 103 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100P ASP* 4.4 15.9 - - - +
102P ALA* 3.8 30.3 - - - +
104P HIS* 3.8 25.4 - - - +
106P LEU* 4.2 21.1 - - - +
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Residues in contact with HIS 104 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103P ALA* 3.8 24.7 - - - +
105P PHE* 3.7 29.4 - - - +
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Residues in contact with PHE 105 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104P HIS* 3.7 30.1 - - - +
106P LEU* 3.8 26.7 - - - +
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Residues in contact with LEU 106 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103P ALA* 4.2 18.6 - - - +
105P PHE* 3.8 29.8 - - - +
107P HIS* 3.8 28.7 - - - +
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Residues in contact with HIS 107 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106P LEU* 3.8 24.9 - - - +
108P GLY* 3.8 28.9 - - - +
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Residues in contact with GLY 108 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107P HIS* 3.8 29.6 - - - +
109P CYS* 3.8 27.1 - - - +
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Residues in contact with CYS 109 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108P GLY* 3.8 29.4 - - - +
110P ASN* 3.8 28.7 - - - +
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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
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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