Contacts of the helix formed by residues 104 - 115 (chain B) in PDB entry 5BXD
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 104 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85A ARG* 3.1 28.2 + - - -
86A TYR* 4.8 0.2 + - - -
99A PRO* 3.2 28.9 - - - +
82B GLN* 4.5 2.1 - - - +
83B MET* 3.3 22.4 - - + +
102B PHE* 3.4 29.0 - - + -
103B LYS* 1.3 77.5 - - - +
105B TYR* 1.3 63.2 + - - +
106B THR 3.4 2.2 - - - -
107B LEU* 3.9 15.7 - - + +
108B LEU* 3.0 16.6 + - - +
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Residues in contact with TYR 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A ASP* 3.9 21.3 - - - +
102B PHE* 3.6 9.9 - + + -
103B LYS 3.1 5.8 + - - -
104B ASP* 1.3 76.7 - - - +
106B THR* 1.3 71.2 + - + +
109B TYR* 2.9 50.4 + + + +
124B MET* 3.2 65.3 + - + +
125B GLU* 3.6 10.6 + - - +
127B TRP* 3.8 28.0 - + + -
128B LYS* 3.8 35.5 - - + +
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Residues in contact with THR 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A LEU* 3.7 18.5 - - - +
98A ILE 3.1 29.3 + - - +
100A ASP* 4.8 8.4 + - - +
103B LYS 5.0 0.2 + - - -
105B TYR* 1.3 89.8 + - + +
107B LEU* 1.3 70.3 + - - +
109B TYR* 3.8 5.2 - - - +
110B GLU* 3.2 22.9 + - - +
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Residues in contact with LEU 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A ARG* 3.6 37.9 - - + +
86A TYR* 4.1 12.3 - - + -
89A ASN* 4.1 17.4 + - - +
97A LEU* 3.3 44.0 - - + +
98A ILE 3.9 11.0 - - - -
99A PRO* 4.0 5.2 - - + -
80B ASP* 4.5 2.0 - - - +
83B MET* 4.0 12.3 - - + -
104B ASP* 3.8 19.5 - - + +
105B TYR 3.3 0.4 - - - -
106B THR* 1.3 88.0 + - - +
108B LEU* 1.3 62.8 + - - +
110B GLU* 3.4 4.5 + - - +
111B GLU* 3.2 26.5 + - - +
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Residues in contact with LEU 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B MET* 3.7 38.5 - - + +
86B TYR* 3.9 20.0 - - + -
87B ILE* 3.9 8.3 - - + -
96B LEU* 4.2 2.5 - - + -
98B ILE* 4.0 20.9 - - + -
102B PHE* 4.0 8.5 - - + -
104B ASP 3.0 16.9 + - - +
107B LEU* 1.3 73.9 - - - +
109B TYR* 1.3 59.5 + - - +
111B GLU* 3.2 2.2 + - + +
112B ALA* 2.9 27.4 + - - +
120B MET* 3.8 24.7 - - + -
124B MET* 3.8 24.0 - - + -
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Residues in contact with TYR 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B TYR* 2.9 48.2 + + + +
106B THR* 3.8 8.3 - - - +
108B LEU* 1.3 77.6 - - - +
110B GLU* 1.3 56.7 + - - +
112B ALA* 3.3 2.4 + - - +
113B LYS* 2.8 61.5 + - - +
121B LEU* 3.6 42.8 - - + +
124B MET* 3.5 16.1 - - + +
125B GLU* 3.1 22.8 + - + -
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Residues in contact with GLU 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A THR* 3.9 15.0 - - + +
95A LYS* 2.8 44.2 + - - +
97A LEU* 3.6 34.5 - - + +
79B ARG* 3.9 16.1 + - - +
106B THR 3.2 8.8 + - - +
107B LEU 3.7 2.7 - - - +
108B LEU 3.3 0.2 - - - -
109B TYR* 1.3 81.5 - - - +
111B GLU* 1.3 57.3 + - - +
113B LYS* 3.3 13.0 + - - +
114B TYR* 2.8 32.7 + - - +
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Residues in contact with GLU 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A ASN* 4.2 8.8 + - - +
93A THR* 4.0 9.4 - - - +
79B ARG* 2.7 56.9 + - - +
80B ASP* 4.2 12.0 + - + +
83B MET* 3.8 21.5 - - + -
84B PHE* 5.5 0.4 - - - +
87B ILE* 4.1 16.6 - - + -
107B LEU 3.2 14.5 + - - +
108B LEU* 3.2 8.6 + - - +
110B GLU* 1.3 78.2 - - - +
112B ALA* 1.3 56.4 + - - +
114B TYR* 3.2 1.4 + - - +
115B PHE* 2.9 47.9 + - + -
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Residues in contact with ALA 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B ILE* 3.7 18.3 - - + +
108B LEU 2.9 16.5 + - - +
109B TYR* 3.6 5.8 - - - +
111B GLU* 1.3 76.2 - - - +
113B LYS* 1.3 61.6 + - - +
115B PHE* 3.5 2.2 + - - +
116B GLN 3.1 4.2 + - - -
117B LEU* 2.9 31.6 + - + +
120B MET* 4.0 22.0 - - + -
121B LEU* 3.7 18.2 - - + -
124B MET* 4.7 2.7 - - - -
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Residues in contact with LYS 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A LYS* 3.7 23.4 - - - +
55B ARG* 4.9 1.7 + - - -
109B TYR* 2.8 45.1 + - - +
110B GLU* 3.6 15.8 + - - +
112B ALA* 1.3 77.4 - - - +
114B TYR* 1.3 63.3 + - - +
116B GLN* 3.3 18.4 + - - +
121B LEU* 3.9 21.3 - - + +
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Residues in contact with TYR 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B ARG* 2.7 71.1 + - + +
59B LEU* 5.7 4.6 - - + +
77B ILE* 5.6 1.5 - - + +
79B ARG* 3.4 56.0 - - + +
110B GLU* 2.8 24.1 + - - +
111B GLU 3.2 3.1 + - - +
113B LYS* 1.3 77.7 - - - +
115B PHE* 1.3 83.8 + + - +
116B GLN* 3.1 3.9 + - - +
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Residues in contact with PHE 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B SER* 3.2 8.5 - - - -
55B ARG* 3.2 17.3 + - + -
56B ILE* 3.5 39.2 - - + +
59B LEU* 5.0 5.4 - - + -
77B ILE* 4.3 16.2 - - + -
79B ARG* 4.3 14.6 - - + -
84B PHE* 3.8 35.4 - + - -
87B ILE* 4.1 18.4 - - + -
111B GLU* 2.9 42.0 + - + +
112B ALA 4.3 0.2 - - - +
113B LYS 3.4 0.2 - - - -
114B TYR* 1.3 98.7 - + - +
116B GLN* 1.3 69.3 + - - +
117B LEU* 3.4 12.7 + - + +
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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