Contacts of the helix formed by residues 114 - 129 (chain B) in PDB entry 2B9R
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 114 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106B ALA* 4.7 2.5 - - - -
112B THR 5.8 0.2 - - - +
113B TYR* 1.3 76.1 - - - +
115B LYS* 1.3 65.4 + - - +
116B HIS* 3.3 12.5 + - - +
117B GLN* 2.5 39.8 + - + +
118B ILE* 3.1 19.8 + - - +
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Residues in contact with LYS 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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102B ILE* 3.2 39.8 - - + +
103B GLY* 5.1 3.4 - - - +
106B ALA* 4.3 12.0 - - + +
114B THR* 1.3 72.4 - - - +
116B HIS* 1.3 51.6 + - - +
118B ILE* 3.2 5.8 + - - -
119B ARG* 2.5 40.4 + - - +
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Residues in contact with HIS 116 (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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98A TYR* 3.7 31.6 - + + -
99A PRO* 6.1 1.6 - - + -
114B THR* 3.1 8.9 + - - +
115B LYS* 1.3 76.9 - - - +
117B GLN* 1.3 59.9 + - + +
119B ARG* 3.0 36.5 + - - +
120B GLN* 2.7 60.9 + - - +
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Residues in contact with GLN 117 (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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82B LEU* 3.9 14.8 - - + +
112B THR 3.8 4.5 + - - +
113B TYR* 2.9 32.6 - - + +
114B THR* 2.5 52.6 + - + +
116B HIS* 1.3 77.1 - - + +
118B ILE* 1.3 61.2 + - - +
120B GLN* 3.3 7.4 + - - +
121B MET* 2.9 29.5 + - - +
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Residues in contact with ILE 118 (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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82B LEU* 3.8 23.3 - - + -
85B VAL* 4.6 10.8 - - + -
86B THR* 4.0 14.4 - - + +
89B PHE* 4.2 20.0 - - + -
102B ILE* 3.5 25.8 - - + +
105B PHE* 4.1 13.2 - - + +
106B ALA* 3.9 34.8 - - + +
109B THR* 5.0 0.4 - - + -
113B TYR* 4.8 5.2 - - + +
114B THR 3.1 11.9 + - - +
115B LYS* 3.4 6.3 - - - +
117B GLN* 1.3 74.8 - - - +
119B ARG* 1.3 69.2 + - - +
120B GLN 3.1 0.3 + - - -
121B MET* 3.1 1.0 + - - +
122B GLU* 2.8 23.9 + - - +
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Residues in contact with ARG 119 (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 LYS* 6.0 3.8 - - - +
99A PRO* 4.7 21.6 + - + +
101A GLU* 3.2 57.2 + - - +
102B ILE* 3.4 22.7 - - + +
115B LYS* 2.5 19.0 + - - +
116B HIS* 3.0 50.2 + - - +
118B ILE* 1.3 72.8 - - - +
120B GLN* 1.3 62.4 + - - +
122B GLU* 3.5 15.5 - - - +
123B MET* 3.4 26.8 + - - +
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Residues in contact with GLN 120 (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 MET* 2.6 31.9 + - - +
98A TYR* 4.3 14.4 - - - +
99A PRO* 4.8 1.8 - - - +
116B HIS* 2.7 50.5 + - + +
117B GLN* 3.5 8.3 - - - +
119B ARG* 1.3 75.9 - - - +
121B MET* 1.3 66.5 + - - +
123B MET* 3.0 24.8 + - + +
124B LYS* 3.0 20.6 + - - +
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Residues in contact with MET 121 (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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69B PHE* 4.6 3.1 - - - -
79B MET* 3.6 31.9 - - + -
82B LEU* 3.6 30.1 - - + +
83B VAL* 3.6 24.0 - - + -
86B THR* 3.4 28.7 - - + +
117B GLN 2.9 17.2 + - - +
120B GLN* 1.3 75.2 - - - +
122B GLU* 1.3 63.6 + - - +
124B LYS* 2.9 27.5 + - + +
125B ILE* 2.8 33.9 + - + +
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Residues in contact with GLU 122 (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 LYS* 2.6 39.4 + - - +
126A LEU* 5.9 0.5 - - - +
86B THR* 3.2 15.8 - - + +
89B PHE* 3.8 15.1 - - + -
90B ILE* 3.7 24.9 - - + +
93B LYS* 2.9 18.6 + - - +
118B ILE 2.8 16.2 + - - +
119B ARG* 3.5 15.6 - - - +
121B MET* 1.3 77.4 - - - +
123B MET* 1.3 51.4 + - - +
125B ILE* 3.2 1.9 + - - +
126B LEU* 2.6 55.8 + - + +
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Residues in contact with MET 123 (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 LYS* 2.9 35.4 - - + +
96A GLU 3.5 15.7 - - - +
97A MET* 3.5 17.3 - - + +
99A PRO* 3.8 30.7 - - - -
119B ARG* 3.4 15.0 + - - +
120B GLN* 3.0 22.5 + - + +
122B GLU* 1.3 77.8 - - - +
124B LYS* 1.3 64.0 + - - +
126B LEU* 3.1 9.2 + - - +
127B ARG* 2.9 53.3 + - - +
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Residues in contact with LYS 124 (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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69B PHE* 4.1 16.0 - - + -
73B ASN* 6.0 1.6 - - - +
74B SER 5.7 2.4 + - - -
79B MET* 3.8 31.3 - - - +
120B GLN 3.0 9.7 + - - +
121B MET* 2.9 34.5 + - + +
123B MET* 1.3 76.4 - - - +
125B ILE* 1.3 58.4 + - - +
127B ARG* 3.4 8.9 + - - +
128B ALA* 3.0 28.1 + - - +
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Residues in contact with ILE 125 (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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65B ILE* 3.6 33.2 - - + -
69B PHE* 3.5 37.9 - - + -
83B VAL* 4.2 28.9 - - + +
86B THR* 4.7 3.1 - - + -
87B ALA* 4.6 7.9 - - + +
90B ILE* 3.9 13.2 - - + -
121B MET* 2.8 24.5 + - + +
122B GLU 3.7 5.2 - - - +
124B LYS* 1.3 73.9 - - - +
126B LEU* 1.3 68.0 - - + +
128B ALA* 2.8 11.4 + - - +
129B LEU* 2.9 22.8 + - + +
133B LEU* 5.2 1.3 - - + -
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Residues in contact with LEU 126 (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 LYS* 4.2 15.9 - - + +
94A TYR* 3.1 46.7 + - + +
126A LEU* 6.0 6.3 - - + -
90B ILE* 3.6 37.0 - - + -
94B TYR* 5.8 1.8 - - + +
122B GLU* 2.6 48.0 + - + +
123B MET* 3.5 7.9 - - - +
125B ILE* 1.3 73.6 - - - +
127B ARG* 1.3 61.5 + - - +
129B LEU* 3.8 3.9 + - - +
130B ASN 3.8 1.0 + - - -
131B PHE* 3.3 15.6 + - - -
133B LEU* 4.6 14.1 - - + +
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Residues in contact with ARG 127 (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 LYS 2.8 24.1 + - - +
94A TYR* 2.8 46.9 + - + +
95A GLU 3.4 2.4 - - - +
96A GLU 3.0 26.1 + - - +
97A MET* 5.1 0.4 - - - +
123B MET* 2.9 51.2 + - - +
124B LYS* 3.8 7.1 - - - +
126B LEU* 1.3 74.3 - - - +
128B ALA* 1.3 59.2 + - - +
130B ASN* 2.8 27.4 + - - +
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Residues in contact with ALA 128 (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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69B PHE* 3.6 27.8 - - + -
73B ASN* 4.2 15.3 - - - +
124B LYS 3.0 17.4 + - - +
125B ILE 2.8 5.8 + - - +
127B ARG* 1.3 73.9 - - - +
129B LEU* 1.3 62.0 + - + +
130B ASN* 2.7 14.8 + - - +
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Residues in contact with LEU 129 (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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65B ILE* 3.6 32.8 - - + -
68B ARG* 3.8 38.1 - - + +
69B PHE* 4.2 23.1 - - + -
125B ILE* 2.9 20.0 + - + +
126B LEU 3.9 2.2 - - - +
128B ALA* 1.3 80.4 - - + +
130B ASN* 1.3 69.2 + - - +
131B PHE 2.6 18.8 + - - -
132B GLY 3.1 19.9 + - - +
133B LEU* 3.7 23.1 - - + -
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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