Contacts of the helix formed by residues 100 - 110 (chain B) in PDB entry 1BO1
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 PRO 100 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84A PHE* 3.4 37.0 - - + -
57B LEU* 4.1 7.2 - - + +
73B ALA* 4.5 2.0 - - + -
74B TYR* 3.9 12.6 - - - +
75B SER* 4.1 8.3 - - - +
97B GLU* 3.2 50.3 - - - +
98B TYR 3.3 0.8 - - - +
99B CYS* 1.3 88.3 - - - +
101B MET* 1.3 63.0 + - + +
103B PHE* 3.6 1.2 + - + -
104B ARG* 3.0 26.4 + - - +
107B ARG* 4.0 3.8 + - - -
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Residues in contact with MET 101 (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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84A PHE* 3.9 24.9 - - + -
57B LEU* 4.1 3.6 - - - -
60B VAL* 3.6 22.9 - - + -
61B PRO 3.8 6.5 - - - +
63B PRO* 3.5 37.2 - - + -
66B LEU* 3.7 12.9 - - + +
70B ASP* 3.5 29.6 - - + +
99B CYS 3.2 1.0 + - - -
100B PRO* 1.3 75.9 - - - +
102B VAL* 1.3 57.4 + - - +
104B ARG* 3.5 22.3 + - - +
105B ASN* 3.1 27.5 + - - +
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Residues in contact with VAL 102 (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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66B LEU* 3.6 11.7 - - + -
70B ASP* 3.6 24.9 - - + +
71B PHE* 3.4 48.2 - - + -
99B CYS* 3.2 13.1 + - + +
101B MET* 1.3 73.8 - - - +
103B PHE* 1.3 61.9 + - - +
105B ASN* 3.4 3.5 + - - +
106B LEU* 2.9 39.5 + - + +
164B LEU* 4.1 13.9 - - + -
168B HIS* 4.1 10.3 - - + -
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Residues in contact with PHE 103 (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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97B GLU* 5.6 2.0 - - + +
98B TYR* 3.2 31.0 - - + -
99B CYS* 3.3 13.0 + - + +
100B PRO* 4.3 1.3 - - + +
102B VAL* 1.3 74.0 - - - +
104B ARG* 1.3 57.2 + - - +
105B ASN 3.0 1.6 - - - -
106B LEU* 2.9 20.9 + - + +
107B ARG* 2.7 45.2 + - - +
160B MET* 3.3 29.4 - - + -
161B HIS* 6.0 0.2 - - - -
164B LEU* 3.8 16.8 - - + -
183B PHE* 3.7 27.6 - - + -
184B LEU 3.5 12.9 - - - +
185B GLY* 3.7 22.2 - - - -
186B MET* 3.9 25.8 - - + -
199B VAL* 6.3 0.2 - - + -
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Residues in contact with ARG 104 (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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34A LYS* 4.4 4.0 - - - +
57B LEU* 3.2 35.6 + - + +
58B SER* 5.2 1.0 - - - +
60B VAL 2.5 24.7 + - - -
61B PRO* 3.2 21.0 + - - +
62B VAL* 3.4 34.4 - - - +
63B PRO* 3.8 3.1 - - - +
100B PRO 3.0 19.6 + - - +
101B MET* 3.6 28.1 - - - +
103B PHE* 1.3 77.1 - - - +
105B ASN* 1.3 62.0 + - - +
107B ARG* 3.2 33.0 - - - +
108B GLU* 3.4 9.4 + - - +
114B ASP* 4.2 19.0 + - - +
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Residues in contact with ASN 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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62B VAL* 5.7 4.0 - - - +
63B PRO* 6.2 1.6 - - - +
66B LEU* 4.1 16.6 - - + +
101B MET 3.1 16.6 + - - +
102B VAL 3.6 4.9 - - - +
103B PHE 3.0 0.4 - - - -
104B ARG* 1.3 76.9 - - - +
106B LEU* 1.3 58.2 + - - +
107B ARG 3.0 2.6 + - - -
108B GLU* 3.2 24.1 + - - +
109B ARG* 2.9 59.6 + - - +
168B HIS* 3.0 24.8 + - - -
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Residues in contact with LEU 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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102B VAL* 2.9 27.1 + - + +
103B PHE* 2.9 29.7 + - + +
105B ASN* 1.3 73.7 - - - +
107B ARG* 1.3 60.0 + - - +
109B ARG* 3.4 5.4 + - - +
110B PHE* 2.8 35.9 + - + -
164B LEU* 3.9 23.3 - - + -
167B TYR* 4.0 22.9 - - + -
168B HIS* 3.6 23.8 - - + -
171B ILE* 4.1 22.2 - - + -
183B PHE 3.6 16.6 - - - +
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Residues in contact with ARG 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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54B ILE* 3.8 19.4 - - - +
57B LEU* 4.1 4.8 - - - +
97B GLU* 4.0 14.5 + - - -
100B PRO 4.0 4.8 + - - -
103B PHE* 2.7 12.3 + - - +
104B ARG* 3.2 42.0 - - - +
105B ASN 3.0 0.2 - - - -
106B LEU* 1.3 73.3 - - - +
108B GLU* 1.3 61.0 + - - +
109B ARG 3.0 1.1 - - - -
110B PHE* 2.8 20.1 + - - +
112B ILE* 3.0 31.3 + - + +
114B ASP* 2.7 49.3 + - - +
117B TYR* 3.9 26.1 - - - -
184B LEU* 2.9 46.5 + - + +
185B GLY* 5.4 0.8 - - - -
187B TYR* 5.4 1.2 + - - -
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Residues in contact with GLU 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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62B VAL* 4.3 18.9 - - - +
104B ARG 3.4 7.6 + - - +
105B ASN* 3.2 30.7 + - - +
107B ARG* 1.3 78.7 - - - +
109B ARG* 1.3 65.2 + - + +
111B GLY* 2.9 18.4 + - - +
112B ILE 4.0 10.7 + - - +
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Residues in contact with ARG 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 ASN* 2.9 44.8 + - - +
106B LEU* 3.5 9.6 - - - +
108B GLU* 1.3 82.9 - - - +
110B PHE* 1.3 56.9 + - - +
111B GLY 3.2 1.2 + - - -
168B HIS* 4.6 4.6 + - - -
171B ILE* 3.6 35.0 - - + +
172B VAL* 3.0 51.2 + - - +
175B HIS* 4.2 6.2 - - - +
176B GLY* 3.5 19.6 + - - +
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Residues in contact with PHE 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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106B LEU* 2.8 27.1 + - + +
107B ARG 2.8 6.3 + - - +
109B ARG* 1.3 75.3 - - - +
111B GLY* 1.3 64.5 + - - +
112B ILE* 3.4 4.0 + - + +
167B TYR* 3.6 13.9 - + - -
171B ILE* 3.6 39.3 - - + -
176B GLY* 3.8 23.8 - - - -
178B THR* 5.0 0.7 - - - -
182B GLN* 3.2 53.6 - - + +
183B PHE 3.7 9.6 - - - -
184B LEU* 3.7 17.5 - - + -
202B ARG* 2.8 34.8 + - - +
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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