Contacts of the strand formed by residues 66 - 72 (chain B) in PDB entry 1BUH
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 ILE 66 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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207A SER* 4.4 8.3 - - - -
209A ILE* 4.1 15.5 - - + -
21B HIS* 3.9 35.0 - - + -
22B VAL 3.3 5.2 - - - +
23B MET* 3.2 38.4 - - + -
56B HIS* 5.2 2.1 - - - -
58B MET 5.3 0.9 - - - +
59B ILE* 5.5 3.6 - - - +
60B HIS* 5.3 4.7 + - + -
63B GLU* 3.3 38.7 + - + +
64B PRO* 4.5 3.1 - - - +
65B HIS* 1.3 94.1 - - + +
67B LEU* 1.3 66.6 + - - +
68B LEU* 3.7 11.4 + - + +
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Residues in contact with LEU 67 (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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21B HIS* 3.2 4.6 - - - -
22B VAL* 2.7 41.2 + - + +
24B LEU* 4.0 24.9 - - + -
32B VAL* 4.4 8.3 - - + -
38B MET* 3.7 33.7 - - + -
43B TRP* 4.4 1.6 - - + -
46B LEU* 4.1 10.5 - - + -
48B VAL* 4.1 22.2 - - + -
56B HIS* 3.8 13.9 - - + +
64B PRO 4.8 5.4 - - - +
65B HIS 3.9 0.2 + - - -
66B ILE* 1.3 75.7 - - - +
68B LEU* 1.3 60.6 + - - +
69B PHE* 3.6 30.8 + - + -
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Residues in contact with LEU 68 (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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209A ILE* 3.9 20.0 - - + -
213A PHE* 3.7 29.2 - - + -
12B TYR* 4.0 2.2 - - - +
20B ARG 4.0 1.1 - - - +
21B HIS* 3.5 24.2 - - + -
56B HIS* 3.5 12.6 + - - -
57B TYR* 3.3 37.7 + - + +
58B MET* 3.7 47.9 + - + +
59B ILE* 4.8 0.2 - - - -
60B HIS* 4.2 12.3 - - + +
66B ILE* 3.7 9.5 + - + +
67B LEU* 1.3 73.5 - - - +
69B PHE* 1.3 60.4 + - - +
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Residues in contact with PHE 69 (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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19B TYR* 3.3 8.0 - - - +
20B ARG* 2.9 42.1 + - + +
22B VAL* 3.9 14.8 - - + -
43B TRP* 3.6 37.0 - + + -
48B VAL* 4.3 4.3 - - + -
50B GLN* 3.2 33.9 - - - -
54B TRP* 3.7 18.8 - - + -
55B VAL 3.3 6.5 - - - -
56B HIS* 3.5 28.5 - - + -
57B TYR* 3.5 4.9 - - - -
67B LEU* 3.6 46.7 - - + -
68B LEU* 1.3 70.8 - - - +
70B ARG* 1.3 61.2 + - - +
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Residues in contact with ARG 70 (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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239A SER* 3.8 23.0 + - - +
17B PHE* 3.2 52.7 - - + -
18B GLU 3.6 4.3 - - - -
19B TYR* 3.7 20.1 + - + -
53B GLY 3.8 0.2 - - - +
54B TRP* 3.6 2.1 - - - -
55B VAL* 2.7 46.0 + - + +
57B TYR* 3.1 50.8 - - + +
69B PHE* 1.3 73.9 - - - +
71B ARG* 1.3 66.7 + - - +
72B PRO* 4.7 0.2 - - - -
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Residues in contact with ARG 71 (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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11B LYS* 5.7 1.6 - - - +
17B PHE* 3.7 3.6 - - - -
18B GLU* 2.8 63.2 + - - +
51B SER* 3.6 15.6 + - - -
52B GLN 3.1 20.0 + - - -
53B GLY* 3.4 29.4 - - - +
54B TRP* 3.5 41.2 - - + +
70B ARG* 1.3 79.1 - - - +
72B PRO* 1.3 77.6 + - + +
74B PRO 5.8 0.8 + - - -
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Residues in contact with PRO 72 (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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16B GLU 3.4 10.5 - - - +
17B PHE* 3.6 18.8 - - + -
18B GLU* 5.2 0.3 - - - +
53B GLY 4.8 3.6 - - - +
55B VAL* 5.6 4.5 - - + -
70B ARG 4.7 0.9 - - - +
71B ARG* 1.3 101.5 + - + +
73B LEU* 1.3 63.9 + - - +
74B PRO 2.9 12.6 - - - +
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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