Contacts of the helix formed by residues 44 - 54 (chain B) in PDB entry 3OOY
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 ALA 44 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40B SER 4.2 6.3 - - - +
41B CYS* 3.0 11.8 + - - +
43B SER* 1.3 79.6 + - - +
45B ALA* 1.3 63.9 + - - +
46B GLU 3.4 2.2 - - - -
47B ILE* 3.3 12.4 + - + +
48B MET* 3.0 27.9 + - + +
75B LYS* 4.4 2.5 - - - +
78B ALA* 5.7 0.2 - - + -
81B ILE* 4.3 4.9 - - + -
152B LEU* 3.9 25.8 - - + -
183B ASP* 3.6 15.7 - - - +
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Residues in contact with ALA 45 (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 ALA* 3.4 28.7 - - - +
22B LEU* 3.9 2.3 - - - +
23B ARG* 3.6 34.8 - - + +
41B CYS 3.5 1.9 + - - +
42B CYS 3.4 6.2 + - - +
43B SER 3.5 1.8 + - - -
44B ALA* 1.3 76.5 - - - +
46B GLU* 1.3 62.6 + - - +
48B MET* 3.5 2.3 + - - +
49B ALA* 3.1 22.9 + - - +
81B ILE* 3.7 17.5 - - + -
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Residues in contact with GLU 46 (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 LYS* 5.3 2.4 - - + +
19B ALA* 3.6 17.5 - - + +
20B ASN* 5.4 1.0 + - - -
23B ARG* 2.8 44.6 + - - -
44B ALA 3.4 0.2 - - - -
45B ALA* 1.3 73.5 - - - +
47B ILE* 1.3 65.9 + - - +
49B ALA* 3.3 2.0 + - - +
50B VAL* 3.0 29.5 + - - +
218B GLY 3.5 13.6 + - - +
219B HIS* 2.8 43.6 + - - +
221B VAL* 3.9 16.4 - - + -
224B LEU* 3.8 10.1 - - + -
246B ARG* 5.8 0.4 + - - -
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Residues in contact with ILE 47 (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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43B SER 4.4 6.3 - - - +
44B ALA* 3.3 20.1 + - - +
46B GLU* 1.3 79.4 - - - +
48B MET* 1.3 62.8 + - - +
50B VAL* 3.4 2.3 + - - +
51B LEU* 3.0 41.7 + - + +
152B LEU* 4.0 25.1 - - + -
181B ILE* 3.8 34.3 - - + -
183B ASP* 4.5 7.9 - - + -
218B GLY 4.3 3.3 + - - +
224B LEU* 3.8 24.0 - - + +
228B PHE* 5.0 3.0 - - + -
240B ALA* 4.1 16.4 - - + -
242B THR* 4.4 6.5 - - + -
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Residues in contact with MET 48 (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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22B LEU* 4.1 6.5 - - + -
44B ALA* 3.0 22.9 + - + +
45B ALA 3.8 3.6 - - - +
47B ILE* 1.3 74.1 - - - +
49B ALA* 1.3 65.5 + - - +
51B LEU* 4.5 4.0 - - - -
52B PHE* 2.9 53.6 + - + +
71B PHE* 3.6 33.9 - - + -
73B LEU* 5.2 2.2 - - + -
81B ILE* 4.2 18.8 - - + +
82B LEU* 4.0 30.5 - - + +
85B VAL* 4.1 17.5 - - + -
152B LEU* 3.8 13.0 - - + -
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Residues in contact with ALA 49 (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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15B LEU* 3.6 31.3 - - + +
18B THR* 4.1 9.2 - - + -
19B ALA* 3.8 14.6 - - + +
22B LEU* 4.1 5.8 - - + +
45B ALA 3.1 17.2 + - - +
46B GLU* 3.7 4.7 - - - +
47B ILE 3.3 0.2 - - - -
48B MET* 1.3 75.1 - - - +
50B VAL* 1.3 59.1 + - + +
53B PHE* 2.9 41.7 + - - +
221B VAL* 5.6 0.4 - - + -
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Residues in contact with VAL 50 (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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15B LEU* 4.2 11.9 - - + -
46B GLU 3.0 17.8 + - - +
47B ILE 4.0 2.7 - - - +
49B ALA* 1.3 77.1 - - + +
51B LEU* 1.3 59.2 + - - +
54B HIS* 3.1 7.3 + - + -
55B THR* 2.8 31.6 + - - +
221B VAL* 4.0 29.6 - - + +
224B LEU* 4.1 15.7 - - + -
225B CYS* 4.0 26.2 - - - +
228B PHE* 3.7 30.1 - - + -
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Residues in contact with LEU 51 (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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47B ILE* 3.0 38.0 + - + +
48B MET* 3.2 6.7 + - - +
50B VAL* 1.3 78.1 - - - +
52B PHE* 1.3 69.1 + - + +
53B PHE 3.5 0.2 + - - -
55B THR* 4.3 5.4 - - - -
56B MET* 2.7 41.4 + - + +
71B PHE* 3.7 32.1 - - + -
150B TYR* 3.6 38.4 - - + -
152B LEU* 5.4 0.2 - - + -
181B ILE* 4.3 8.7 - - + -
228B PHE* 3.7 23.6 - - + -
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Residues in contact with PHE 52 (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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48B MET* 2.9 43.4 + - + +
51B LEU* 1.3 82.6 - - + +
53B PHE* 1.3 80.6 + - + +
54B HIS 3.7 0.4 - - - -
56B MET* 3.9 17.0 - - + +
58B TYR* 2.6 50.0 + + - +
71B PHE* 3.6 39.0 - + + -
82B LEU* 4.4 0.9 - - + -
85B VAL* 3.9 24.0 - - + -
86B TRP* 3.7 34.1 - + - -
286B ALA* 4.5 4.2 - - - +
625B EDO 5.5 0.2 - - - -
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Residues in contact with PHE 53 (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* 2.7 32.6 + - - -
15B LEU* 3.7 12.0 - - + +
18B THR* 3.9 17.9 - - + -
49B ALA* 2.9 19.3 + - - +
52B PHE* 1.3 100.1 - - + +
54B HIS* 1.3 53.6 + - - +
58B TYR* 4.2 3.1 - - - -
85B VAL* 3.7 16.2 - - + -
88B GLU* 3.5 36.1 - - + -
89B ALA* 3.7 24.5 - - + -
284B ILE* 3.5 45.0 - - + +
285B LEU 4.6 7.4 - - - -
286B ALA* 4.8 4.3 - - - +
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Residues in contact with HIS 54 (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* 3.7 24.2 - - + +
15B LEU* 4.1 14.8 - - + +
50B VAL* 3.1 11.5 + - + +
52B PHE 3.7 0.8 - - - -
53B PHE* 1.3 79.9 - - - +
55B THR* 1.3 74.6 + - - +
56B MET 3.8 1.5 + - - -
57B ARG* 2.9 26.1 + - - -
225B CYS* 3.8 38.7 + - + +
228B PHE* 5.8 0.2 - - + -
287B THR* 5.3 0.7 + - - -
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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