Contacts of the helix formed by residues 45 - 56 (chain B) in PDB entry 1ORZ
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 MET 45 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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352A ILE* 4.2 23.6 - - + +
353A PHE* 4.2 31.2 - - + -
43B GLY 4.9 4.9 - - - +
44B PRO* 1.3 83.9 - - - +
46B VAL* 1.3 65.8 + - - +
47B LEU* 3.1 3.8 - - + +
48B ASP* 3.0 31.8 + - - +
49B ALA 3.4 4.2 + - - -
86B ALA 3.8 2.5 - - - +
87B CYS* 2.7 31.6 - - - +
88B ILE 4.2 10.3 - - - +
89B CYS 3.4 8.5 - - - +
90B LYS* 4.6 3.6 - - + +
91B ILE* 3.6 5.0 - - - +
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Residues in contact with VAL 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 PHE* 5.7 3.6 - - + -
45B MET* 1.3 70.2 - - - +
47B LEU* 1.3 68.0 + - - +
49B ALA* 3.1 6.0 + - + +
50B LEU* 3.0 24.7 + - + +
77B MET* 5.5 0.2 - - - -
79B ILE* 3.6 17.0 - - + -
86B ALA* 3.3 12.5 + - + +
89B CYS* 3.0 42.4 + - + +
90B LYS 4.4 2.2 - - - +
91B ILE* 3.7 21.8 - - + -
99B LEU* 6.3 1.1 - - + -
101B ILE* 4.0 26.5 - - + -
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Residues in contact with LEU 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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233A HIS* 3.5 31.0 - - + +
45B MET* 3.1 2.4 - - + -
46B VAL* 1.3 77.2 - - - +
48B ASP* 1.3 70.4 + - - +
50B LEU* 3.1 6.0 + - + +
51B LEU* 2.8 22.4 + - + +
63B PHE* 3.6 13.0 - - + -
65B ARG* 3.0 40.6 - - + -
68B ARG* 4.3 18.6 - - + -
75B CYS* 4.6 9.6 - - - -
77B MET* 6.0 0.2 - - + -
86B ALA* 3.1 16.0 + - + +
87B CYS* 4.0 22.0 - - + -
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Residues in contact with ASP 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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44B PRO* 3.4 26.5 - - + +
45B MET* 3.0 26.2 + - - +
47B LEU* 1.3 85.4 - - - +
49B ALA* 1.3 62.3 + - - +
51B LEU* 3.1 5.7 + - - +
52B LYS* 2.9 47.8 + - - +
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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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13B LEU* 4.3 15.3 - - + -
16B PHE* 4.4 7.9 - - + -
37B VAL* 5.2 3.4 - - + -
39B LEU* 6.4 1.3 - - + -
44B PRO* 5.2 2.0 - - + +
45B MET 3.4 2.2 + - - -
46B VAL* 3.1 11.6 + - + +
48B ASP* 1.3 78.5 - - - +
50B LEU* 1.3 64.6 + - + +
52B LYS* 3.1 9.9 + - - +
53B ILE* 2.8 38.1 + - + +
91B ILE* 3.7 23.8 - - + -
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Residues in contact with LEU 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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16B PHE* 6.2 0.4 - - + -
18B VAL* 5.3 3.4 - - + -
46B VAL* 3.0 24.1 + - + +
47B LEU* 3.6 7.2 - - - +
49B ALA* 1.3 78.7 - - + +
51B LEU* 1.3 52.8 + - - +
53B ILE* 3.1 15.2 + - + +
54B LYS* 2.6 39.5 + - - +
61B LEU* 3.9 21.5 - - + -
63B PHE* 3.9 23.3 - - + -
77B MET* 3.7 37.9 - - + -
86B ALA* 4.8 4.3 - - + -
101B ILE* 4.3 18.6 - - + -
113B LEU* 3.9 11.2 - - + -
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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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233A HIS* 4.8 17.5 - - + +
529A GLU* 5.4 4.9 - - - +
47B LEU* 2.8 14.7 + - + +
48B ASP* 3.1 10.1 + - - +
50B LEU* 1.3 75.3 - - - +
52B LYS* 1.3 72.2 + - + +
54B LYS* 4.4 1.1 - - + -
55B ASP* 2.7 53.6 + - + +
56B GLU* 4.8 3.1 - - - +
63B PHE* 4.3 7.6 - - + -
65B ARG* 4.4 31.6 - - - +
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Residues in contact with LYS 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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37B VAL* 4.6 15.9 - - + -
48B ASP* 2.9 40.6 + - - +
49B ALA* 3.5 7.9 - - - +
51B LEU* 1.3 90.1 - - + +
53B ILE* 1.3 64.9 + - - +
56B GLU* 2.6 50.9 + - - +
57B GLN* 3.4 2.2 + - - +
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Residues in contact with ILE 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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16B PHE* 4.5 15.0 - - + -
35B TYR* 3.4 41.3 - - + -
37B VAL* 2.9 33.4 - - + -
49B ALA* 2.8 37.2 + - + +
50B LEU* 3.5 21.8 - - + +
52B LYS* 1.3 76.3 - - - +
54B LYS* 1.3 53.5 + - + +
57B GLN* 2.7 24.6 + - + +
58B ASP* 2.6 31.8 + - + +
61B LEU* 4.6 8.5 - - + -
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Residues in contact with LYS 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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525A SER* 3.7 12.6 - - - -
526A ASP* 3.1 37.2 - - - +
529A GLU* 3.0 31.2 + - - +
50B LEU 2.6 21.0 + - - +
51B LEU* 3.9 2.7 - - + +
53B ILE* 1.3 71.7 - - - +
55B ASP* 1.3 74.5 + - + +
58B ASP 2.5 32.4 - - - +
59B SER* 3.0 14.6 + - - +
61B LEU* 2.7 38.6 - - + +
63B PHE* 3.3 24.7 - - + -
65B ARG* 5.2 0.7 - - - +
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Residues in contact with ASP 55 (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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473A THR* 4.5 5.0 - - - +
474A ALA* 3.8 23.9 - - - +
477A ARG* 3.9 24.6 + - - -
526A ASP* 5.3 2.4 - - - +
529A GLU* 4.5 6.5 - - - +
51B LEU* 2.7 39.1 + - + +
54B LYS* 1.3 87.5 + - + +
56B GLU* 1.3 74.4 + - - +
59B SER* 3.5 14.4 + - - -
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Residues in contact with GLU 56 (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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474A ALA* 5.0 13.8 - - + +
51B LEU* 3.7 3.5 - - - +
52B LYS* 2.6 52.8 + - - +
55B ASP* 1.3 101.3 - - + +
57B GLN* 1.4 71.0 + - + +
58B ASP* 4.7 0.2 - - - -
59B SER* 5.1 1.0 + - - -
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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