Contacts of the helix formed by residues 62 - 80 (chain B) in PDB entry 1OIZ
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 ASP 62 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B ARG* 2.9 16.2 + - - +
60B ASP 3.1 3.1 + - - +
61B PHE* 1.3 74.6 - - - +
63B LEU* 1.3 54.9 + - - +
64B ASP* 3.3 11.8 + - - +
65B LEU* 3.1 42.1 + - + +
66B ALA* 2.8 35.6 + - - +
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Residues in contact with LEU 63 (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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27B GLY* 4.2 6.7 - - - +
30B ALA* 3.7 13.7 - - + +
31B LEU* 3.8 39.9 - - + +
33B ARG* 3.6 26.9 - - - +
34B ARG* 3.9 19.3 - - - +
56B LEU* 4.6 7.0 - - + -
61B PHE 3.2 8.7 + - - +
62B ASP* 1.3 71.7 + - - +
64B ASP* 1.3 58.8 + - - +
66B ALA* 3.3 4.6 + - - +
67B TRP* 2.9 31.6 + - - +
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Residues in contact with ASP 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B ARG* 2.7 44.6 + - - +
62B ASP* 3.3 8.3 + - - +
63B LEU* 1.3 78.5 - - - +
65B LEU* 1.3 61.9 + - + +
67B TRP* 3.3 4.7 + - - +
68B ARG* 2.9 28.8 + - - +
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Residues in contact with LEU 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B ARG* 3.7 27.7 + - + +
62B ASP* 3.1 34.8 + - + +
64B ASP* 1.3 77.4 - - + +
66B ALA* 1.3 60.6 + - - +
68B ARG* 3.5 42.2 + - - +
69B LEU* 2.9 30.1 + - - +
185B ASP* 5.0 1.0 - - - +
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Residues in contact with ALA 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B LEU* 4.3 8.9 - - + +
55B PHE* 3.6 27.3 - - - +
56B LEU* 4.0 24.5 - - + +
59B ARG* 3.8 11.8 - - + +
62B ASP 2.8 20.8 + - - +
63B LEU 3.7 3.8 - - - +
65B LEU* 1.3 72.9 - - - +
67B TRP* 1.3 57.5 + - - +
69B LEU* 3.5 3.4 + - - +
70B LEU* 3.0 28.4 + - - +
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Residues in contact with TRP 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B LEU* 3.8 22.4 - - + +
34B ARG* 3.5 58.0 - - + +
35B ALA* 3.7 22.2 - - + -
38B ALA* 4.1 17.0 - - + -
40B VAL* 4.2 11.9 - - + -
63B LEU 2.9 18.4 + - - +
64B ASP 3.5 4.5 - - - +
66B ALA* 1.3 73.6 - - - +
68B ARG* 1.3 66.3 + - + +
70B LEU* 3.1 19.1 + - + -
71B LYS* 3.0 64.0 + - + +
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Residues in contact with ARG 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B ARG* 5.6 0.8 - - - +
64B ASP 2.9 17.1 + - - +
65B LEU* 3.5 35.5 + - - +
67B TRP* 1.3 75.7 - - + +
69B LEU* 1.3 57.6 + - - +
71B LYS* 3.4 17.7 + - - +
72B ASN* 3.0 44.7 + - - +
185B ASP* 2.8 30.6 + - - +
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Residues in contact with LEU 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B PHE* 3.8 24.5 - - + +
58B ALA* 3.7 30.5 - - + -
59B ARG* 3.8 24.0 - - + +
65B LEU 2.9 18.0 + - - +
66B ALA 3.6 4.0 - - - +
68B ARG* 1.3 72.3 - - - +
70B LEU* 1.3 60.3 + - - +
72B ASN* 3.4 1.0 + - - +
73B TYR* 2.9 27.7 + - - +
185B ASP* 3.4 40.7 + - - +
186B SER 3.9 0.2 - - - -
187B PHE 3.7 21.3 - - - +
188B PRO* 3.8 7.6 - - + -
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Residues in contact with LEU 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B LEU* 4.3 9.6 - - + -
35B ALA* 4.3 11.9 - - + -
47B LEU* 5.4 0.7 - - + -
51B PHE* 4.1 6.3 - - + -
52B LEU* 4.0 22.2 - - + -
55B PHE* 3.6 39.9 - - + -
66B ALA 3.0 15.3 + - - +
67B TRP* 3.5 31.2 - - + +
69B LEU* 1.3 76.8 - - - +
71B LYS* 1.3 62.2 + - - +
73B TYR* 3.2 4.9 + - + +
74B TYR* 3.1 59.1 + - + +
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Residues in contact with LYS 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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38B ALA* 6.0 1.3 - - + -
40B VAL* 6.0 0.9 - - + -
67B TRP* 3.0 65.1 + - + +
68B ARG* 3.7 18.8 - - - +
70B LEU* 1.3 74.3 - - - +
72B ASN* 1.3 61.0 + - - +
74B TYR* 3.2 10.7 + - - +
75B LYS* 2.8 29.5 + - - +
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Residues in contact with ASN 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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68B ARG* 3.0 26.7 + - - +
69B LEU 3.7 0.9 - - - +
71B LYS* 1.3 78.0 - - - +
73B TYR* 1.3 59.5 + - - +
75B LYS* 3.6 15.7 - - - +
76B TRP* 2.8 32.4 + - - +
185B ASP* 3.0 48.7 + - - +
186B SER* 3.8 10.4 + - - +
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Residues in contact with TYR 73 (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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45B LEU* 3.9 19.1 - - + +
51B PHE* 3.9 24.7 - + - -
55B PHE* 3.6 21.8 - + + -
69B LEU 2.9 14.3 + - - +
70B LEU* 3.4 9.6 - - + +
72B ASN* 1.3 75.3 - - - +
74B TYR* 1.3 74.9 + + - +
76B TRP* 4.0 1.7 - + - +
77B ARG* 3.1 55.1 + - + +
137B LEU* 5.9 0.7 - - + -
141B GLU* 2.5 35.6 + - - -
186B SER 3.4 24.6 + - - +
187B PHE* 3.7 18.8 - + - -
188B PRO* 3.7 17.7 - - + -
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Residues in contact with TYR 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B VAL* 3.7 28.2 - - + +
41B PRO* 3.7 44.6 + - + +
44B PRO* 6.6 0.2 - - + -
45B LEU* 4.3 21.4 + - + -
47B LEU* 3.4 26.7 - - - +
51B PHE* 3.5 10.9 - + - -
70B LEU* 3.1 46.5 + - + -
71B LYS* 3.6 7.9 - - - +
73B TYR* 1.3 89.1 - + - +
75B LYS* 1.3 64.5 + - - +
77B ARG* 3.5 10.6 + - - +
78B ALA* 3.0 24.8 + - - +
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Residues in contact with LYS 75 (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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71B LYS 2.8 18.0 + - - +
72B ASN* 3.6 16.6 - - - +
74B TYR* 1.3 76.1 - - - +
76B TRP* 1.3 57.7 + - - +
78B ALA* 3.2 7.0 + - - +
79B GLU* 2.9 63.0 + - + +
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Residues in contact with TRP 76 (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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72B ASN 2.8 22.1 + - - +
73B TYR* 4.0 3.6 - + - +
75B LYS* 1.3 72.2 - - - +
77B ARG* 1.3 70.6 + - + +
79B GLU* 3.2 6.2 + - - +
80B CYS* 2.9 51.5 + - + +
83B ILE* 3.9 34.3 - - + -
84B SER* 4.3 11.7 - - - -
133B PHE* 3.7 21.1 - + - -
137B LEU* 3.8 28.5 - - + -
178B LYS* 3.3 21.8 + - + +
181B ALA* 3.5 25.1 - - + +
182B VAL* 3.5 22.1 - - + +
186B SER* 3.9 16.6 - - - +
187B PHE* 6.3 2.0 - + - -
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Residues in contact with ARG 77 (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* 5.0 6.9 - - - +
45B LEU* 3.9 24.9 - - - +
73B TYR* 3.1 54.2 + - + +
74B TYR* 3.7 10.4 - - - +
75B LYS 3.3 0.2 - - - -
76B TRP* 1.3 91.0 - - + +
78B ALA* 1.3 60.8 + - - +
80B CYS 3.5 6.9 + - - -
81B PRO* 3.8 2.4 - - - +
84B SER* 2.6 50.8 + - - +
87B LEU* 4.7 8.3 - - - +
137B LEU* 5.5 3.7 - - + +
141B GLU* 4.3 12.3 + - - -
273B ILE* 3.8 22.2 + - - +
275B GLU 4.3 11.9 - - - +
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Residues in contact with ALA 78 (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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74B TYR 3.0 17.2 + - - +
75B LYS* 3.7 5.2 - - - +
77B ARG* 1.3 76.5 - - - +
79B GLU* 1.3 63.0 + - + +
81B PRO* 3.6 13.0 - - - +
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Residues in contact with GLU 79 (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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75B LYS* 2.9 53.2 + - + +
76B TRP* 3.9 5.4 - - - +
78B ALA* 1.3 77.4 - - + +
80B CYS* 1.3 64.7 + - - +
81B PRO* 3.3 10.9 - - - +
82B GLU* 4.3 2.3 - - - +
178B LYS* 4.6 6.9 + - - -
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Residues in contact with CYS 80 (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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76B TRP* 2.9 43.6 + - + +
77B ARG 3.7 4.5 - - - -
78B ALA 3.4 0.2 - - - -
79B GLU* 1.3 84.7 - - - +
81B PRO* 1.3 58.4 - - - +
82B GLU* 3.2 17.3 - - - +
83B ILE* 2.9 16.6 + - + -
84B SER* 2.8 24.6 + - - -
178B LYS* 3.7 33.0 - - - -
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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
------------------------------------------------------------
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