Contacts of the helix formed by residues 70 - 85 (chain B) in PDB entry 1OJ7
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 70 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65B ILE* 5.6 0.4 - - - +
66B GLU* 5.6 2.1 - - + +
68B ASN 3.3 1.7 + - - +
69B PRO* 1.3 72.5 - - - +
71B TYR* 1.3 66.2 + - - +
72B GLU* 3.8 15.5 - - + +
73B THR* 3.0 20.6 + - - +
74B LEU* 3.0 24.2 + - - +
153B SER* 3.4 5.8 - - - -
155B LYS* 4.1 23.8 - - + -
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Residues in contact with TYR 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B PRO 3.9 1.2 + - - -
70B ALA* 1.3 69.8 - - - +
72B GLU* 1.3 71.0 + - + +
74B LEU* 3.2 6.2 + - - +
75B MET* 2.9 61.8 + - + +
103B PHE* 3.7 19.1 - + - -
115B ASP* 2.4 36.8 + - - -
116B PRO* 4.4 1.7 - - - +
117B TRP* 3.7 39.0 - + + -
152B ILE* 4.0 8.3 - - + +
153B SER 2.8 18.6 + - - +
154B ARG* 4.0 25.1 - - + -
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Residues in contact with GLU 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B ALA* 3.8 9.9 - - + +
71B TYR* 1.3 93.1 + - + +
73B THR* 1.3 62.2 + - - +
75B MET* 3.6 9.3 + - - +
76B ASN* 3.5 16.7 + - - +
154B ARG* 3.4 10.6 - - - +
155B LYS* 3.2 23.9 + - - +
156B THR* 3.0 48.7 + - + +
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Residues in contact with THR 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B PHE* 3.6 25.1 - - + -
63B GLY 5.3 0.2 - - - +
64B GLY* 3.7 25.2 + - - +
65B ILE* 4.8 6.1 - - + -
66B GLU 5.7 0.4 - - - +
70B ALA* 3.0 22.2 + - - +
72B GLU* 1.3 76.8 - - - +
74B LEU* 1.3 68.2 + - + +
76B ASN* 3.1 27.3 + - - +
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Residues in contact with LEU 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B PHE* 5.2 0.4 - - + -
65B ILE* 3.9 25.1 - - + -
69B PRO* 4.1 6.3 - - + -
70B ALA 3.0 21.3 + - - +
71B TYR 3.2 4.2 + - - +
73B THR* 1.3 80.2 - - + +
75B MET* 1.3 56.7 + - - +
77B ALA* 3.0 9.5 + - - +
78B VAL* 3.0 29.0 + - - +
100B GLY* 3.6 39.0 - - - +
103B PHE* 3.8 28.9 - - + -
104B ILE* 3.8 14.4 - - + +
152B ILE* 3.9 23.1 - - + -
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Residues in contact with MET 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B TYR* 2.9 51.4 + - + +
72B GLU* 3.9 7.0 - - - +
73B THR 3.2 0.4 - - - -
74B LEU* 1.3 74.3 - - - +
76B ASN* 1.3 61.7 + - - +
78B VAL* 3.5 22.3 - - + +
79B LYS* 3.0 27.4 + - - +
82B ARG* 4.7 7.0 - - - +
103B PHE* 4.0 13.0 - - - -
116B PRO* 3.6 37.2 - - + -
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Residues in contact with ASN 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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62B PHE* 4.1 13.1 - - + -
72B GLU 3.5 15.5 + - - +
73B THR* 3.1 15.6 + - - +
75B MET* 1.3 79.8 - - - +
77B ALA* 1.3 60.5 + - - +
79B LYS* 3.4 12.4 + - - +
80B LEU* 3.1 20.6 + - - +
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Residues in contact with ALA 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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33B LEU* 4.7 4.7 - - + +
62B PHE* 3.7 38.0 - - + -
73B THR 3.7 1.6 + - - -
74B LEU 3.0 9.9 + - - +
76B ASN* 1.3 75.4 - - - +
78B VAL* 1.3 62.0 + - - +
80B LEU* 3.2 6.0 + - - +
81B VAL* 2.9 34.0 + - - +
104B ILE* 3.5 28.5 - - + -
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Residues in contact with VAL 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B LEU 3.0 19.6 + - - +
75B MET* 3.5 27.8 - - + +
76B ASN 3.3 0.2 - - - -
77B ALA* 1.3 75.9 - - - +
79B LYS* 1.3 63.4 + - - +
81B VAL* 3.2 4.8 + - - +
82B ARG* 3.1 53.8 + - - +
103B PHE* 4.5 1.8 - - + -
104B ILE* 4.0 23.1 - - + +
107B ALA* 3.6 25.4 - - + -
108B ALA* 4.1 13.0 - - - +
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Residues in contact with LYS 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 MET 3.0 13.8 + - - +
76B ASN* 3.5 15.5 - - - +
78B VAL* 1.3 77.4 - - - +
80B LEU* 1.3 62.6 + - - +
82B ARG* 3.3 7.8 + - - +
83B GLU* 2.7 64.4 + - + +
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Residues in contact with LEU 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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33B LEU* 3.7 37.0 - - + -
60B LEU* 4.4 13.0 - - + -
61B GLU 4.9 6.1 - - - +
62B PHE* 4.9 9.6 - - + -
76B ASN 3.1 11.1 + - - +
77B ALA* 3.2 11.0 + - - +
79B LYS* 1.3 80.0 - - - +
81B VAL* 1.3 55.2 + - - +
83B GLU* 3.4 8.0 + - - +
84B GLN* 2.9 64.5 + - + +
86B VAL* 5.0 1.1 - - + -
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Residues in contact with VAL 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B LEU* 3.6 25.8 - - + -
77B ALA 2.9 20.1 + - - +
78B VAL* 3.2 5.6 + - - +
80B LEU* 1.3 75.8 - - - +
82B ARG* 1.3 62.6 + - - +
85B LYS* 3.1 18.4 + - - -
86B VAL* 3.1 31.2 + - + +
89B LEU* 4.2 6.1 - - + -
104B ILE* 3.9 14.6 - - + -
108B ALA* 3.5 13.7 - - + -
131B ILE* 3.2 33.9 - - + -
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Residues in contact with ARG 82 (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 MET* 4.7 10.1 - - - +
78B VAL* 3.1 34.7 + - - +
79B LYS* 3.8 7.3 - - - +
81B VAL* 1.3 77.9 - - - +
83B GLU* 1.3 65.4 + - + +
85B LYS* 3.5 14.4 + - - +
107B ALA 2.8 26.7 + - - -
108B ALA* 3.1 27.1 + - + +
110B TYR* 3.6 18.8 + - - +
111B PRO 5.0 2.4 + - - -
112B GLU* 5.0 8.8 + - - +
114B ILE 5.8 1.0 + - - -
116B PRO* 5.1 6.1 - - - +
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Residues in contact with GLU 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B LYS* 2.7 62.4 + - + +
80B LEU* 3.9 8.0 - - - +
82B ARG* 1.3 79.7 - - + +
84B GLN* 1.3 76.2 + - + +
85B LYS* 3.6 9.9 + - - +
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Residues in contact with GLN 84 (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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31B ARG* 3.0 25.7 + - - -
60B LEU* 4.1 24.8 - - + +
80B LEU* 2.9 41.3 + - + +
83B GLU* 1.3 89.3 + - + +
85B LYS* 1.3 70.7 + - - +
86B VAL* 3.3 3.6 - - + -
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Residues in contact with LYS 85 (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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31B ARG* 3.8 18.5 + - - +
81B VAL 3.1 9.9 + - - -
82B ARG 3.5 10.1 + - - +
83B GLU 3.3 8.1 + - - +
84B GLN* 1.3 81.3 - - - +
86B VAL* 1.3 67.0 + - - +
87B THR* 3.5 14.6 + - + +
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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
------------------------------------------------------------
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