Contacts of the helix formed by residues 70 - 85 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66A GLU* 3.3 30.7 + - - +
68A ASN 3.3 1.7 + - - -
69A PRO* 1.3 72.3 - - - +
71A TYR* 1.3 64.6 + - - +
72A GLU* 3.6 9.2 - - + +
73A THR* 3.0 11.3 + - - +
74A LEU* 2.9 27.0 + - - +
153A SER 3.3 5.8 - - - -
155A LYS* 3.6 26.2 - - + -
118B HIS* 4.5 1.8 - - - +
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Residues in contact with TYR 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A PRO 3.9 1.2 + - - -
70A ALA* 1.3 71.0 - - - +
72A GLU* 1.3 68.3 + - + +
74A LEU* 3.2 5.4 + - - +
75A MET* 3.0 63.8 + - + +
103A PHE* 4.0 15.0 - + - -
115A ASP* 2.5 36.7 + - - -
116A PRO* 4.5 1.0 - - - +
117A TRP* 3.8 40.4 - + + -
152A ILE* 4.1 8.3 - - + +
153A SER 2.7 16.9 + - - +
154A ARG* 4.1 23.6 - - + -
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Residues in contact with GLU 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A ALA* 3.6 11.4 - - + +
71A TYR* 1.3 88.0 + - + +
73A THR* 1.3 57.7 + - - +
75A MET* 4.1 6.6 + - - +
76A ASN* 3.0 20.1 + - - -
154A ARG* 3.4 11.1 - - - +
155A LYS* 3.0 27.0 + - - +
156A THR* 3.0 37.6 + - + +
118B HIS* 4.1 12.1 - - + +
121B GLN* 3.5 44.0 + - + +
122B THR* 5.3 1.1 - - + -
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Residues in contact with THR 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A PHE* 3.7 13.1 - - + -
64A GLY 3.7 20.5 + - - +
65A ILE* 4.1 11.9 - - + -
66A GLU* 2.6 24.6 + - - +
70A ALA* 3.0 10.3 + - - +
72A GLU* 1.3 78.1 - - - +
74A LEU* 1.3 65.4 + - + +
76A ASN* 3.1 28.4 + - - +
114B ILE* 3.9 16.4 - - + -
118B HIS* 2.7 28.7 + - - -
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Residues in contact with LEU 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A PHE* 5.1 0.7 - - + -
65A ILE* 3.9 22.9 - - + -
69A PRO* 4.3 5.4 - - + -
70A ALA 2.9 22.6 + - - +
71A TYR 3.2 4.2 + - - +
73A THR* 1.3 76.8 - - + +
75A MET* 1.3 60.7 + - - +
76A ASN 3.1 0.2 - - - -
77A ALA* 2.9 22.1 + - - +
78A VAL* 3.0 16.6 + - - +
100A GLY* 3.5 42.2 - - - +
103A PHE* 3.8 28.3 - - + -
104A ILE* 3.7 15.4 - - + +
152A ILE* 4.0 20.9 - - + -
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Residues in contact with MET 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A TYR* 3.0 52.8 + - + +
72A GLU* 4.5 5.6 - - - +
73A THR 3.3 0.2 - - - -
74A LEU* 1.3 76.7 - - - +
76A ASN* 1.3 62.8 + - - +
78A VAL* 3.4 25.6 + - + +
79A LYS* 3.1 23.4 + - - +
82A ARG* 4.8 6.3 - - - +
103A PHE* 4.3 4.3 - - - -
116A PRO* 3.5 37.9 - - + -
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Residues in contact with ASN 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A PHE* 3.9 8.0 - - + -
72A GLU 3.0 27.7 + - - -
73A THR 3.1 11.1 + - - +
74A LEU 3.1 0.2 - - - -
75A MET* 1.3 78.8 - - - +
77A ALA* 1.3 56.7 + - - +
79A LYS* 3.5 9.0 + - - +
80A LEU* 3.1 25.5 + - - +
113B ASN* 3.2 24.2 - - - +
114B ILE* 3.8 19.7 - - - +
115B ASP* 3.2 27.0 + - - +
118B HIS* 5.4 0.6 - - - +
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Residues in contact with ALA 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A LEU* 4.7 3.6 - - + -
62A PHE* 3.7 36.8 - - + -
74A LEU 2.9 5.5 + - - +
76A ASN* 1.3 76.2 - - - +
78A VAL* 1.3 61.6 + - - +
80A LEU* 3.6 4.1 - - - +
81A VAL* 2.9 36.0 + - - +
104A ILE* 3.4 33.2 - - + -
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Residues in contact with VAL 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A LEU 3.0 19.2 + - - +
75A MET* 3.7 26.5 - - + +
76A ASN 3.4 0.2 - - - -
77A ALA* 1.3 75.2 - - - +
79A LYS* 1.3 63.3 + - - +
81A VAL* 3.3 6.1 + - - +
82A ARG* 3.1 58.8 + - - +
103A PHE* 4.5 2.7 - - + -
104A ILE* 4.2 17.7 - - + +
107A ALA* 3.7 35.2 - - + +
108A ALA* 4.4 2.9 - - - -
116A PRO* 5.3 0.4 - - + -
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Residues in contact with LYS 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A MET* 3.1 18.0 + - - +
76A ASN* 3.6 8.5 - - - +
78A VAL* 1.3 77.3 - - - +
80A LEU* 1.3 62.1 + - - +
82A ARG* 3.5 8.4 + - - +
83A GLU* 3.0 42.3 + - + +
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Residues in contact with LEU 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A LEU* 4.0 28.5 - - + -
60A LEU* 4.6 6.7 - - + -
61A GLU 4.6 7.6 - - - +
62A PHE* 4.3 12.8 - - + -
76A ASN 3.1 13.5 + - - +
77A ALA* 3.6 5.6 - - - +
79A LYS* 1.3 80.0 - - - +
81A VAL* 1.3 61.4 + - - +
83A GLU* 3.4 10.7 + - - -
84A GLN* 2.9 51.7 + - + +
86A VAL* 4.3 7.2 - - + -
113B ASN* 3.7 32.8 - - + +
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Residues in contact with VAL 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A LEU* 3.6 26.9 - - + -
77A ALA 2.9 24.8 + - - +
78A VAL* 3.7 5.2 - - - +
79A LYS 3.3 0.4 - - - -
80A LEU* 1.3 77.5 - - - +
82A ARG* 1.3 58.1 + - - +
85A LYS* 3.1 22.9 + - - -
86A VAL* 3.1 26.7 + - + +
89A LEU* 4.3 4.3 - - + -
104A ILE* 3.8 14.6 - - + -
108A ALA* 3.6 15.9 - - + -
131A ILE* 3.4 32.3 - - + -
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Residues in contact with ARG 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A MET* 4.8 8.7 - - - +
78A VAL* 3.1 37.9 + - - +
79A LYS* 3.8 6.8 - - - +
81A VAL* 1.3 76.6 - - - +
83A GLU* 1.3 64.0 + - - +
84A GLN 3.4 0.5 + - - -
85A LYS* 3.4 15.9 + - - +
107A ALA 2.8 26.1 + - - -
108A ALA* 3.6 22.8 + - + +
110A TYR* 3.6 19.6 + - - +
111A PRO 4.8 1.2 + - - -
112A GLU* 4.7 20.9 + - - +
114A ILE 5.6 1.6 + - - -
116A PRO* 5.3 7.5 - - - +
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Residues in contact with GLU 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A LYS* 3.0 40.1 + - + +
80A LEU* 3.4 15.9 - - - +
82A ARG* 1.3 77.1 - - - +
84A GLN* 1.3 87.2 + - + +
85A LYS* 3.8 12.6 + - - +
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Residues in contact with GLN 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A ARG* 3.2 40.1 + - - +
60A LEU* 4.0 26.2 - - + +
80A LEU* 2.9 35.0 + - + +
83A GLU* 1.3 105.0 + - + +
85A LYS* 1.3 73.1 + - - +
86A VAL* 4.5 3.4 - - + -
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Residues in contact with LYS 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A ARG* 3.8 15.2 + - - +
81A VAL 3.1 9.7 + - - -
82A ARG 3.4 12.1 + - - +
83A GLU 3.4 9.8 + - - +
84A GLN* 1.3 82.3 - - - +
86A VAL* 1.3 66.2 + - - +
87A THR* 3.5 13.7 + - + +
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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