Contacts of the helix formed by residues 70 - 84 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65D ILE* 5.5 0.8 - - - +
66D GLU 4.8 2.2 + - - +
68D ASN 3.3 2.8 + - - -
69D PRO* 1.3 71.6 - - - +
71D TYR* 1.3 65.8 + - - +
72D GLU* 4.4 7.9 - - + +
73D THR* 3.2 20.4 + - - +
74D LEU* 3.1 25.1 + - - +
153D SER 3.4 5.6 - - - -
155D LYS* 3.9 29.2 - - + +
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Residues in contact with TYR 71 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69D PRO 3.8 0.6 + - - -
70D ALA* 1.3 70.9 - - - +
72D GLU* 1.3 87.8 + - - +
74D LEU* 3.1 5.8 + - - +
75D MET* 3.0 58.7 + - + +
103D PHE* 3.9 14.6 - + - -
115D ASP* 2.4 37.3 + - - -
116D PRO* 4.2 1.6 - - - +
117D TRP* 3.8 35.7 - + + -
152D ILE* 4.5 6.7 - - + -
153D SER 2.6 18.1 + - - +
154D ARG* 4.0 27.7 - - + +
155D LYS 5.3 0.2 - - - +
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Residues in contact with GLU 72 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70D ALA* 3.2 6.4 - - + +
71D TYR* 1.3 104.4 - - - +
73D THR* 1.3 63.4 + - - +
75D MET* 3.5 10.9 + - - +
76D ASN* 3.6 17.2 + - - +
154D ARG* 4.5 2.6 - - - +
155D LYS* 5.2 2.1 + - - +
156D THR* 3.2 23.9 + - - -
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Residues in contact with THR 73 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62D PHE* 3.4 25.8 - - + -
64D GLY* 3.8 28.6 + - - +
65D ILE* 4.5 7.6 - - + +
66D GLU 6.1 0.2 - - - -
70D ALA* 3.2 21.6 + - - +
72D GLU* 1.3 78.9 - - - +
74D LEU* 1.3 64.3 + - - +
76D ASN* 3.2 25.1 + - - +
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Residues in contact with LEU 74 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62D PHE* 5.3 0.2 - - - -
65D ILE* 3.9 27.1 - - + -
69D PRO* 4.1 6.5 - - + -
70D ALA 3.1 18.2 + - - +
71D TYR 3.1 4.2 + - - +
73D THR* 1.3 77.6 - - - +
75D MET* 1.3 58.5 + - - +
77D ALA* 3.1 10.5 + - - +
78D VAL* 2.9 29.2 + - - +
100D GLY* 3.6 39.0 - - - +
103D PHE* 3.8 24.7 - - + -
104D ILE* 3.8 12.6 - - + +
152D ILE* 3.8 28.7 - - + -
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Residues in contact with MET 75 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71D TYR* 3.0 52.3 + - + +
72D GLU* 3.8 6.5 - - - +
73D THR 3.3 0.4 - - - -
74D LEU* 1.3 74.7 - - - +
76D ASN* 1.3 61.3 + - - +
78D VAL* 3.6 21.2 - - + +
79D LYS* 3.1 26.7 + - - +
82D ARG* 4.9 7.0 - - - +
103D PHE* 4.1 11.7 - - - -
116D PRO* 3.6 38.1 - - + -
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Residues in contact with ASN 76 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62D PHE* 4.1 13.5 - - + -
72D GLU 3.6 14.4 + - - +
73D THR* 3.2 14.5 + - - +
75D MET* 1.3 78.9 - - - +
77D ALA* 1.3 60.1 + - - +
79D LYS* 3.6 18.3 + - - +
80D LEU* 3.3 21.0 + - - +
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Residues in contact with ALA 77 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D LEU* 4.6 4.8 - - + +
35D THR* 5.6 0.2 - - + -
62D PHE* 3.7 37.1 - - + -
73D THR 3.5 2.0 + - - -
74D LEU 3.1 11.2 + - - +
76D ASN* 1.3 77.0 - - - +
78D VAL* 1.3 58.5 + - - +
80D LEU* 3.3 6.4 + - - +
81D VAL* 3.0 33.0 + - - +
104D ILE* 3.5 27.4 - - + -
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Residues in contact with VAL 78 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74D LEU 2.9 19.2 + - - +
75D MET* 3.3 26.9 + - + +
77D ALA* 1.3 75.7 - - - +
79D LYS* 1.3 62.4 + - - +
81D VAL* 3.3 8.2 + - - +
82D ARG* 3.1 55.4 + - - +
103D PHE* 4.6 1.6 - - + -
104D ILE* 4.0 21.5 - - + +
107D ALA* 3.8 25.1 - - + +
108D ALA* 4.0 12.1 - - - +
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Residues in contact with LYS 79 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75D MET 3.1 15.3 + - - +
76D ASN* 3.7 16.8 - - - +
77D ALA 3.3 0.2 - - - -
78D VAL* 1.3 78.5 - - - +
80D LEU* 1.3 55.7 + - - +
82D ARG* 3.3 8.8 + - - +
83D GLU* 3.0 66.5 + - + +
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Residues in contact with LEU 80 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D LEU* 4.1 28.5 - - + -
60D LEU* 5.0 9.2 - - + -
61D GLU 4.2 11.7 - - - +
62D PHE* 4.4 16.4 - - + -
76D ASN 3.3 12.2 + - - +
77D ALA 3.5 7.6 - - - +
79D LYS* 1.3 79.6 - - - +
81D VAL* 1.3 57.1 + - - +
83D GLU* 4.6 5.8 - - + +
84D GLN* 3.1 53.8 + - + +
86D VAL* 4.5 0.8 - - + +
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Residues in contact with VAL 81 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33D LEU* 3.5 26.5 - - + -
77D ALA 3.0 20.6 + - - +
78D VAL* 3.6 6.7 - - - +
79D LYS 3.2 0.2 - - - -
80D LEU* 1.3 76.3 - - - +
82D ARG* 1.3 63.3 + - + +
85D LYS* 3.2 4.7 + - - -
86D VAL* 3.2 39.1 + - + +
89D LEU* 4.3 5.4 - - + -
104D ILE* 3.9 14.4 - - + -
108D ALA* 3.6 14.4 - - + -
131D ILE* 3.3 33.2 - - + -
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Residues in contact with ARG 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75D MET* 4.9 8.9 - - - +
78D VAL* 3.1 34.4 + - - +
79D LYS* 3.3 8.2 + - - +
81D VAL* 1.3 77.1 - - + +
83D GLU* 1.3 64.8 + - + +
84D GLN 3.6 0.2 + - - -
85D LYS* 3.6 15.1 + - - +
107D ALA 2.9 26.6 + - - -
108D ALA* 3.2 24.8 + - + +
110D TYR* 3.4 20.8 + - - +
111D PRO 4.6 4.6 + - - -
112D GLU* 4.7 17.5 + - - +
114D ILE 5.7 0.2 + - - -
116D PRO* 5.3 5.7 - - - +
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Residues in contact with GLU 83 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79D LYS* 3.0 56.9 + - + +
80D LEU* 4.2 5.5 - - + +
82D ARG* 1.3 79.7 - - + +
84D GLN* 1.3 76.4 + - + +
85D LYS* 4.5 5.7 - - - +
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Residues in contact with GLN 84 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31D ARG* 3.1 43.1 + - - +
60D LEU* 3.8 23.6 - - + +
80D LEU* 3.1 41.0 + - + +
83D GLU* 1.3 91.7 + - + +
85D LYS* 1.3 69.9 + - - +
86D VAL* 4.4 3.4 - - + -
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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