Contacts of the helix formed by residues 62 - 73 (chain A) in PDB entry 1JZO
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 VAL 62 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23A PRO* 4.5 19.3 - - + -
38A TYR* 3.5 6.3 - - + +
51A MET* 2.9 53.7 + - + +
52A TYR 4.1 1.3 - - - -
53A ASP* 3.6 36.1 - - + +
60A VAL* 3.8 4.3 - - + +
61A ASN* 1.3 70.3 - - - +
63A THR* 1.3 66.5 + - - +
65A LYS* 3.6 12.3 - - + +
66A MET* 3.0 23.7 + - - +
45B HIS* 4.6 0.9 - - + +
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Residues in contact with THR 63 (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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36A VAL* 3.9 31.4 - - + -
38A TYR* 2.6 23.4 + - + -
49A GLY* 5.6 1.6 - - - -
50A PRO* 3.3 13.6 - - + +
51A MET 3.0 18.4 + - - -
61A ASN* 3.1 9.3 + - - -
62A VAL* 1.3 78.9 - - - +
64A ASN* 1.3 60.5 + - - +
66A MET* 3.2 8.5 + - - +
67A LEU* 2.9 42.2 + - + +
176A GLN 5.3 3.6 - - - +
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Residues in contact with ASN 64 (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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50A PRO* 5.4 0.7 - - - +
61A ASN* 3.1 32.9 + - - +
63A THR* 1.3 81.4 - - - +
65A LYS* 1.3 64.9 + - - +
67A LEU* 3.1 15.0 + - - +
68A LEU* 3.1 17.5 + - - +
176A GLN 4.1 2.9 - - - +
177A LEU* 3.2 56.0 + - + +
186A VAL* 5.8 0.4 - - - +
190A GLY* 2.9 30.8 + - - +
192A LEU* 4.2 9.5 - - - +
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Residues in contact with LYS 65 (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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60A VAL* 4.6 15.8 - - + +
61A ASN 3.0 17.9 + - - +
62A VAL* 3.6 12.3 - - + +
64A ASN* 1.3 75.5 - - - +
66A MET* 1.3 61.2 + - - +
68A LEU* 3.3 26.1 - - + +
69A LYS 4.6 0.5 + - - -
188A SER 5.7 0.4 + - - -
189A ASN* 3.7 32.4 + - - +
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Residues in contact with MET 66 (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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20A GLN* 3.6 38.6 - - + +
21A PRO* 4.0 11.2 - - + +
29A THR* 4.0 26.2 - - + +
31A LEU* 6.5 0.4 - - + -
36A VAL* 5.6 4.9 - - + -
62A VAL 3.0 13.8 + - - +
63A THR* 3.3 10.8 - - - +
65A LYS* 1.3 75.4 - - - +
67A LEU* 1.3 65.4 + - + +
68A LEU 3.0 5.9 + - - -
69A LYS* 3.1 31.5 + - - +
70A GLN* 5.5 0.3 - - - +
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Residues in contact with LEU 67 (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 LEU* 4.4 7.9 - - + -
36A VAL* 3.7 20.9 - - + -
63A THR* 2.9 30.0 + - + +
64A ASN* 3.1 15.4 + - - +
66A MET* 1.3 72.0 - - + +
68A LEU* 1.3 56.1 + - - +
69A LYS 2.9 6.3 - - - -
70A GLN* 2.8 32.8 + - + +
71A LEU* 2.9 12.9 + - - +
173A LEU* 4.3 10.2 - - + +
176A GLN* 3.7 42.0 - - + +
177A LEU* 3.6 28.7 - - + -
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Residues in contact with LEU 68 (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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64A ASN 3.1 15.1 + - - +
65A LYS* 3.3 20.9 - - + +
66A MET 3.0 0.8 - - - -
67A LEU* 1.3 76.5 - - - +
69A LYS* 1.3 55.3 + - - +
71A LEU* 3.6 30.5 - - + +
72A ASN* 2.8 46.3 + - - +
177A LEU* 6.0 1.8 - - + -
186A VAL* 4.3 3.4 - - + -
187A LEU 4.1 8.7 - - - +
188A SER* 3.0 28.0 - - - +
189A ASN* 3.7 5.2 - - - -
190A GLY* 3.6 24.7 - - - +
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Residues in contact with LYS 69 (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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18A ASP* 4.6 6.5 + - - -
20A GLN* 4.5 20.3 - - + +
65A LYS 4.6 0.4 + - - -
66A MET* 3.1 25.3 + - - +
68A LEU* 1.3 80.2 - - - +
70A GLN* 1.3 68.6 + - + +
72A ASN* 3.6 4.9 + - - +
73A ALA* 3.1 26.5 + - - +
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Residues in contact with GLN 70 (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 LEU* 3.7 33.1 - - + +
66A MET 5.5 0.2 - - - +
67A LEU* 2.8 21.3 + - + +
69A LYS* 1.3 89.3 - - + +
71A LEU* 1.3 65.8 + - - +
73A ALA* 3.2 20.7 + - - +
74A LEU* 3.5 15.4 + - - +
173A LEU* 4.3 15.5 - - + -
176A GLN* 6.0 0.7 - - - +
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Residues in contact with LEU 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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67A LEU 2.9 12.4 + - - +
68A LEU* 3.6 29.6 - - + +
69A LYS 3.2 0.2 - - - -
70A GLN* 1.3 73.3 - - - +
72A ASN* 1.3 69.2 + - - +
73A ALA 3.0 4.5 - - - -
74A LEU* 2.9 18.8 + - - +
78A MET* 3.3 27.6 - - + +
91A THR* 4.2 17.3 - - + +
93A PHE* 5.1 0.4 - - + -
119A ARG* 3.2 29.8 - - - +
121A LEU* 4.7 2.0 - - + -
173A LEU* 3.7 20.6 - - + +
177A LEU* 4.7 11.9 - - + -
186A VAL* 4.0 20.6 - - + -
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Residues in contact with ASN 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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68A LEU* 2.8 36.0 + - - +
69A LYS* 4.1 4.6 - - - +
71A LEU* 1.3 85.4 - - - +
73A ALA* 1.3 61.3 + - - +
75A GLU* 3.1 43.3 + - - +
78A MET* 5.0 0.2 - - - -
119A ARG* 3.8 5.7 + - - -
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Residues in contact with ALA 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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69A LYS 3.1 14.5 + - - +
70A GLN* 3.2 21.8 - - - +
71A LEU 3.0 0.2 - - - -
72A ASN* 1.3 78.8 - - - +
74A LEU* 1.3 63.4 + - + +
75A GLU 3.3 1.2 + - - -
76A LYS* 4.9 4.3 + - - +
77A GLU* 5.4 0.9 - - - +
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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