Contacts of the helix formed by residues 64 - 79 (chain A) in PDB entry 2JAZ
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 SER 64 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A ARG* 4.2 1.2 - - - +
62A ASP* 3.1 16.8 + - - +
63A ASP* 1.3 78.2 + - - +
65A PRO* 1.3 77.7 - - - +
66A GLU* 3.5 15.1 + - - +
67A GLY 3.0 16.8 + - - -
68A ILE* 2.9 28.7 + - - +
515B ARG* 3.7 13.5 - - - +
515D ARG* 5.8 1.1 - - - -
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Residues in contact with PRO 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A VAL* 4.1 18.6 - - + -
19A LEU* 3.6 23.2 - - + +
20A LYS* 3.6 15.5 - - - +
23A GLU* 3.5 24.7 - - - +
64A SER* 1.3 87.4 - - - +
66A GLU* 1.3 67.2 + - - +
68A ILE* 3.3 6.0 + - + +
69A VAL* 3.0 29.9 + - - +
515B ARG* 5.5 0.7 - - - +
519D ASP* 3.7 16.8 - - - +
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Residues in contact with GLU 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A VAL* 4.8 1.2 - - - +
64A SER* 3.5 15.0 + - - +
65A PRO* 1.3 84.6 - - - +
67A GLY* 1.3 57.0 + - - +
69A VAL* 3.5 6.0 + - - +
70A LYS* 3.0 30.2 + - - +
504D SER* 5.0 11.7 - - - +
515D ARG 5.3 0.2 - - - +
518D ASN* 4.4 18.3 - - + +
519D ASP* 2.6 41.4 - - - +
522D LYS* 3.5 39.4 + - + +
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Residues in contact with GLY 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A ARG* 3.7 12.4 + - - +
62A ASP* 3.5 23.8 - - - +
64A SER* 3.0 15.0 + - - -
66A GLU* 1.3 78.3 - - - +
68A ILE* 1.3 55.5 + - - +
70A LYS* 3.4 8.5 + - - +
71A GLU* 2.9 30.8 + - - +
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Residues in contact with ILE 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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19A LEU* 3.8 31.4 - - + -
23A GLU* 6.1 0.4 - - - +
41A PHE* 4.3 9.4 - - + -
53A LEU* 3.6 21.4 - - + +
54A ILE* 4.0 22.9 - - + +
61A ARG* 3.4 20.4 - - - +
63A ASP* 5.5 2.7 - - - +
64A SER 2.9 23.7 + - - +
65A PRO* 3.6 8.3 - - + +
67A GLY* 1.3 76.3 - - - +
69A VAL* 1.3 63.0 + - - +
71A GLU* 3.3 2.3 + - - +
72A ILE* 3.0 42.4 + - + +
516B ASN* 5.3 5.4 - - - +
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Residues in contact with VAL 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A GLU* 3.6 44.2 - - + +
15A PHE* 3.8 23.3 - - + -
16A VAL* 3.9 22.7 - - + -
19A LEU* 4.2 2.2 - - + -
65A PRO 3.0 20.3 + - - +
66A GLU* 3.9 5.4 - - - +
68A ILE* 1.3 75.7 - - - +
70A LYS* 1.3 59.1 + - - +
72A ILE* 3.3 7.3 + - - +
73A LYS* 2.8 29.3 + - + +
84A PHE* 3.7 13.3 - - + -
522D LYS* 4.7 3.6 - - - +
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Residues in contact with LYS 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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12A GLU* 6.0 0.2 - - - -
61A ARG* 6.5 0.7 - - + -
66A GLU 3.0 18.9 + - - +
67A GLY* 3.7 8.1 - - - +
68A ILE 3.3 0.2 - - - -
69A VAL* 1.3 79.0 - - - +
71A GLU* 1.3 62.4 + - - +
73A LYS* 3.4 9.8 + - + +
74A GLU* 3.0 52.8 + - - +
505D LYS* 5.3 8.5 + - - +
507D PRO* 6.3 3.3 - - - +
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Residues in contact with GLU 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A HIS* 4.8 6.9 + - + +
53A LEU* 3.3 24.7 - - + +
57A PRO* 5.4 0.2 - - - +
58A SER* 4.1 13.6 + - - -
60A ASN* 5.4 0.9 - - - +
61A ARG* 2.8 49.0 + - + +
67A GLY 2.9 17.5 + - - +
68A ILE 3.9 2.5 - - - +
70A LYS* 1.3 77.8 - - - +
72A ILE* 1.3 60.3 + - - +
74A GLU* 3.3 7.4 + - - +
75A TRP* 2.8 33.7 + - + +
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Residues in contact with ILE 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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7A ILE* 4.9 5.8 - - + -
15A PHE* 3.5 36.8 - - + -
41A PHE* 4.0 5.2 - - + -
45A THR* 3.9 17.0 - - + +
47A HIS* 5.7 2.0 - - + -
53A LEU* 3.9 20.4 - - + -
68A ILE* 3.0 32.0 + - + +
69A VAL* 3.7 3.8 - - - +
71A GLU* 1.3 74.8 - - - +
73A LYS* 1.3 56.2 + - - +
75A TRP* 3.2 5.9 + - + +
76A ARG* 2.8 60.5 + - + +
84A PHE* 3.9 15.5 - - + -
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Residues in contact with LYS 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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12A GLU* 2.9 31.4 + - - +
69A VAL 2.8 18.2 + - - +
70A LYS* 3.5 11.7 - - + +
72A ILE* 1.3 76.8 - - - +
74A GLU* 1.3 60.0 + - + +
76A ARG* 4.0 4.1 - - - +
77A ALA* 3.1 32.5 + - + +
83A GLY* 6.2 2.2 - - - -
84A PHE* 4.2 18.6 - - + +
86A GLN* 6.0 2.0 - - - +
505D LYS* 5.1 13.7 - - - +
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Residues in contact with GLU 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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70A LYS* 3.0 54.3 + - - +
71A GLU* 3.9 5.3 - - - +
73A LYS* 1.3 77.2 - - + +
75A TRP* 1.3 60.8 + - - +
77A ALA* 3.5 5.0 + - - +
78A ALA* 2.9 32.1 + - - +
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Residues in contact with TRP 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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45A THR 4.1 11.0 - - - -
46A GLU 3.4 23.8 - - - -
47A HIS* 3.4 39.0 + + + +
48A PRO* 3.4 22.3 - - + +
71A GLU* 2.8 25.0 + - + +
72A ILE* 3.8 3.8 - - + +
74A GLU* 1.3 73.9 - - - +
76A ARG* 1.3 74.5 + - + +
78A ALA* 3.3 5.1 + - + +
79A ASN* 2.8 54.6 + - - +
81A LYS* 4.0 32.3 - - + -
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Residues in contact with ARG 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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7A ILE* 3.8 30.2 - - - +
8A SER 5.5 0.2 - - - +
44A ILE 3.7 4.9 + - - -
45A THR 2.9 23.7 + - - +
46A GLU* 3.0 28.3 + - - -
72A ILE* 2.8 42.2 + - + +
73A LYS* 4.1 4.5 - - - +
75A TRP* 1.3 91.1 - - + +
77A ALA* 1.3 60.4 + - - +
79A ASN* 3.1 6.8 + - - -
81A LYS* 2.9 50.2 + - + +
82A PRO* 2.8 48.7 + - - +
83A GLY* 5.3 5.2 - - - -
84A PHE* 5.7 0.4 - - - -
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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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73A LYS* 3.1 20.3 + - + +
74A GLU* 3.8 5.2 - - - +
76A ARG* 1.3 76.3 - - - +
78A ALA* 1.3 63.0 + - - +
80A GLY* 3.1 13.4 + - - -
81A LYS 4.5 5.6 - - - +
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Residues in contact with ALA 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 GLU 2.9 19.7 + - - +
75A TRP* 3.6 8.3 - - + +
76A ARG 3.2 0.2 - - - -
77A ALA* 1.3 76.8 - - - +
79A ASN* 1.3 63.9 + - - +
80A GLY 3.4 0.6 + - - -
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Residues in contact with ASN 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 TRP* 2.8 65.7 + - + +
76A ARG 3.1 5.2 + - - +
78A ALA* 1.3 83.4 - - - +
80A GLY* 1.3 62.4 + - - +
81A LYS* 3.1 20.5 + - + +
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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