Contacts of the helix formed by residues 59 - 77 (chain A) in PDB entry 5ZJS
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 THR 59 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A LYS* 5.6 4.5 - - - +
53A ALA* 3.6 2.7 - - - -
58A LEU* 1.3 77.4 - - - +
60A GLU* 1.3 62.1 + - - +
61A ARG* 3.2 10.2 + - - +
62A GLN* 2.7 50.8 + - + +
63A VAL* 3.2 24.4 + - - +
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Residues in contact with GLU 60 (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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46A LYS 3.7 18.9 - - - +
49A ARG* 3.3 30.9 + - - +
50A TRP* 3.3 35.3 - - + +
53A ALA* 4.2 12.1 - - + -
59A THR* 1.3 72.0 - - - +
61A ARG* 1.3 61.0 + - - +
63A VAL* 3.4 1.0 + - - +
64A LYS* 2.9 25.7 + - - +
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Residues in contact with ARG 61 (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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21A LYS* 6.0 1.3 - - - +
59A THR* 3.2 7.8 + - - +
60A GLU* 1.3 77.0 - - - +
62A GLN* 1.3 58.7 + - + +
64A LYS* 3.3 22.1 - - + +
65A ILE* 2.9 50.5 + - + +
10D A 5.0 0.8 - - - +
11D T 2.7 54.9 + - - +
12D G 5.3 1.6 + - - -
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Residues in contact with GLN 62 (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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21A LYS* 4.8 14.2 - - - +
26A TYR* 3.3 24.1 + - - +
57A GLN 4.6 0.7 - - - +
58A LEU* 3.3 30.1 - - + +
59A THR* 2.7 56.6 + - + +
60A GLU 3.3 0.2 - - - -
61A ARG* 1.3 74.7 - - - +
63A VAL* 1.3 56.8 + - - +
65A ILE* 3.4 6.9 + - - +
66A TRP* 2.9 29.3 + - - +
10D A 3.1 28.8 + - - +
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Residues in contact with VAL 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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34A LEU* 4.7 5.8 - - + -
44A VAL* 4.9 2.7 - - + -
49A ARG* 3.8 19.7 - - + +
52A LEU* 3.9 22.4 - - + -
53A ALA* 3.9 27.6 - - + +
58A LEU* 4.4 15.7 - - + -
59A THR 3.2 14.6 + - - +
60A GLU 3.8 6.1 - - - +
61A ARG 3.3 0.2 - - - -
62A GLN* 1.3 72.5 - - - +
64A LYS* 1.3 68.0 + - - +
66A TRP* 3.1 6.4 + - - +
67A PHE* 3.0 42.5 + - + -
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Residues in contact with LYS 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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49A ARG* 4.1 29.6 - - - +
60A GLU 2.9 18.6 + - - +
61A ARG* 3.3 23.1 - - + +
63A VAL* 1.3 78.5 - - - +
65A ILE* 1.3 71.9 + - + +
67A PHE* 3.3 5.2 + - - +
68A GLN* 3.0 52.9 + - + +
71A ARG* 5.2 0.2 + - - -
1C G 5.9 2.9 + - - -
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Residues in contact with ILE 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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26A TYR* 5.9 1.8 - - - +
61A ARG* 2.9 43.1 + - + +
62A GLN* 3.6 6.5 - - - +
64A LYS* 1.3 83.6 - - + +
66A TRP* 1.3 65.7 + - - +
68A GLN* 3.1 20.0 + - - +
69A ASN* 2.9 42.8 + - - +
9D A 5.1 5.4 - - + -
10D A 3.6 25.8 - - + +
11D T 3.6 23.3 - - + +
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Residues in contact with TRP 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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26A TYR* 3.8 25.1 - + + -
31A THR* 4.4 12.8 + - + +
34A LEU* 3.5 64.8 - - + +
35A GLU* 3.8 20.6 - - + -
38A PHE* 4.3 6.7 - + + -
62A GLN 2.9 14.9 + - - +
63A VAL* 3.1 9.8 + - - +
65A ILE* 1.3 76.8 - - - +
67A PHE* 1.3 79.6 + + + +
69A ASN* 3.9 6.0 - - + +
70A ARG* 2.9 65.5 + - + +
9D A 4.1 16.3 + - - -
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Residues in contact with PHE 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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34A LEU* 4.0 20.6 - - + -
37A GLU* 4.3 10.5 - - + -
38A PHE* 3.8 17.7 - + - -
41A ASN 3.2 22.9 - - - -
42A ALA 3.4 18.6 - - - -
44A VAL* 4.2 24.7 - - + -
52A LEU* 3.7 29.8 - - + -
63A VAL* 3.0 32.0 + - + +
64A LYS* 3.8 4.5 - - - +
66A TRP* 1.3 90.7 - + - +
68A GLN* 1.3 65.8 + - - +
70A ARG* 3.4 2.7 + - - +
71A ARG* 2.9 39.9 + - - +
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Residues in contact with GLN 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 LYS* 3.0 48.7 + - + +
65A ILE* 3.1 25.0 + - - +
67A PHE* 1.3 75.4 - - - +
69A ASN* 1.3 65.7 + - - +
71A ARG* 3.0 40.3 + - - +
72A MET* 3.1 18.3 + - - +
1C G 4.8 9.5 + - - -
2C T 3.4 33.2 + - + +
3C C 4.5 12.9 + - + +
11D T 5.0 1.9 - - - +
12D G 4.9 2.9 - - - +
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Residues in contact with ASN 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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65A ILE* 2.9 29.4 + - - +
66A TRP* 3.9 5.5 - - - +
68A GLN* 1.3 74.8 - - - +
70A ARG* 1.3 57.9 + - - +
72A MET* 3.1 11.2 + - - +
73A LYS* 2.9 29.0 + - - +
3C C 5.8 1.7 + - - -
4C A 4.8 3.1 + - - -
9D A 3.6 22.6 + - - +
10D A 3.2 44.3 + - - +
11D T 5.2 1.7 - - - +
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Residues in contact with ARG 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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35A GLU* 2.7 42.9 + - - -
38A PHE* 3.6 32.4 - - + -
66A TRP* 2.9 46.3 + - + +
67A PHE 3.7 4.9 - - - +
69A ASN* 1.3 76.2 - - - +
71A ARG* 1.3 57.8 + - - +
73A LYS* 3.3 30.3 + - - +
74A ASN* 2.9 51.7 + - - +
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Residues in contact with ARG 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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38A PHE* 4.2 13.5 - - + -
42A ALA* 3.2 29.6 + - + +
43A TYR* 3.4 35.2 - - - +
44A VAL 5.4 0.2 - - - +
67A PHE* 2.9 37.4 + - - +
68A GLN* 3.0 31.3 + - - +
70A ARG* 1.3 76.6 - - - +
72A MET* 1.3 69.3 + - + +
74A ASN* 3.2 5.5 + - - +
75A LYS* 2.9 22.5 + - - +
1C G 3.7 15.4 + - - -
2C T 2.7 46.7 + - - +
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Residues in contact with MET 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 GLN 3.1 15.5 + - - +
69A ASN* 3.1 12.1 + - - +
71A ARG* 1.3 80.6 - - + +
73A LYS* 1.3 62.6 + - - +
75A LYS* 3.0 19.5 + - + +
76A LYS* 3.0 21.1 + - - +
2C T 3.7 33.9 - - + +
3C C 3.7 63.0 - - + +
4C A 6.1 1.1 - - - +
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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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35A GLU* 4.8 9.3 + - - -
69A ASN 2.9 12.6 + - - +
70A ARG* 3.4 35.6 - - - +
71A ARG 3.2 0.2 - - - -
72A MET* 1.3 77.7 - - - +
74A ASN* 1.3 63.4 + - - +
76A LYS* 3.1 15.9 + - - +
77A ASN* 3.2 33.7 + - - +
8D T 3.0 41.8 + - - +
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Residues in contact with ASN 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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38A PHE* 4.0 19.1 - - + -
42A ALA* 6.2 0.2 - - - +
70A ARG* 2.9 32.0 + - - +
71A ARG* 3.2 8.5 + - - +
73A LYS* 1.3 76.9 - - - +
75A LYS* 1.3 61.9 + - - +
77A ASN* 3.9 19.0 - - - +
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Residues in contact with LYS 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 ARG 2.9 10.3 + - - +
72A MET* 3.0 26.0 + - + +
74A ASN* 1.3 77.2 - - - +
76A LYS* 1.3 68.1 + - - +
77A ASN 4.4 1.7 - - - -
2C T 3.7 13.3 + - - -
3C C 2.4 43.8 + - - +
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Residues in contact with LYS 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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72A MET 3.0 12.2 + - - +
73A LYS* 3.1 11.2 + - - +
75A LYS* 1.3 81.7 - - - +
77A ASN* 1.3 71.0 + - - +
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Residues in contact with ASN 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* 3.2 37.4 + - - +
74A ASN* 3.9 18.0 - - - +
75A LYS 3.6 2.2 - - - -
76A LYS* 1.3 87.5 - - - +
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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