Contacts of the helix formed by residues 59 - 78 (chain P) in PDB entry 1ZD2
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 P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53P LEU* 3.5 1.6 - - - -
58P ILE* 1.3 75.4 - - - +
60P LEU* 1.3 65.0 + - - +
61P SER* 3.1 1.9 + - - -
62P GLN* 2.7 45.5 + - + +
63P TRP* 2.9 20.6 + - - +
127P LEU* 3.8 21.1 - - + -
129P ASP* 2.7 32.9 + - + +
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Residues in contact with LEU 60 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53P LEU* 3.4 14.9 - - + +
59P THR* 1.3 73.1 - - - +
61P SER* 1.3 57.7 + - - +
63P TRP* 3.0 30.3 + - + +
64P ILE* 2.9 38.0 + - + +
92P PHE* 5.2 9.2 - - + -
96P ILE* 4.4 2.9 - - + -
126P TRP* 3.0 48.2 - - + +
127P LEU 3.1 17.8 + - - +
128P ASP* 4.0 4.9 - - - +
129P ASP* 4.3 1.3 - - - +
130P ARG* 3.3 40.2 - - + +
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Residues in contact with SER 61 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59P THR* 3.1 0.9 + - - -
60P LEU* 1.3 78.7 - - - +
62P GLN* 1.3 56.8 + - - +
64P ILE* 4.2 11.3 - - - +
65P PRO* 3.1 23.7 - - - +
129P ASP* 2.7 46.9 + - - -
130P ARG* 4.1 7.4 + - - +
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Residues in contact with GLN 62 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57P GLU 4.4 0.7 - - - +
58P ILE* 2.9 28.6 - - + +
59P THR* 2.7 52.4 + - + +
61P SER* 1.3 77.2 - - - +
63P TRP* 1.3 63.4 + - - +
65P PRO* 3.5 7.1 - - - +
66P LEU* 3.3 23.9 - - + +
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Residues in contact with TRP 63 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41P PHE* 3.4 31.2 - + - -
49P ALA* 3.5 31.7 - - + +
50P THR* 2.7 36.5 + - + +
53P LEU* 3.6 24.9 - - + -
58P ILE* 4.1 7.8 - - + +
59P THR 2.9 11.5 + - - +
60P LEU* 3.0 25.5 + - + +
62P GLN* 1.3 77.0 - - - +
64P ILE* 1.3 84.3 + - + +
66P LEU* 2.7 17.1 + - - +
67P MET* 2.8 46.4 + - + +
88P ILE* 4.2 6.7 - - + -
92P PHE* 3.5 29.8 - + - -
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Residues in contact with ILE 64 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60P LEU* 2.9 26.6 + - + +
61P SER* 4.2 11.9 - - - +
63P TRP* 1.3 89.3 - - + +
65P PRO* 1.3 72.9 - - + +
67P MET* 3.0 13.4 + - - +
68P GLU* 3.1 22.2 + - - +
88P ILE* 4.0 10.4 - - + +
89P LYS* 3.8 51.8 - - + +
92P PHE* 6.1 4.3 - - + -
130P ARG* 4.8 13.0 - - + -
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Residues in contact with PRO 65 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61P SER 3.1 23.6 - - - +
62P GLN* 3.5 9.4 - - - +
64P ILE* 1.3 89.7 - - + +
66P LEU* 1.3 61.6 + - + +
68P GLU* 3.0 35.9 + - + +
69P GLU* 3.4 8.3 + - - +
72P ARG* 4.7 1.0 + - - -
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Residues in contact with LEU 66 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49P ALA* 4.0 24.5 - - + +
52P ARG* 5.6 6.5 - - - +
58P ILE* 3.4 33.7 - - + -
62P GLN* 3.3 14.6 - - + +
63P TRP* 2.7 15.5 + - - +
65P PRO* 1.3 78.6 - - + +
67P MET* 1.3 51.4 + - - -
68P GLU 3.2 0.8 + - - -
69P GLU* 4.0 10.9 + - - +
70P ASN* 2.8 30.8 + - - +
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Residues in contact with MET 67 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23P LEU* 4.2 13.7 - - + -
37P LEU 3.9 8.3 - - - +
40P ALA* 3.7 11.2 - - - +
41P PHE* 3.3 58.1 - - + +
49P ALA* 6.0 0.4 - - - -
63P TRP* 2.8 46.4 + - + +
64P ILE 3.0 8.5 + - - +
66P LEU* 1.3 74.9 - - - +
68P GLU* 1.3 59.4 + - - +
70P ASN* 3.8 6.2 - - - +
71P CYS* 3.3 19.9 + - - -
88P ILE* 3.8 22.8 - - + +
92P PHE* 4.2 5.2 - - + -
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Residues in contact with GLU 68 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64P ILE* 3.1 14.0 + - - +
65P PRO* 3.0 29.3 + - + +
67P MET* 1.3 75.2 - - - +
69P GLU* 1.3 61.3 + - - +
70P ASN 3.1 1.6 - - - -
71P CYS* 2.8 24.1 + - - +
72P ARG* 3.2 42.4 + - - +
86P PHE* 5.0 8.5 - - + +
87P SER* 4.6 5.2 + - - -
88P ILE* 3.8 34.5 + - + +
89P LYS* 4.8 1.2 + - - +
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Residues in contact with GLU 69 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65P PRO 3.4 5.6 + - - +
66P LEU* 4.1 14.8 - - - +
68P GLU* 1.3 80.0 - - - +
70P ASN* 1.3 56.4 + - - +
72P ARG* 2.7 44.3 + - + +
73P LYS* 2.9 44.5 + - + +
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Residues in contact with ASN 70 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40P ALA* 2.7 38.6 + - + +
41P PHE 5.0 0.6 + - - -
43P LYS* 3.1 41.2 + - + +
49P ALA* 5.0 10.4 - - - +
66P LEU 2.8 24.3 + - - +
67P MET* 3.8 10.8 - - - +
68P GLU 3.1 0.4 - - - -
69P GLU* 1.3 82.7 - - - +
71P CYS* 1.3 56.5 + - - +
72P ARG 3.1 0.2 - - - -
73P LYS* 3.9 3.7 - - - +
74P CYS* 3.0 34.3 + - - +
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Residues in contact with CYS 71 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36P LEU* 4.4 3.6 - - - +
37P LEU* 3.8 19.5 - - + -
40P ALA* 3.8 17.0 - - - -
67P MET* 3.3 20.4 - - - -
68P GLU* 2.8 13.4 + - + +
70P ASN* 1.3 76.0 - - - +
72P ARG* 1.3 58.7 + - - +
74P CYS* 4.8 1.6 - - - -
75P SER* 3.2 15.7 + - - -
82P LEU* 3.0 27.7 - - + +
86P PHE* 4.2 13.5 - - + -
88P ILE* 3.7 23.6 - - - -
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Residues in contact with ARG 72 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65P PRO 4.7 1.4 + - - -
68P GLU* 3.3 38.7 - - - +
69P GLU* 2.7 43.0 + - + +
71P CYS* 1.3 82.0 - - - +
73P LYS* 1.3 56.9 + - + +
75P SER* 3.0 9.4 + - - -
76P GLU* 2.7 36.0 + - - +
82P LEU* 4.3 11.1 - - + +
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Residues in contact with LYS 73 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43P LYS* 4.6 23.8 - - + +
69P GLU* 2.9 47.7 + - + +
70P ASN* 4.1 5.8 - - - +
72P ARG* 1.3 78.6 - - + +
74P CYS* 1.3 57.9 + - - +
76P GLU* 2.9 37.0 + - - +
77P THR* 3.1 14.3 + - - +
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Residues in contact with CYS 74 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36P LEU* 3.2 30.2 - - + +
39P ASP* 3.6 17.0 - - + -
40P ALA* 3.3 34.5 - - + -
43P LYS* 5.0 11.4 - - - -
70P ASN 3.0 14.9 + - - +
71P CYS* 4.8 0.9 - - - -
73P LYS* 1.3 77.0 - - - +
75P SER* 1.3 58.7 + - - +
77P THR* 2.8 27.5 - - + +
78P ALA* 3.6 5.2 + - - +
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Residues in contact with SER 75 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36P LEU* 3.6 13.9 - - - +
71P CYS 3.2 19.2 + - - -
72P ARG* 3.0 15.6 + - - -
73P LYS 3.1 0.6 - - - -
74P CYS* 1.3 78.7 - - - +
76P GLU* 1.3 60.4 + - - +
79P LYS 3.5 1.9 + - - -
80P VAL* 2.8 49.6 + - - +
81P CYS* 4.1 17.0 - - - -
82P LEU* 4.2 7.6 - - - +
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Residues in contact with GLU 76 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72P ARG 2.7 13.8 + - - +
73P LYS* 2.9 30.3 + - - +
75P SER* 1.3 79.1 - - - +
77P THR* 1.3 59.5 + - - +
79P LYS* 3.8 13.4 + - - +
80P VAL 5.1 1.1 - - - -
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Residues in contact with THR 77 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73P LYS 3.1 5.7 + - - +
74P CYS* 2.8 41.5 - - + +
76P GLU* 1.3 75.0 - - - +
78P ALA* 1.3 62.1 + - + +
79P LYS* 3.0 20.4 + - - +
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Residues in contact with ALA 78 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33P PRO* 4.7 13.4 - - + +
36P LEU* 5.0 2.9 - - + -
74P CYS 3.6 9.7 + - - +
75P SER 4.0 0.2 + - - -
76P GLU 3.7 0.2 - - - -
77P THR* 1.3 80.2 - - + +
79P LYS* 1.3 74.2 + - - +
80P VAL* 3.1 19.8 - - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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