Contacts of the helix formed by residues 66 - 84 (chain A) in PDB entry 1HZ4
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 GLU 66 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A LEU* 2.9 33.8 + - + +
64A LYS* 4.1 28.0 - - + +
65A GLY* 1.3 76.1 - - - +
67A LEU* 1.3 57.3 + - - +
69A ARG* 3.1 39.4 + - + +
70A SER* 2.8 28.1 + - - -
782A SO4 3.3 22.8 + - - +
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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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62A HIS* 3.8 39.3 - - + +
65A GLY* 3.1 17.3 + - - +
66A GLU* 1.3 74.6 - - - +
68A THR* 1.3 60.9 + - - +
70A SER* 3.6 3.5 - - - -
71A LEU* 2.9 35.3 + - - +
100A ILE* 4.0 14.7 - - + +
103A ALA* 5.6 1.6 - - + -
104A GLN* 3.9 29.8 - - + +
248A HIS* 4.3 5.6 - - - +
284A LEU* 4.3 14.4 - - + +
286A LEU* 3.8 28.5 - - + -
782A SO4 3.3 3.7 + - - +
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Residues in contact with THR 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A LEU* 1.3 77.8 - - - +
69A ARG* 1.3 65.3 + - + +
71A LEU* 3.4 9.7 + - - +
72A ALA* 3.2 19.4 + - - +
104A GLN* 5.1 5.5 + - - +
782A SO4 3.0 23.7 + - - +
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Residues in contact with ARG 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A LEU* 3.6 19.1 - - + -
66A GLU* 3.1 36.1 + - - +
68A THR* 1.3 75.9 - - + +
70A SER* 1.3 66.1 + - - +
72A ALA* 3.2 9.5 + - + +
73A LEU* 3.1 25.8 + - - +
782A SO4 2.9 45.8 + - - +
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Residues in contact with SER 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A GLY* 2.7 22.8 + - - -
61A LEU* 3.7 9.6 - - - +
62A HIS* 3.3 19.9 + - - +
66A GLU 2.8 19.0 + - - -
67A LEU* 3.6 5.8 - - - -
68A THR 3.3 0.2 - - - -
69A ARG* 1.3 77.5 - - - +
71A LEU* 1.3 58.2 + - - +
73A LEU* 3.1 6.3 + - - +
74A MET* 2.8 48.4 + - - +
100A ILE* 3.9 7.4 - - - -
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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
----------------------------------------------------------
67A LEU 2.9 21.7 + - - +
68A THR* 3.7 9.0 - - - +
69A ARG 3.3 0.2 - - - -
70A SER* 1.3 76.3 - - - +
72A ALA* 1.3 57.4 + - - +
74A MET* 3.2 4.6 + - - +
75A GLN* 2.9 48.1 + - - +
97A GLN* 3.9 38.8 - - + +
100A ILE* 3.9 31.2 - - + -
101A LEU* 4.8 12.1 - - + -
104A GLN* 4.3 13.5 - - - +
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Residues in contact with ALA 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 THR 3.2 10.4 + - - +
69A ARG* 3.2 12.7 + - - +
70A SER 3.2 0.4 - - - -
71A LEU* 1.3 80.0 - - - +
73A LEU* 1.3 58.0 + - + +
75A GLN* 3.3 14.8 + - - +
76A GLN* 3.0 36.9 + - - +
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Residues in contact with LEU 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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54A THR* 4.0 12.9 - - + +
57A LEU* 3.7 36.1 - - + -
58A GLY* 3.8 11.9 - - - +
61A LEU* 3.5 29.2 - - + -
69A ARG 3.1 11.1 + - - +
70A SER 3.1 7.7 + - - +
72A ALA* 1.3 76.9 - - + +
74A MET* 1.3 60.6 + - - +
76A GLN* 3.3 28.4 + - - +
77A THR* 2.9 32.9 + - - -
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Residues in contact with MET 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A SER* 6.1 0.7 - - - +
58A GLY* 4.3 8.1 - - - +
62A HIS* 3.9 11.9 - - + +
70A SER* 2.8 38.0 + - - +
71A LEU* 3.2 9.4 + - - +
73A LEU* 1.3 75.4 - - - +
75A GLN* 1.3 57.2 + - - +
77A THR* 3.2 6.4 + - - -
78A GLU* 2.8 17.7 + - - +
93A SER* 2.7 24.2 + - - +
96A GLN* 3.5 48.9 - - + +
97A GLN* 3.7 31.0 - - + -
100A ILE* 3.4 22.2 - - + -
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Residues in contact with GLN 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 LEU* 2.9 39.3 + - - +
72A ALA* 3.5 13.1 - - - +
74A MET* 1.3 74.3 - - - +
76A GLN* 1.3 65.2 + - - +
78A GLU* 3.3 7.0 + - - +
79A GLN* 3.0 30.8 + - + +
97A GLN* 4.2 22.8 + - - +
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Residues in contact with GLN 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A THR* 4.3 11.1 - - + +
72A ALA* 3.0 21.4 + - - +
73A LEU* 3.3 30.7 + - - +
75A GLN* 1.3 76.0 - - - +
77A THR* 1.3 62.3 + - - +
79A GLN* 3.4 6.5 + - - +
80A MET* 3.1 34.8 + - + +
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Residues in contact with THR 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A ILE* 4.0 17.8 - - + +
54A THR* 3.4 5.0 - - - +
55A SER* 3.3 47.6 + - - +
73A LEU 2.9 14.6 + - - -
74A MET* 3.4 10.9 - - - -
76A GLN* 1.3 78.4 - - - +
78A GLU* 1.3 58.1 + - - +
80A MET* 3.3 10.4 + - - +
81A ALA* 2.9 28.2 + - - +
89A TYR* 4.4 15.0 - - + +
93A SER* 4.6 4.3 - - - -
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Residues in contact with GLU 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 MET 2.8 9.6 + - - +
75A GLN* 3.6 8.4 - - - +
77A THR* 1.3 77.0 - - - +
79A GLN* 1.3 68.2 + - - +
81A ALA* 3.3 5.5 + - - +
82A ARG* 2.9 72.4 + - + +
90A ALA* 4.2 15.9 - - + +
93A SER* 3.5 18.8 + - - +
94A LEU* 3.5 19.3 - - + +
97A GLN* 3.0 21.0 + - - +
116A LYS* 5.2 5.3 + - - +
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Residues in contact with GLN 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 GLN* 3.0 21.3 + - + +
76A GLN* 3.7 6.5 - - - +
77A THR 3.3 0.2 - - - -
78A GLU* 1.3 88.1 + - - +
80A MET* 1.3 63.3 + - + +
82A ARG* 3.3 21.3 + - - +
83A GLN* 3.0 23.6 + - - +
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Residues in contact with MET 80 (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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47A PHE 5.6 0.2 - - - +
50A ARG* 4.5 15.7 - - - +
51A ILE* 3.7 24.5 - - + +
54A THR* 3.6 37.7 - - + +
76A GLN* 3.1 28.5 + - + +
77A THR* 3.9 4.5 - - - +
79A GLN* 1.3 76.9 - - + +
81A ALA* 1.3 64.2 + - - +
83A GLN* 3.3 6.3 + - - -
84A HIS* 3.2 33.5 + - + +
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Residues in contact with ALA 81 (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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51A ILE* 3.8 13.0 - - + +
77A THR 2.9 18.7 + - - +
78A GLU 3.7 3.8 - - - +
80A MET* 1.3 77.4 - - - +
82A ARG* 1.3 61.8 + - - +
84A HIS 3.2 1.7 + - - -
85A ASP 3.0 4.0 + - - -
86A VAL* 2.8 47.9 + - + +
89A TYR* 4.0 11.4 - - + -
90A ALA* 3.6 18.6 - - + +
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Residues in contact with ARG 82 (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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78A GLU* 2.9 53.2 + - - +
79A GLN* 3.7 19.8 - - - +
81A ALA* 1.3 76.3 - - - +
83A GLN* 1.3 63.8 + - - +
84A HIS 3.1 0.7 + - - -
85A ASP* 3.2 17.3 + - - +
87A TRP* 4.2 20.1 - - + -
90A ALA* 4.2 10.8 - - + -
94A LEU* 3.9 19.3 - - - +
116A LYS* 4.8 9.9 + - - +
120A LEU* 4.1 26.2 - - - +
123A GLU* 5.0 6.1 + - - -
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Residues in contact with GLN 83 (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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79A GLN 3.0 14.1 + - - +
80A MET* 3.5 12.8 - - - +
81A ALA 3.2 0.4 - - - -
82A ARG* 1.3 77.2 - - - +
84A HIS* 1.3 76.9 + - + +
85A ASP* 3.9 4.2 + - - +
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Residues in contact with HIS 84 (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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47A PHE* 3.4 67.9 - + + +
51A ILE* 4.4 3.8 - - + -
80A MET* 3.2 31.1 + - + +
82A ARG 3.1 0.4 - - - -
83A GLN* 1.3 95.4 + - + +
85A ASP* 1.3 73.5 + - - +
86A VAL* 3.1 13.6 + - + +
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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
------------------------------------------------------------
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