Contacts of the helix formed by residues 64 - 83 (chain E) in PDB entry 4HHM
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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62E GLY 3.7 2.0 + - - -
63E ALA* 1.3 75.0 - - - +
65E ASP* 1.3 63.1 + - - +
66E THR* 3.4 11.1 + - - -
67E GLU* 2.7 38.6 + - - +
68E ARG* 2.8 29.8 + - - +
121E ARG* 6.3 0.2 - - - -
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Residues in contact with ASP 65 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63E ALA 5.1 0.5 - - - +
64E SER* 1.3 75.6 - - - +
66E THR* 1.3 66.1 + - - +
68E ARG* 3.6 9.0 - - - +
69E GLU* 3.0 26.3 + - - +
121E ARG* 3.0 29.3 + - - -
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Residues in contact with THR 66 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64E SER* 3.2 9.2 + - - -
65E ASP* 1.3 81.1 + - - +
67E GLU* 1.3 64.9 + - - +
69E GLU* 3.4 5.9 + - - +
70E ALA* 3.2 20.3 + - - +
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Residues in contact with GLU 67 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62E GLY 4.4 1.0 - - - +
63E ALA* 3.1 16.9 - - + +
64E SER* 2.7 41.3 + - - +
66E THR* 1.3 74.3 - - - +
68E ARG* 1.3 67.2 + - - +
70E ALA* 2.8 20.2 + - - +
71E HIS* 2.9 26.9 + - + +
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Residues in contact with ARG 68 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55E ASP* 5.9 4.9 - - - +
59E ILE* 3.6 51.8 - - + +
63E ALA* 4.7 2.2 + - - +
64E SER 2.8 21.7 + - - +
65E ASP* 3.6 7.8 + - - +
67E GLU* 1.3 72.3 - - - +
69E GLU* 1.3 68.0 + - - +
71E HIS* 3.1 13.1 + - - +
72E VAL* 3.1 19.2 + - + +
121E ARG* 3.3 66.8 + - - +
122E ASN* 5.3 2.2 + - - +
125E LEU* 4.0 19.4 - - + +
357F TYR* 4.4 2.4 + - - -
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Residues in contact with GLU 69 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65E ASP 3.0 18.5 + - - +
66E THR* 3.7 6.3 - - - +
67E GLU 3.2 0.2 - - - -
68E ARG* 1.3 81.7 - - - +
70E ALA* 1.3 57.4 + - - +
72E VAL* 3.1 21.8 - - - +
73E LYS* 3.0 34.8 + - + +
76E ARG* 5.7 0.9 + - - -
128E GLU* 4.2 11.6 - - - +
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Residues in contact with ALA 70 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66E THR 3.2 12.3 + - - +
67E GLU* 2.8 18.9 + - - +
69E GLU* 1.3 71.1 - - - +
71E HIS* 1.3 62.7 + - + +
73E LYS* 4.7 6.2 - - - +
74E ARG* 3.0 31.2 + - - +
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Residues in contact with HIS 71 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58E LEU* 3.4 24.3 + - - +
59E ILE* 4.2 7.2 - - + -
60E PRO* 3.4 35.5 - - + +
63E ALA* 5.2 0.6 - - + +
67E GLU* 2.9 34.8 + - + +
68E ARG* 3.1 9.6 + - - +
70E ALA* 1.3 79.0 - - + +
72E VAL* 1.3 60.8 + - - +
74E ARG* 3.6 14.7 + - - +
75E PHE* 2.9 28.8 + - - +
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Residues in contact with VAL 72 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58E LEU* 4.4 10.1 - - + -
59E ILE* 4.0 10.5 - - + -
68E ARG* 3.4 16.4 - - + +
69E GLU* 3.1 33.2 - - - +
71E HIS* 1.3 73.3 - - - +
73E LYS* 1.3 64.4 + - - +
75E PHE* 3.0 10.3 + - - +
76E ARG* 2.7 43.0 + - - +
125E LEU* 3.7 39.0 - - + -
128E GLU* 4.6 8.7 - - - +
129E LEU* 5.4 6.2 - - + +
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Residues in contact with LYS 73 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69E GLU* 3.0 17.4 + - + +
70E ALA* 4.3 6.1 - - - +
72E VAL* 1.3 82.4 - - + +
74E ARG* 1.3 64.7 + - + +
76E ARG* 3.1 16.4 + - - +
77E GLN* 3.0 51.0 + - + +
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Residues in contact with ARG 74 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35E ASP* 2.7 43.9 + - - -
36E PRO* 5.1 2.8 - - - +
37E VAL* 3.3 28.9 - - + +
70E ALA 3.0 19.5 + - - +
71E HIS* 3.7 14.1 + - - +
73E LYS* 1.3 80.0 - - - +
75E PHE* 1.3 62.0 + - - +
77E GLN* 3.4 29.4 - - - +
78E ALA* 3.7 3.6 + - - +
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Residues in contact with PHE 75 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15E LEU* 3.9 22.7 - - + -
36E PRO* 4.1 13.9 - - + -
37E VAL* 4.7 6.5 - - - -
40E VAL* 3.7 23.6 - - + -
51E VAL* 3.9 22.9 - - + -
53E PHE* 5.1 4.7 - + - -
58E LEU* 3.5 38.4 - - + -
71E HIS 2.9 16.2 + - - +
72E VAL* 3.2 11.9 - - - +
74E ARG* 1.3 73.9 - - - +
76E ARG* 1.3 62.0 + - - +
77E GLN 3.0 4.0 - - - -
78E ALA* 3.1 16.6 + - - +
79E LEU* 3.3 33.5 + - + +
86E VAL* 4.1 10.3 - - + -
129E LEU* 4.8 11.2 - - + -
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Residues in contact with ARG 76 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69E GLU* 5.7 1.0 + - - -
72E VAL* 2.7 22.9 + - - +
73E LYS* 3.7 17.2 - - - +
75E PHE* 1.3 72.7 - - - +
77E GLN* 1.3 56.8 + - - +
78E ALA 3.3 0.2 - - - -
79E LEU* 3.8 16.6 - - + +
80E ASP* 3.0 48.6 + - - +
128E GLU* 2.9 51.3 + - - +
129E LEU* 3.7 31.2 - - + +
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Residues in contact with GLN 77 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73E LYS* 3.0 37.2 + - + +
74E ARG* 3.4 29.4 - - - +
75E PHE 3.0 0.2 - - - -
76E ARG* 1.3 77.8 - - - +
78E ALA* 1.3 58.3 + - - +
80E ASP* 3.5 4.3 + - - +
81E ALA* 2.9 31.6 + - - +
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Residues in contact with ALA 78 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37E VAL* 4.0 34.3 - - + +
40E VAL* 3.9 20.4 - - + -
41E GLN* 4.9 7.2 - - + +
74E ARG 3.7 1.4 + - - +
75E PHE* 3.1 10.2 + - - +
77E GLN* 1.3 77.9 - - - +
79E LEU* 1.3 54.2 + - - +
81E ALA* 4.4 4.7 - - - -
82E THR* 2.6 43.7 + - - +
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Residues in contact with LEU 79 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40E VAL* 4.2 9.0 - - + -
51E VAL* 3.9 22.4 - - + -
75E PHE* 3.3 31.1 + - + +
76E ARG* 3.8 20.9 - - + +
77E GLN 3.3 0.2 - - - -
78E ALA* 1.3 78.2 - - - +
80E ASP* 1.3 55.1 + - - +
82E THR* 3.6 3.1 - - - -
83E GLY* 2.6 33.4 + - - -
84E MET* 2.9 44.9 + - + +
85E THR* 4.2 2.0 - - - +
86E VAL* 3.4 25.8 - - + -
129E LEU* 5.0 1.1 - - + -
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Residues in contact with ASP 80 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76E ARG* 3.0 37.0 + - - +
77E GLN* 4.0 4.4 - - - +
79E LEU* 1.3 80.1 - - - +
81E ALA* 1.3 62.3 + - - +
82E THR 3.4 0.3 + - - -
83E GLY* 3.7 6.6 + - - -
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Residues in contact with ALA 81 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77E GLN 2.9 19.9 + - - +
78E ALA* 3.9 5.8 - - - +
79E LEU 3.3 0.2 - - - -
80E ASP* 1.3 77.4 - - - +
82E THR* 1.3 61.4 + - + +
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Residues in contact with THR 82 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40E VAL* 3.4 11.7 - - + +
41E GLN* 4.1 22.4 - - + -
44E ALA* 3.7 31.2 - - + +
78E ALA* 2.6 23.2 + - - +
79E LEU 3.2 2.6 + - - -
81E ALA* 1.3 79.8 - - + +
83E GLY* 1.3 63.8 + - - +
84E MET* 3.1 18.7 + - - +
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Residues in contact with GLY 83 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49E TYR* 4.4 4.3 - - - +
79E LEU 2.6 17.0 + - - -
80E ASP* 3.7 6.9 + - - -
81E ALA 3.6 1.4 - - - -
82E THR* 1.3 75.6 - - - +
84E MET* 1.3 61.0 + - - -
85E THR* 3.9 2.1 + - - +
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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