Contacts of the helix formed by residues 63 - 78 (chain E) in PDB entry 4DHX
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 63 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96C ALA 4.9 1.0 + - - -
1192D LEU* 3.8 7.9 - - - -
61E HIS 4.2 6.1 - - - +
62E VAL* 1.3 85.4 - - - +
64E VAL* 1.3 66.9 + - - +
65E ASP* 3.6 12.4 + - - +
66E ASP* 2.9 42.5 + - - +
67E LEU* 3.2 9.7 + - - +
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Residues in contact with VAL 64 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1185D ARG* 4.3 23.3 - - - +
1188D CYS* 4.1 7.0 - - + +
1189D SER* 3.7 44.2 - - - +
1192D LEU* 3.6 21.0 - - + +
63E THR* 1.3 73.6 - - - +
65E ASP* 1.3 59.0 + - - +
67E LEU* 3.1 9.4 + - - +
68E VAL* 3.0 28.8 + - + +
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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
----------------------------------------------------------
96C ALA* 3.2 47.7 - - - +
97C GLN* 3.6 14.5 - - + +
1185D ARG* 2.8 42.6 + - - -
63E THR* 3.2 9.8 + - - +
64E VAL* 1.3 76.3 + - - +
66E ASP* 1.3 65.0 + - - +
68E VAL* 3.5 4.1 + - - -
69E ALA* 3.1 23.0 + - - +
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Residues in contact with ASP 66 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96C ALA 4.3 8.3 - - - +
97C GLN* 5.6 1.7 - - - +
99C ALA* 5.8 2.3 + - - -
53E VAL* 5.5 0.2 - - - -
57E LYS* 4.0 21.8 + - + +
61E HIS 3.6 11.8 - - - +
62E VAL* 3.8 8.2 - - + -
63E THR* 2.9 38.6 + - - +
65E ASP* 1.3 79.1 - - - +
67E LEU* 1.3 62.4 + - - +
69E ALA* 3.4 5.2 + - - +
70E GLU* 3.1 29.1 + - - +
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Residues in contact with LEU 67 (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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1188D CYS* 3.6 25.1 - - + +
1192D LEU* 3.8 32.1 - - + -
50E CYS* 3.9 17.3 - - - +
53E VAL* 3.5 32.8 - - + -
54E ILE* 4.0 15.7 - - + -
62E VAL* 3.6 25.8 - - + -
63E THR 3.2 4.7 + - - +
64E VAL* 3.1 8.3 + - - +
66E ASP* 1.3 76.2 - - - +
68E VAL* 1.3 66.0 + - - +
70E GLU* 3.2 4.7 + - - +
71E ILE* 3.1 29.2 + - + +
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Residues in contact with VAL 68 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97C GLN* 3.7 25.8 - - - +
1181D MET* 5.7 7.6 - - + +
1184D VAL* 4.3 6.7 - - + -
1185D ARG* 3.9 41.3 - - + +
1188D CYS* 3.7 13.9 - - + -
64E VAL* 3.0 22.1 + - + +
65E ASP* 3.7 9.9 - - - +
66E ASP 3.3 0.2 - - - -
67E LEU* 1.3 75.8 - - - +
69E ALA* 1.3 62.5 + - - +
72E THR* 2.7 44.8 + - - +
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Residues in contact with ALA 69 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97C GLN* 3.7 31.4 - - + +
98C HIS* 6.3 0.2 - - + -
65E ASP 3.1 14.2 + - - +
66E ASP* 3.7 5.8 - - - +
67E LEU 3.3 0.2 - - - -
68E VAL* 1.3 81.5 - - - +
70E GLU* 1.3 64.1 + - + +
72E THR* 4.6 2.0 - - - -
73E PRO* 3.3 18.9 - - - +
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Residues in contact with GLU 70 (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 HIS* 4.3 7.0 + - - -
53E VAL* 4.1 23.4 - - + +
57E LYS* 2.9 36.6 + - - +
66E ASP 3.1 17.8 + - - +
67E LEU 3.2 3.8 + - - +
69E ALA* 1.3 81.1 - - + +
71E ILE* 1.3 62.7 + - + +
73E PRO* 3.6 10.4 - - - +
74E LYS* 5.2 1.0 + - - +
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Residues in contact with ILE 71 (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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1184D VAL* 3.8 13.7 - - + -
1187D THR* 5.5 0.7 - - + -
1188D CYS* 3.3 26.9 - - - +
46E LEU* 3.9 36.6 - - + +
49E HIS* 3.4 36.9 - - + +
50E CYS* 4.4 9.9 - - - -
53E VAL* 3.7 23.3 - - + -
67E LEU* 3.1 19.0 + - - +
70E GLU* 1.3 74.8 - - - +
72E THR* 1.3 67.1 + - - +
73E PRO* 3.4 2.7 - - - -
74E LYS* 3.7 4.3 + - - +
75E GLY* 3.1 19.6 + - - -
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Residues in contact with THR 72 (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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1180D MET* 4.4 12.8 - - + +
1181D MET* 4.8 13.3 - - + +
1184D VAL* 3.6 16.1 - - - +
68E VAL* 2.7 39.6 + - - +
69E ALA* 4.6 2.5 - - - -
71E ILE* 1.3 78.5 - - - +
73E PRO* 1.3 70.8 - - + +
75E GLY* 3.0 2.3 + - - -
76E ARG* 2.8 50.7 + - - +
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Residues in contact with PRO 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 ALA 3.3 19.5 - - - +
70E GLU 3.6 8.1 - - - +
71E ILE 3.5 2.7 - - - -
72E THR* 1.3 95.2 - - + +
74E LYS* 1.3 62.7 + - - +
76E ARG* 3.1 28.3 + - - +
77E ALA* 3.3 11.7 + - - +
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Residues in contact with LYS 74 (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 HIS* 4.2 40.6 + - + +
70E GLU 5.2 0.8 + - - +
71E ILE* 3.7 6.1 + - - +
72E THR 3.4 0.6 - - - -
73E PRO* 1.3 79.0 - - - +
75E GLY* 1.3 62.8 + - - +
77E ALA* 3.0 16.1 + - + +
78E LEU* 3.1 54.0 + - + +
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Residues in contact with GLY 75 (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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1180D MET* 4.4 3.8 - - - +
1184D VAL* 5.2 2.0 - - - -
42E TRP* 3.2 40.6 + - - -
46E LEU* 4.5 11.0 - - - +
49E HIS* 5.8 0.2 - - - -
71E ILE 3.1 12.7 + - - -
72E THR* 3.0 8.9 + - - -
74E LYS* 1.3 77.7 - - - +
76E ARG* 1.3 59.1 + - - +
77E ALA 3.4 0.3 + - - -
78E LEU* 3.5 5.9 + - - -
79E VAL* 3.7 5.0 - - - +
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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
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1177D GLU* 2.9 39.0 + - - +
1180D MET* 3.5 21.0 - - + +
1181D MET* 4.6 6.1 - - - +
72E THR* 2.8 34.9 + - - +
73E PRO* 3.1 19.6 + - - +
75E GLY* 1.3 77.4 - - - +
77E ALA* 1.3 59.3 + - - +
79E VAL* 3.3 21.4 - - - +
84E LYS* 4.7 3.5 + - - -
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Residues in contact with ALA 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 PRO 3.3 9.2 + - - +
74E LYS* 3.0 12.1 + - + +
76E ARG* 1.3 76.8 - - - +
78E LEU* 1.3 70.3 + - + +
79E VAL* 3.5 4.7 - - - +
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Residues in contact with LEU 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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42E TRP* 3.6 21.5 - - + +
45E GLN* 3.4 33.0 - - + +
46E LEU 6.1 0.2 - - - +
74E LYS* 3.1 55.6 + - + +
75E GLY* 3.5 2.0 + - - -
76E ARG 3.4 0.2 - - - -
77E ALA* 1.3 89.2 - - + +
79E VAL* 1.3 65.4 + - - +
80E PRO* 3.1 13.3 - - - +
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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