Contacts of the helix formed by residues 80 - 99 (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 PRO 80 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37E LEU* 4.1 19.3 - - + -
40E CYS* 3.8 26.5 - - + -
42E TRP* 4.6 1.3 - - + -
78E LEU 3.1 10.7 - - - +
79E VAL* 1.3 87.4 - - + +
81E ASP* 1.3 63.7 + - - +
82E SER* 4.0 16.8 - - - +
83E VAL* 3.3 12.8 + - + +
84E LYS* 3.3 18.4 + - - +
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Residues in contact with ASP 81 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79E VAL 4.3 3.6 - - - +
80E PRO* 1.3 72.3 - - - +
82E SER* 1.3 54.1 + - - +
84E LYS* 3.1 24.5 + - + +
85E LYS* 2.7 35.1 + - - +
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Residues in contact with SER 82 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80E PRO* 4.0 12.5 - - - +
81E ASP* 1.3 77.7 - - - +
83E VAL* 1.3 61.9 + - - +
85E LYS* 3.3 12.1 + - - +
86E GLU* 3.0 28.2 + - - +
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Residues in contact with VAL 83 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1176D MET* 4.0 9.6 - - + -
33E LEU* 3.6 26.8 - - + +
36E LYS* 4.1 35.0 - - + +
37E LEU* 4.4 14.6 - - + -
40E CYS* 4.8 3.8 - - + -
80E PRO* 3.5 33.0 - - + +
81E ASP 3.2 0.2 - - - -
82E SER* 1.3 85.9 + - - +
84E LYS* 1.3 57.6 + - - +
86E GLU* 3.3 6.0 + - - +
87E LEU* 3.0 27.0 + - - +
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Residues in contact with LYS 84 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1172D ALA* 5.5 1.7 - - - +
1176D MET* 3.5 32.1 - - + -
76E ARG 4.7 3.0 + - - -
79E VAL* 3.4 33.5 + - + +
80E PRO 3.3 12.0 + - - +
81E ASP* 3.1 25.2 + - - +
83E VAL* 1.3 78.4 - - - +
85E LYS* 1.3 62.8 + - - +
87E LEU* 3.5 6.2 + - + +
88E LEU* 3.1 23.4 + - - +
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Residues in contact with LYS 85 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81E ASP 2.7 19.3 + - - +
82E SER* 3.4 13.5 - - - +
83E VAL 3.2 0.4 - - - -
84E LYS* 1.3 74.4 - - - +
86E GLU* 1.3 56.8 + - - +
88E LEU* 3.3 9.2 + - + +
89E GLN* 2.9 30.4 + - + +
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Residues in contact with GLU 86 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32E LEU* 4.4 20.3 - - + +
36E LYS* 3.6 34.8 + - + -
82E SER 3.0 15.5 + - - +
83E VAL* 3.8 5.8 - - - +
85E LYS* 1.3 74.2 - - - +
87E LEU* 1.3 66.6 + - - +
89E GLN* 3.3 25.6 + - - +
90E ARG* 3.0 31.8 + - - +
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Residues in contact with LEU 87 (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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1172D ALA* 3.6 30.1 - - + +
1175D LEU* 4.1 16.4 - - + -
1176D MET* 4.1 21.1 - - + +
29E LEU* 4.3 17.5 - - + +
32E LEU* 4.9 8.3 - - + -
33E LEU* 4.1 29.2 - - + -
83E VAL 3.0 17.4 + - - +
84E LYS* 3.6 7.0 - - + +
85E LYS 3.3 0.2 - - - -
86E GLU* 1.3 77.3 - - - +
88E LEU* 1.3 61.8 + - - +
90E ARG* 3.3 3.5 + - - +
91E ILE* 3.0 45.0 + - + +
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Residues in contact with LEU 88 (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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1168D SER* 4.0 22.2 - - - -
1169D GLN* 3.0 41.7 - - - +
1172D ALA* 4.1 10.3 - - + -
84E LYS 3.1 14.8 + - - +
85E LYS* 3.6 7.0 - - + +
87E LEU* 1.3 80.0 - - - +
89E GLN* 1.3 64.0 + - - +
91E ILE* 3.1 9.4 + - + +
92E ARG* 2.9 56.6 + - + +
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Residues in contact with GLN 89 (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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85E LYS* 2.9 18.0 + - + +
86E GLU* 3.4 28.0 + - - +
88E LEU* 1.3 76.6 - - - +
90E ARG* 1.3 73.2 + - - +
92E ARG* 3.2 10.8 + - - +
93E THR* 3.1 33.2 + - - +
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Residues in contact with ARG 90 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25E GLU* 3.7 13.5 + - - +
28E ARG* 4.5 28.3 + - - +
29E LEU* 4.1 18.1 - - + +
32E LEU* 3.7 39.5 - - + +
86E GLU* 3.0 26.6 + - - +
87E LEU 4.0 2.7 - - - +
89E GLN* 1.3 86.5 - - + +
91E ILE* 1.3 63.8 + - - +
92E ARG 3.3 0.2 - - - -
93E THR* 3.9 12.4 - - + +
94E PHE* 3.3 20.6 + - - +
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Residues in contact with ILE 91 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1168D SER* 4.1 29.6 - - - +
1171D LEU* 4.3 19.1 - - + +
1172D ALA* 3.6 29.4 - - + +
1175D LEU* 4.8 4.5 - - + -
20E LEU* 6.1 1.1 - - + -
29E LEU* 4.0 19.7 - - + -
87E LEU* 3.0 43.0 + - + +
88E LEU* 3.1 6.5 + - - +
90E ARG* 1.3 77.1 - - - +
92E ARG* 1.3 59.5 + - - +
94E PHE* 3.2 7.1 + - + +
95E LEU* 3.0 36.3 + - + +
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Residues in contact with ARG 92 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1166D GLU 5.3 2.6 - - - +
1168D SER* 3.4 31.7 + - - -
1169D GLN* 3.9 4.0 + - - -
88E LEU* 2.9 49.7 + - + +
89E GLN* 3.3 11.0 - - - +
91E ILE* 1.3 75.1 - - - +
93E THR* 1.3 65.0 + - - +
94E PHE 3.1 0.2 + - - -
95E LEU* 3.2 6.3 + - - +
96E ALA* 2.9 27.5 + - - +
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Residues in contact with THR 93 (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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89E GLN* 3.1 18.9 + - - +
90E ARG* 4.0 14.3 - - + +
91E ILE 3.4 0.2 - - - -
92E ARG* 1.3 77.8 - - - +
94E PHE* 1.3 60.3 + - - +
96E ALA* 3.8 6.7 + - - +
97E GLN* 3.4 29.8 + - - +
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Residues in contact with PHE 94 (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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16E ILE* 5.0 2.0 - - + -
19E LYS* 3.5 24.7 - - + -
20E LEU* 3.4 27.4 - - + -
23E THR* 3.4 28.3 - - + -
25E GLU* 3.5 32.8 - - + +
28E ARG* 4.8 1.8 - - - -
90E ARG 3.3 16.5 + - - +
91E ILE* 3.2 9.1 + - + +
92E ARG 3.0 0.8 - - - -
93E THR* 1.3 78.9 - - - +
95E LEU* 1.3 78.8 + - + +
97E GLN* 3.2 4.8 + - - -
98E HIS* 3.1 66.6 + + + +
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Residues in contact with LEU 95 (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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1167D LEU* 5.0 8.7 - - + -
1168D SER* 4.1 33.0 - - - +
1171D LEU* 5.1 9.6 - - + -
16E ILE* 4.4 27.8 - - + -
91E ILE* 3.0 24.6 + - + +
92E ARG* 3.9 6.1 - - - +
94E PHE* 1.3 92.4 - - + +
96E ALA* 1.3 57.7 + - - +
97E GLN 3.1 0.2 - - - -
98E HIS* 5.2 0.4 - - + -
99E ALA* 2.8 48.3 + - + +
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Residues in contact with ALA 96 (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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92E ARG 2.9 18.0 + - - +
93E THR* 4.1 7.0 - - - +
95E LEU* 1.3 77.0 - - - +
97E GLN* 1.3 57.4 + - - +
98E HIS 3.6 0.2 - - - -
99E ALA 4.4 6.4 - - - +
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Residues in contact with GLN 97 (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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93E THR* 3.4 25.5 + - - +
94E PHE* 3.2 7.4 + - - +
95E LEU 3.1 0.6 - - - -
96E ALA* 1.3 80.8 - - - +
98E HIS* 1.3 85.4 + - + +
99E ALA 5.3 0.2 - - - -
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Residues in contact with HIS 98 (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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19E LYS* 3.8 43.8 + - + +
23E THR* 3.8 20.3 - - + +
28E ARG* 6.0 0.4 + - - -
94E PHE* 3.1 51.3 + + + +
95E LEU* 5.2 0.2 - - - -
97E GLN* 1.3 113.4 + - + +
99E ALA* 1.3 61.3 + - + +
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Residues in contact with ALA 99 (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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16E ILE* 5.2 9.2 - - + -
19E LYS* 6.3 1.3 - - + -
95E LEU* 2.8 40.1 + - + +
96E ALA* 4.4 7.6 - - - +
97E GLN 3.8 0.2 - - - -
98E HIS* 1.3 82.1 - - + +
100E SER* 1.3 64.4 + - - +
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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