Contacts of the helix formed by residues 41 - 58 (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 GLY 41 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38E ILE 3.3 10.2 + - - -
39E GLU 3.3 4.2 - - - -
40E CYS* 1.3 79.3 - - - +
42E TRP* 1.3 65.0 + - - +
43E LYS 3.3 2.0 - - - -
44E ASP* 3.3 17.9 + - - +
45E GLN* 3.1 33.8 + - - +
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Residues in contact with TRP 42 (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* 4.1 17.7 - - + -
1183D PHE* 4.0 22.4 - + + -
1184D VAL* 4.2 10.8 - - + -
37E LEU* 2.9 43.8 + - + +
40E CYS* 3.4 16.5 - - - -
41E GLY* 1.3 78.4 - - - +
43E LYS* 1.3 71.4 + - + +
45E GLN* 3.4 11.3 + - - +
46E LEU* 3.0 53.4 + - + +
75E GLY* 3.2 35.6 + - - -
78E LEU* 3.6 35.0 - - + +
79E VAL* 3.7 15.0 - - + +
80E PRO* 4.6 0.4 - - + -
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Residues in contact with LYS 43 (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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1183D PHE* 4.8 5.1 + - + +
1186D GLU* 4.3 20.2 + - - -
1187D THR* 3.2 27.8 + - - +
1190D GLN* 4.4 10.0 + - - +
34E ARG* 4.9 6.2 - - + +
37E LEU 3.2 3.8 + - - +
38E ILE* 4.1 38.4 - - + +
41E GLY 3.3 0.4 - - - -
42E TRP* 1.3 90.1 - - + +
44E ASP* 1.3 66.9 + - - +
46E LEU* 3.2 8.1 + - + +
47E LYS* 2.9 50.0 + - - +
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Residues in contact with ASP 44 (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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38E ILE 5.1 3.2 - - - +
41E GLY* 3.3 19.0 + - - +
43E LYS* 1.3 81.4 - - - +
45E GLN* 1.3 58.1 + - + +
47E LYS* 3.0 17.1 + - - +
48E ALA* 2.8 29.8 + - - +
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Residues in contact with GLN 45 (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 CYS 4.8 5.1 + - - -
41E GLY* 3.1 23.6 + - - +
42E TRP* 3.7 9.7 - - + +
44E ASP* 1.3 75.7 - - + +
46E LEU* 1.3 57.9 + - - +
48E ALA* 3.3 7.3 + - - +
49E HIS* 2.9 30.8 + - - +
78E LEU* 3.4 36.7 - - + +
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Residues in contact with LEU 46 (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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1183D PHE 4.3 0.7 - - - +
1184D VAL* 3.9 24.2 - - + -
1187D THR* 3.5 32.1 - - + +
42E TRP* 3.0 50.9 + - + +
43E LYS* 3.3 10.8 - - + +
45E GLN* 1.3 77.7 - - - +
47E LYS* 1.3 59.7 + - - +
49E HIS* 3.5 7.2 + - + +
50E CYS* 3.0 23.8 + - - +
71E ILE* 3.9 28.4 - - + +
75E GLY* 4.5 12.3 - - - -
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Residues in contact with LYS 47 (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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1187D THR* 4.0 13.7 - - + +
1190D GLN* 3.8 20.0 + - - +
1191D GLU* 2.6 39.6 + - - +
43E LYS* 2.9 40.1 + - + +
44E ASP* 3.0 19.7 + - - +
46E LEU* 1.3 74.3 - - - +
48E ALA* 1.3 64.9 + - - +
50E CYS* 3.1 16.7 + - - +
51E LYS* 3.1 25.9 + - - +
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Residues in contact with ALA 48 (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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44E ASP 2.8 15.6 + - - +
45E GLN* 3.6 8.3 - - - +
47E LYS* 1.3 75.5 - - - +
49E HIS* 1.3 62.9 + - - +
51E LYS* 3.1 17.7 + - - +
52E GLU* 3.1 27.0 - - + +
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Residues in contact with HIS 49 (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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45E GLN 2.9 17.5 + - - +
46E LEU* 3.8 7.4 - - + +
48E ALA* 1.3 77.5 - - - +
50E CYS* 1.3 63.5 + - - +
52E GLU* 3.1 22.3 + - + +
53E VAL* 3.3 23.7 + - + +
70E GLU 4.3 5.6 + - - -
71E ILE* 3.4 42.1 - - + +
74E LYS* 4.2 39.5 + - + +
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Residues in contact with CYS 50 (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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1187D THR* 5.0 1.6 - - + -
1188D CYS* 3.9 23.6 - - - -
1191D GLU* 3.8 29.8 - - + -
46E LEU 3.0 14.8 + - - +
47E LYS* 3.1 11.0 + - - +
49E HIS* 1.3 77.2 - - - +
51E LYS* 1.3 60.5 + - - +
53E VAL* 3.4 4.4 + - - +
54E ILE* 3.2 28.4 + - - +
67E LEU* 3.9 26.5 - - - -
71E ILE* 4.4 13.0 - - + +
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Residues in contact with LYS 51 (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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1191D GLU* 3.3 24.9 - - + +
47E LYS* 3.1 19.2 + - - +
48E ALA* 3.1 14.1 + - - +
50E CYS* 1.3 77.2 - - + +
52E GLU* 1.3 69.2 + - - +
54E ILE* 3.5 14.7 + - + +
55E LYS* 3.4 23.2 + - - +
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Residues in contact with GLU 52 (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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48E ALA* 3.1 25.2 - - - +
49E HIS* 3.1 18.3 + - + +
51E LYS* 1.3 84.6 - - - +
53E VAL* 1.3 65.4 + - + +
55E LYS* 3.2 24.1 + - - +
56E GLU* 3.1 42.3 + - - +
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Residues in contact with VAL 53 (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* 3.3 25.4 + - + +
50E CYS 3.4 6.9 + - - +
52E GLU* 1.3 75.6 - - + +
54E ILE* 1.3 58.3 + - - +
56E GLU* 4.5 7.0 - - - +
57E LYS* 2.9 45.3 + - + +
67E LEU* 3.5 22.4 - - + -
70E GLU* 4.1 28.5 - - + +
71E ILE* 3.7 22.2 - - + -
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Residues in contact with ILE 54 (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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1191D GLU* 4.3 19.1 - - + +
1192D LEU* 4.3 14.6 - - + +
1195D ALA* 4.3 20.2 - - + -
50E CYS* 3.2 19.9 + - - +
51E LYS* 3.6 17.7 - - + +
52E GLU 3.2 0.2 - - - -
53E VAL* 1.3 77.7 - - - +
55E LYS* 1.3 58.9 + - - +
58E GLY* 2.8 29.0 + - - +
59E LEU* 3.9 27.8 + - + +
62E VAL* 4.7 5.6 - - + -
67E LEU* 4.0 17.5 - - + -
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Residues in contact with LYS 55 (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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51E LYS 3.4 7.9 + - - +
52E GLU* 3.2 32.3 + - - +
54E ILE* 1.3 79.4 - - + +
56E GLU* 1.3 73.9 + - + +
57E LYS 3.4 0.2 - - - -
58E GLY* 4.0 6.5 + - - -
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Residues in contact with GLU 56 (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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52E GLU* 3.1 29.7 + - - +
53E VAL* 3.3 5.8 + - - +
55E LYS* 1.3 88.7 - - + +
57E LYS* 1.3 64.1 + - + +
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Residues in contact with LYS 57 (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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53E VAL* 2.9 20.6 + - + +
56E GLU* 1.3 80.5 - - + +
58E GLY* 1.3 65.4 + - - +
61E HIS* 3.1 29.3 - - + +
62E VAL* 3.0 26.9 - - + -
66E ASP* 4.0 25.4 + - + +
70E GLU* 2.9 43.6 + - - +
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Residues in contact with GLY 58 (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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54E ILE 2.8 18.4 + - - -
55E LYS* 4.0 6.5 + - - -
56E GLU 3.6 1.2 - - - -
57E LYS* 1.3 84.6 - - - +
59E LEU* 1.3 64.0 + - - -
60E GLU* 2.9 9.4 + - - -
61E HIS* 3.1 8.7 + - - -
62E VAL* 3.1 11.0 - - - +
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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