Contacts of the helix formed by residues 43 - 57 (chain E) in PDB entry 3SHD
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 43 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70D GLN* 3.5 6.6 + - - +
38E LEU* 3.9 1.4 - - - +
42E GLU* 1.3 75.2 - - - +
44E LEU* 1.3 65.3 + - - +
45E VAL* 3.3 19.3 - - + +
46E GLU* 2.9 44.1 + - + +
47E ALA* 3.0 21.7 + - - +
143E ASP* 3.4 37.6 + - - +
146E TRP* 3.9 10.4 + - - -
150E LYS* 4.3 4.2 - - - -
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Residues in contact with LEU 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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68D MET* 4.2 7.6 - - + -
70D GLN* 3.2 19.0 + - - +
80D LEU* 5.2 2.9 - - + -
6E VAL* 4.6 1.8 - - + -
8E VAL* 3.7 26.7 - - + +
38E LEU* 3.8 27.4 - - + -
43E THR* 1.3 74.8 - - - +
45E VAL* 1.3 58.7 + - - +
47E ALA* 3.3 3.2 + - - +
48E ALA* 2.9 28.2 + - - +
82E PHE* 3.4 49.4 - - + -
84E PHE* 4.3 5.8 - - + -
141E ILE* 3.8 34.5 - - + +
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Residues in contact with VAL 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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43E THR* 3.3 13.0 - - + +
44E LEU* 1.3 74.8 - - + +
46E GLU* 1.3 60.6 + - + +
48E ALA* 3.4 6.9 - - - +
49E ALA* 2.7 37.4 + - - +
61E GLN* 4.1 19.3 - - + +
62E PRO* 4.0 13.2 - - + +
84E PHE* 4.3 18.4 - - + -
138E LEU* 4.4 25.1 - - + +
141E ILE* 4.8 8.5 - - + -
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Residues in contact with GLU 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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41E ASP 4.2 4.0 - - - +
42E GLU* 3.5 16.4 - - + +
43E THR* 2.9 38.7 + - + +
45E VAL* 1.3 86.2 - - + +
47E ALA* 1.3 52.2 + - - +
49E ALA* 3.5 5.8 + - - +
50E ARG* 2.8 33.4 + - - +
61E GLN* 5.6 3.8 - - - +
146E TRP* 4.6 5.1 + - - -
148E PHE* 5.9 0.7 - - - +
149E THR 4.5 5.4 - - - +
150E LYS* 3.4 32.3 - - + +
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Residues in contact with ALA 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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8E VAL* 3.7 15.5 - - + -
38E LEU* 3.8 14.8 - - + -
42E GLU* 3.4 29.3 - - - +
43E THR 3.0 11.6 + - - +
44E LEU 3.6 7.9 - - - +
46E GLU* 1.3 72.5 - - - +
48E ALA* 1.3 59.3 + - - +
50E ARG* 3.1 10.2 + - - +
51E GLU* 2.7 38.8 + - - +
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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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8E VAL* 3.5 13.9 - - + +
10E CYS* 4.0 15.3 - - - -
34E PRO 5.7 0.5 - - - +
44E LEU 2.9 17.3 + - - +
45E VAL* 3.1 5.1 + - - +
47E ALA* 1.3 78.3 - - - +
49E ALA* 1.3 62.1 + - - +
51E GLU* 4.1 1.4 - - - +
52E LEU* 3.2 19.8 + - - +
62E PRO* 3.8 11.0 - - + -
84E PHE* 3.6 32.1 - - + -
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Residues in contact with ALA 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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10E CYS* 5.7 0.2 - - - -
45E VAL 2.7 20.6 + - - +
46E GLU* 3.7 6.1 - - - +
48E ALA* 1.3 70.9 - - - +
50E ARG* 1.3 62.4 + - - +
52E LEU* 3.3 8.5 - - - +
53E TRP* 3.2 19.8 + - - +
58E ILE 4.9 0.7 - - - +
59E SER* 6.0 0.3 - - - -
60E ALA 3.6 24.3 + - - +
61E GLN* 3.6 20.2 - - - +
62E PRO* 4.1 6.3 - - + +
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Residues in contact with ARG 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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37E HIS 3.3 19.6 + - - -
39E GLU* 3.6 18.0 + - - -
42E GLU* 2.5 44.1 + - - +
46E GLU 2.8 20.9 + - - +
47E ALA* 3.7 10.1 - - - +
49E ALA* 1.3 73.2 - - - +
51E GLU* 1.3 94.9 + - - +
53E TRP* 2.9 20.6 + - + +
54E GLU* 2.9 41.5 + - + +
154E MN 4.0 0.8 + - - -
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Residues in contact with GLU 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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8E VAL* 4.9 2.5 - - + -
35E ALA* 3.4 18.0 - - - +
36E GLY* 3.7 18.5 - - - +
37E HIS 4.0 0.7 + - - +
47E ALA 2.7 21.6 + - - +
48E ALA 4.3 2.0 - - - +
50E ARG* 1.3 91.6 + - - +
52E LEU* 1.3 63.3 + - - +
54E GLU* 3.3 7.1 + - - +
55E GLU* 3.0 38.3 + - - +
154E MN 2.0 39.6 + - - -
155E MN 2.4 24.7 + - - -
156E SO4 3.0 7.1 + - - -
157E SO4 3.0 6.4 + - - -
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Residues in contact with LEU 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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10E CYS* 4.6 11.0 - - - -
12E VAL* 4.5 11.2 - - + -
19E LEU* 4.3 8.7 - - + -
34E PRO* 3.8 24.3 - - + +
48E ALA 3.2 13.2 + - - +
49E ALA* 3.3 11.7 - - - +
51E GLU* 1.3 76.8 - - - +
53E TRP* 1.3 60.9 + - - +
56E THR* 2.6 67.0 + - + +
58E ILE* 3.9 17.9 - - + +
60E ALA* 4.0 31.0 - - + +
86E ILE* 4.0 15.9 - - + -
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Residues in contact with TRP 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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99B SER* 4.5 7.8 + - - -
49E ALA 3.2 7.3 + - - +
50E ARG* 2.9 13.7 + - + +
52E LEU* 1.3 79.2 - - - +
54E GLU* 1.3 81.8 + - + +
55E GLU 2.7 8.3 + - - -
57E GLY* 2.6 45.5 + - - +
58E ILE 3.5 11.0 - - - +
59E SER* 3.4 26.0 + - - -
97E HIS* 3.8 48.8 + + + -
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Residues in contact with GLU 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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50E ARG* 2.9 57.3 + - + +
51E GLU* 3.7 19.8 - - - +
53E TRP* 1.3 98.1 - - + +
55E GLU* 1.3 57.5 + - + +
97E HIS* 3.1 8.3 + - + -
98E ASP* 2.7 52.3 + - + +
154E MN 4.2 2.8 + - - -
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Residues in contact with GLU 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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21E VAL* 3.9 10.8 - - + +
34E PRO* 3.3 7.3 - - + +
35E ALA 3.0 21.0 + - - -
51E GLU* 3.0 23.2 + - - +
52E LEU 4.1 1.6 - - - +
53E TRP 2.7 6.5 + - - -
54E GLU* 1.3 78.6 - - - +
56E THR* 1.3 58.6 + - + +
57E GLY 3.8 0.2 - - - -
96E PRO* 3.7 7.7 - - - +
98E ASP* 4.9 0.2 - - + -
101E ILE* 3.3 46.2 - - + +
104E CYS* 3.5 9.0 - - - -
155E MN 3.0 7.9 + - - +
157E SO4 2.2 50.2 + - - -
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Residues in contact with THR 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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19E LEU* 3.7 28.9 - - + -
21E VAL* 3.7 20.6 - - + -
34E PRO* 3.8 10.8 - - + -
52E LEU* 2.6 27.7 + - + +
55E GLU* 1.3 81.1 - - - +
57E GLY* 1.3 61.4 + - - +
58E ILE* 3.1 15.5 + - - +
94E THR* 3.4 6.3 - - - -
95E GLN 2.5 35.0 + - - -
104E CYS* 3.8 14.1 - - - -
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Residues in contact with GLY 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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52E LEU 3.3 0.2 + - - -
53E TRP* 2.6 39.5 + - - -
56E THR* 1.3 72.4 + - - +
58E ILE* 1.3 62.2 + - - +
59E SER* 3.8 2.1 + - - -
94E THR* 5.8 0.2 - - - -
95E GLN* 3.2 15.5 + - - +
97E HIS* 3.8 11.8 + - - -
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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