Contacts of the helix formed by residues 43 - 57 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38F LEU* 4.3 0.2 - - - -
42F GLU* 1.3 78.1 - - - +
44F LEU* 1.3 60.9 + - - +
45F VAL* 3.0 18.6 - - + +
46F GLU* 3.0 41.2 + - + +
47F ALA* 2.8 26.5 + - - +
143F ASP* 3.5 37.3 + - - +
146F TRP* 3.8 9.5 + - - -
150F LYS* 4.8 6.1 + - - +
70K GLN* 3.5 7.9 + - - -
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Residues in contact with LEU 44 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6F VAL* 3.9 5.8 - - + -
8F VAL* 3.9 16.5 - - + +
38F LEU* 3.9 26.9 - - + -
43F THR* 1.3 73.0 + - - +
45F VAL* 1.3 58.6 + - - +
47F ALA* 3.2 4.9 + - - +
48F ALA* 3.0 28.2 + - - +
82F PHE* 3.8 50.7 - - + -
84F PHE* 4.2 14.0 - - + -
141F ILE* 4.1 26.9 - - + +
68K MET* 4.3 12.1 - - + -
70K GLN* 3.2 17.3 + - - +
80K LEU* 5.0 3.6 - - + -
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Residues in contact with VAL 45 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43F THR* 3.0 13.9 - - + +
44F LEU* 1.3 72.2 - - - +
46F GLU* 1.3 71.5 + - + +
47F ALA 3.1 0.2 + - - -
48F ALA* 3.4 5.0 + - - +
49F ALA* 2.8 29.0 + - - +
61F GLN* 4.6 13.2 - - + +
62F PRO* 4.1 14.2 - - + +
84F PHE* 4.0 12.8 - - + -
138F LEU* 3.9 38.8 - - + -
141F ILE* 4.9 6.3 - - + -
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Residues in contact with GLU 46 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41F ASP 4.5 1.9 - - - +
42F GLU* 3.6 17.3 - - + +
43F THR* 3.0 38.6 + - + +
45F VAL* 1.3 78.1 - - + +
47F ALA* 1.3 65.7 + - - +
49F ALA* 4.1 4.6 - - - +
50F ARG* 3.1 22.3 + - - +
61F GLN* 5.3 3.4 - - - +
146F TRP* 4.5 4.3 + - - -
149F THR 4.2 5.4 - - - +
150F LYS* 3.2 42.0 - - - +
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Residues in contact with ALA 47 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8F VAL* 4.0 15.5 - - + -
38F LEU* 3.8 18.4 - - + -
42F GLU* 3.6 26.0 + - - +
43F THR 2.8 14.3 + - - +
44F LEU* 3.3 9.0 - - - +
45F VAL 3.0 0.2 - - - -
46F GLU* 1.3 72.6 - - - +
48F ALA* 1.3 68.9 + - - +
50F ARG* 2.7 20.4 + - - +
51F GLU* 2.9 13.9 + - - +
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Residues in contact with ALA 48 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8F VAL* 3.3 16.9 - - + +
9F ALA* 6.0 0.2 - - - +
10F CYS* 3.8 16.9 - - - -
44F LEU 3.0 14.9 + - - +
45F VAL 3.7 0.2 - - - +
47F ALA* 1.3 74.5 - - - +
49F ALA* 1.3 63.8 + - - +
51F GLU* 3.0 2.9 + - - +
52F LEU* 2.8 22.2 + - - +
62F PRO* 3.6 21.3 - - + -
84F PHE* 3.8 22.2 - - + -
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Residues in contact with ALA 49 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93B PRO* 5.7 2.0 - - - +
10F CYS* 5.7 0.4 - - - -
45F VAL 2.8 19.8 + - - +
46F GLU* 4.2 3.8 - - - +
48F ALA* 1.3 72.1 - - - +
50F ARG* 1.3 58.6 + - - +
52F LEU* 3.1 22.3 - - - +
53F TRP* 3.2 10.2 + - - +
58F ILE 4.9 0.9 - - - +
60F ALA 3.6 25.1 + - - +
61F GLN* 3.6 23.8 - - - +
62F PRO* 3.8 6.3 - - + +
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Residues in contact with ARG 50 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93B PRO* 6.2 2.0 - - - -
37F HIS 3.3 14.5 + - - -
39F GLU* 4.0 12.8 + - - +
42F GLU* 3.0 38.6 + - - -
46F GLU 3.1 13.7 + - - +
47F ALA* 2.7 18.1 + - - +
49F ALA* 1.3 67.9 - - - +
51F GLU* 1.3 101.4 + - - +
52F LEU 3.0 1.6 + - - -
53F TRP* 3.1 10.3 + - + +
54F GLU* 2.8 64.6 + - + +
155F MN 4.3 1.4 + - - -
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Residues in contact with GLU 51 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8F VAL* 4.7 6.1 - - + -
34F PRO* 4.3 3.5 - - - +
35F ALA* 3.1 18.8 - - - +
36F GLY* 3.4 22.7 - - - +
37F HIS 3.9 1.6 - - - +
47F ALA 2.9 14.3 + - - +
48F ALA* 3.9 7.0 - - - +
50F ARG* 1.3 103.0 + - - +
52F LEU* 1.3 60.8 + - - +
54F GLU* 3.6 6.1 - - - +
55F GLU* 3.1 27.9 - - - +
154F MN 2.3 30.6 + - - -
155F MN 2.2 30.4 + - - -
156F SO4 3.9 0.2 + - - -
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Residues in contact with LEU 52 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10F CYS* 4.9 4.7 - - + -
12F VAL* 4.3 9.9 - - + -
19F LEU* 4.2 10.5 - - + -
34F PRO* 3.8 27.4 - - + -
48F ALA 2.8 12.4 + - - +
49F ALA* 3.1 12.3 - - - +
50F ARG 3.0 0.6 - - - -
51F GLU* 1.3 78.4 - - - +
53F TRP* 1.3 57.0 + - - +
55F GLU 3.3 1.0 + - - -
56F THR* 2.6 61.2 + - + +
58F ILE* 4.0 13.0 - - + +
60F ALA* 3.5 43.5 - - + +
86F ILE* 3.9 14.6 - - + -
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Residues in contact with TRP 53 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B GLU* 5.3 2.0 - - - -
90B GLN* 5.4 11.0 - - + -
91B ILE* 2.7 47.3 - - + +
92B CYS 4.5 0.2 - - - -
93B PRO* 3.5 36.1 - - + +
49F ALA 3.2 6.7 + - - +
50F ARG* 3.1 11.3 + - + +
52F LEU* 1.3 75.6 - - - +
54F GLU* 1.3 77.0 + - + +
55F GLU 2.8 5.8 + - - -
57F GLY* 2.8 43.7 + - - +
58F ILE 3.6 15.0 - - - +
59F SER* 3.8 11.7 + - - -
97F HIS* 3.3 45.8 - + + +
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Residues in contact with GLU 54 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50F ARG* 2.8 59.0 + - + +
51F GLU* 3.6 13.4 - - - +
53F TRP* 1.3 87.3 - - + +
55F GLU* 1.3 65.0 + - + +
97F HIS* 3.2 23.4 + - + +
98F ASP* 3.0 35.2 - - + +
154F MN 4.0 4.7 + - - -
155F MN 4.1 3.6 + - - -
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Residues in contact with GLU 55 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21F VAL* 3.7 6.2 - - + +
34F PRO* 3.5 6.9 - - + +
35F ALA 3.1 21.2 + - - +
51F GLU* 3.1 16.4 - - - +
52F LEU 3.3 1.9 + - - +
53F TRP 2.9 0.6 - - - -
54F GLU* 1.3 84.6 - - + +
56F THR* 1.3 68.1 + - + +
96F PRO* 4.1 6.3 - - - +
98F ASP* 5.0 1.3 - - + -
101F ILE* 3.4 46.6 - - + +
104F CYS* 3.4 4.0 - - - -
154F MN 2.5 15.4 + - - +
157F SO4 2.3 48.3 + - - -
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Residues in contact with THR 56 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19F LEU* 4.0 7.2 - - + -
21F VAL* 3.6 20.4 - - + -
34F PRO* 3.8 20.0 - - + -
52F LEU* 2.6 25.2 + - + +
53F TRP 3.2 0.2 + - - -
55F GLU* 1.3 83.6 - - - +
57F GLY* 1.3 61.1 + - - +
58F ILE* 2.8 33.4 + - - +
94F THR* 3.6 8.2 - - - -
95F GLN 3.2 26.9 + - - -
96F PRO* 4.1 1.8 - - - +
104F CYS* 3.8 16.4 - - - -
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Residues in contact with GLY 57 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53F TRP* 2.8 30.9 + - - -
56F THR* 1.3 78.9 + - - +
58F ILE* 1.3 63.5 + - - +
59F SER* 3.7 3.5 + - - -
93F PRO 5.6 2.1 - - - +
95F GLN* 3.4 17.1 + - - -
97F HIS* 3.9 11.9 + - - -
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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