Contacts of the helix formed by residues 43 - 57 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A GLN* 3.2 13.2 - - - +
38I LEU* 3.6 1.4 - - - +
42I GLU* 1.3 76.1 - - - +
44I LEU* 1.3 76.5 + - + +
45I VAL* 3.3 26.3 - - + +
46I GLU* 3.2 31.5 + - - +
47I ALA* 3.0 22.2 + - - +
141I ILE* 5.4 3.8 - - + +
142I GLY* 5.4 1.6 - - - -
143I ASP* 3.7 23.3 + - - +
146I TRP* 3.8 8.9 + - - -
150I LYS* 3.9 18.1 + - - +
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Residues in contact with LEU 44 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A MET* 3.9 12.1 - - + -
70A GLN* 3.1 13.7 + - - +
80A LEU* 4.7 4.5 - - + -
6I VAL* 3.8 17.3 - - + -
8I VAL* 3.6 13.3 - - + +
38I LEU* 3.8 13.7 - - + -
43I THR* 1.3 76.5 - - - +
45I VAL* 1.3 64.9 + - - +
47I ALA* 3.1 6.3 + - - +
48I ALA* 3.0 22.7 + - - +
82I PHE* 3.5 48.9 - - + -
84I PHE* 4.2 9.0 - - + -
141I ILE* 3.8 37.5 - - + +
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Residues in contact with VAL 45 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43I THR* 3.3 20.3 - - + +
44I LEU* 1.3 76.4 - - - +
46I GLU* 1.3 71.9 + - + +
48I ALA* 3.1 3.9 + - - +
49I ALA* 2.9 24.9 + - - +
61I GLN* 4.9 15.0 - - - +
62I PRO* 3.9 17.8 - - + +
84I PHE* 3.8 20.6 - - + -
138I LEU* 3.8 33.9 - - + -
141I ILE* 4.7 4.5 - - + -
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Residues in contact with GLU 46 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41I ASP 4.4 2.8 - - - +
42I GLU* 3.5 22.0 - - + +
43I THR* 3.2 37.5 + - - +
44I LEU 3.2 0.4 - - - -
45I VAL* 1.3 86.5 - - + +
47I ALA* 1.3 64.9 + - - +
49I ALA* 3.1 5.7 + - - +
50I ARG* 2.9 24.3 + - - +
61I GLN* 5.8 5.4 - - - +
146I TRP* 4.6 5.6 + - - -
149I THR 4.9 0.7 - - - +
150I LYS* 3.4 39.5 - - + +
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Residues in contact with ALA 47 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8I VAL* 3.8 19.3 - - + -
38I LEU* 3.6 14.4 - - + -
42I GLU* 3.3 29.3 - - - +
43I THR 3.0 10.9 + - - +
44I LEU 3.3 9.0 - - - +
46I GLU* 1.3 78.0 - - - +
48I ALA* 1.3 52.7 + - - +
50I ARG* 3.2 7.3 + - - +
51I GLU* 2.7 37.1 + - - +
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Residues in contact with ALA 48 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8I VAL* 3.6 23.8 - - + -
9I ALA 4.6 1.3 - - - +
10I CYS* 4.0 14.0 - - - -
34I PRO 4.9 1.7 - - - +
44I LEU 3.0 15.7 + - - +
45I VAL 3.7 3.4 - - - +
47I ALA* 1.3 77.0 - - - +
49I ALA* 1.3 60.9 + - - +
51I GLU* 4.0 2.2 - - - +
52I LEU* 3.3 21.7 + - - +
62I PRO* 3.9 11.9 - - + -
84I PHE* 3.8 23.6 - - + -
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Residues in contact with ALA 49 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10I CYS* 6.0 0.2 - - - -
45I VAL 2.9 12.8 + - - +
46I GLU* 3.5 9.6 - - - +
48I ALA* 1.3 73.6 - - - +
50I ARG* 1.3 67.4 - - - +
52I LEU* 3.2 9.0 + - - +
53I TRP* 3.0 23.3 + - - +
60I ALA 4.1 19.2 + - - +
61I GLN* 4.2 11.0 - - + +
62I PRO* 4.0 15.2 - - + +
150K LYS* 5.7 4.3 - - - +
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Residues in contact with ARG 50 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37I HIS 3.0 25.9 + - - -
39I GLU* 3.1 23.7 + - - -
42I GLU* 2.5 38.2 + - - +
46I GLU 2.9 15.4 + - - +
47I ALA* 3.5 5.4 - - - +
49I ALA* 1.3 76.4 - - - +
51I GLU* 1.3 78.3 + - - +
53I TRP* 3.1 19.5 + - + +
54I GLU* 2.7 78.5 + - - +
155I MN 3.7 4.8 + - - -
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Residues in contact with GLU 51 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8I VAL* 4.2 6.1 - - + -
34I PRO 4.1 1.9 - - - +
35I ALA 3.1 18.1 - - - +
36I GLY* 3.1 11.3 - - - -
37I HIS 2.9 12.2 + - - +
47I ALA 2.7 21.1 + - - +
48I ALA 4.4 3.4 - - - +
50I ARG* 1.3 94.7 + - - +
52I LEU* 1.3 54.7 + - - +
54I GLU* 3.0 19.9 - - - +
55I GLU* 2.8 36.9 + - - +
154I MN 2.7 25.9 + - - -
155I MN 2.7 2.2 + - - -
156I SO4 2.6 30.3 + - - -
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Residues in contact with LEU 52 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10I CYS* 4.9 3.1 - - + -
12I VAL* 4.1 23.1 - - + -
19I LEU* 4.4 3.8 - - + -
34I PRO* 4.1 23.3 + - + +
48I ALA 3.3 15.8 + - - +
49I ALA* 3.2 9.4 + - - +
50I ARG 3.1 0.4 - - - -
51I GLU* 1.3 72.9 - - - +
53I TRP* 1.3 60.7 + - - +
55I GLU 3.2 1.0 + - - -
56I THR* 2.8 48.6 + - + +
58I ILE* 2.8 45.5 - - + +
60I ALA* 3.8 26.0 - - + +
86I ILE* 4.6 12.3 - - + -
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Residues in contact with TRP 53 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49I ALA 3.0 11.4 + - - +
50I ARG* 3.6 20.9 - - + +
52I LEU* 1.3 72.4 - - - +
54I GLU* 1.3 81.6 + - + +
55I GLU 3.0 2.0 - - - -
56I THR 3.0 0.7 + - - -
57I GLY* 2.8 47.5 + - - +
58I ILE 3.3 17.0 + - - +
59I SER* 4.7 11.4 - - - -
97I HIS* 3.6 39.9 + + + +
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Residues in contact with GLU 54 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39I GLU* 5.2 0.2 - - - +
50I ARG* 2.7 64.0 + - - +
51I GLU* 3.0 20.1 - - - +
53I TRP* 1.3 86.8 - - + +
55I GLU* 1.3 59.7 + - - +
97I HIS* 3.9 6.5 + - + -
98I ASP* 3.3 41.8 + - + +
101I ILE* 4.2 0.3 - - - +
154I MN 4.5 3.6 - - - +
155I MN 3.7 8.3 + - - -
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Residues in contact with GLU 55 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21I VAL* 4.0 17.3 - - + +
33I GLN 4.3 0.2 - - - +
34I PRO* 3.5 23.7 - - + +
35I ALA 3.5 8.1 + - - -
51I GLU 2.8 25.1 + - - +
52I LEU 4.0 2.2 - - - +
53I TRP 3.0 0.8 - - - -
54I GLU* 1.3 82.8 - - - +
56I THR* 1.3 66.5 + - + +
96I PRO* 3.4 23.2 - - - +
101I ILE* 3.7 28.0 - - + +
104I CYS* 4.7 0.3 - - - -
154I MN 2.9 14.0 + - - +
157I SO4 2.6 39.9 + - - -
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Residues in contact with THR 56 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19I LEU* 3.8 22.7 - - + -
21I VAL* 4.1 10.8 - - + -
34I PRO* 4.0 15.3 - - + -
52I LEU* 2.8 21.7 + - + +
53I TRP 3.0 0.8 + - - -
55I GLU* 1.3 86.3 - - - +
57I GLY* 1.3 59.5 + - - +
58I ILE* 3.0 33.8 + - - +
93I PRO 4.6 0.3 - - - +
94I THR* 4.1 3.5 - - - -
95I GLN 3.0 34.0 + - - +
96I PRO* 3.9 6.0 - - - +
104I CYS* 4.5 9.9 - - - -
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Residues in contact with GLY 57 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53I TRP* 2.8 32.7 + - - -
56I THR* 1.3 77.6 + - - +
58I ILE* 1.3 62.8 + - - +
59I SER* 3.4 5.4 + - - -
93I PRO 5.5 4.0 - - - -
95I GLN 3.7 2.6 + - - -
97I HIS* 3.6 18.7 + - - -
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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