Contacts of the helix formed by residues 47 - 61 (chain I) in PDB entry 3SWD
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 LEU 47 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22I LYS* 4.1 21.3 - - + -
45I PRO* 3.2 27.2 + - + +
46I LYS* 1.3 76.3 - - - +
48I LYS* 1.3 66.7 + - - +
49I ASP 3.2 1.1 - - - +
50I VAL* 3.0 43.2 + - + +
51I ASP* 3.4 15.8 + - - +
231I ASP* 5.9 0.4 - - - +
396I ASP 3.5 13.2 - - - +
397I ARG 3.6 12.3 - - - +
398I GLY 3.6 29.4 - - - +
399I TYR 3.8 6.7 - - - +
400I GLU 3.9 9.9 - - - +
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Residues in contact with LYS 48 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47I LEU* 1.3 70.1 - - - +
49I ASP* 1.3 62.6 + - - +
51I ASP* 3.1 25.2 + - - +
52I THR* 3.1 31.5 + - - +
393I TYR 5.4 0.7 - - - +
396I ASP* 3.1 25.7 + - + +
397I ARG* 3.8 20.0 - - + -
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Residues in contact with ASP 49 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22I LYS* 3.1 26.5 + - - -
26I LEU* 4.0 18.1 - - + +
47I LEU* 3.1 3.9 + - + -
48I LYS* 1.3 76.2 - - - +
50I VAL* 1.3 60.0 + - - +
52I THR* 3.5 2.6 + - - -
53I SER* 3.0 26.4 + - - -
89I THR 5.3 0.2 - - - +
90I MET* 3.6 27.3 - - - +
370I LEU* 3.4 8.1 - - - +
397I ARG* 2.9 52.5 + - - +
501I EPZ 4.5 1.7 - - - +
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Residues in contact with VAL 50 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25I ALA* 4.5 7.2 - - + -
26I LEU* 4.2 13.5 - - + -
29I LEU* 4.1 14.1 - - + -
44I VAL* 3.8 15.7 - - + -
45I PRO* 3.6 21.3 - - + +
47I LEU* 3.0 22.8 + - + +
49I ASP* 1.3 72.8 - - - +
51I ASP* 1.3 67.5 + - - +
53I SER* 3.0 8.6 + - - -
54I MET* 2.9 36.3 + - + +
66I ARG* 3.9 21.8 - - - +
70I VAL* 4.7 0.9 - - + -
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Residues in contact with ASP 51 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47I LEU 3.8 14.9 + - - +
48I LYS* 3.1 31.9 + - + +
50I VAL* 1.3 78.4 - - - +
52I THR* 1.3 57.4 + - - +
54I MET* 3.2 27.0 + - + +
55I LYS* 2.9 28.6 + - - +
66I ARG* 5.3 1.9 - - - -
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Residues in contact with THR 52 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48I LYS* 3.1 24.6 + - - +
49I ASP* 3.9 9.1 + - - -
51I ASP* 1.3 75.0 - - - +
53I SER* 1.3 60.9 + - - +
55I LYS* 3.4 8.4 + - + -
56I LEU* 3.0 22.3 + - - +
86I LEU* 3.8 20.9 - - + +
89I THR* 3.9 21.6 + - - +
90I MET* 4.0 26.5 - - + +
93I SER* 5.0 1.6 - - - +
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Residues in contact with SER 53 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26I LEU* 3.5 19.8 - - - +
29I LEU* 3.9 22.2 - - - -
30I PHE* 3.8 22.4 - - - -
49I ASP 3.0 15.1 + - - -
50I VAL* 3.0 9.9 + - - -
52I THR* 1.3 77.7 - - - +
54I MET* 1.3 57.4 + - - +
56I LEU* 3.3 3.9 + - - +
57I LEU* 2.9 34.4 + - - +
90I MET* 3.5 9.1 - - - +
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Residues in contact with MET 54 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29I LEU* 4.6 8.5 - - + -
50I VAL* 2.9 22.3 + - + +
51I ASP* 3.2 36.8 - - + +
53I SER* 1.3 73.4 - - - +
55I LYS* 1.3 58.1 + - - +
57I LEU* 3.2 9.6 + - + +
58I SER* 2.8 33.6 + - - -
64I VAL* 3.8 31.1 - - + +
65I GLU* 5.2 1.6 - - - -
66I ARG* 3.8 36.3 - - + -
70I VAL* 4.3 8.3 - - + -
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Residues in contact with LYS 55 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51I ASP 2.9 16.2 + - - +
52I THR* 3.8 9.4 - - + +
54I MET* 1.3 76.6 - - - +
56I LEU* 1.3 62.2 + - - +
58I SER* 3.4 6.2 + - - -
59I GLN* 3.0 38.1 + - + +
86I LEU* 4.0 24.3 - - + +
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Residues in contact with LEU 56 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30I PHE* 3.5 27.6 - - + -
52I THR 3.0 12.4 + - - +
53I SER* 3.8 4.5 - - - +
54I MET 3.2 0.2 - - - -
55I LYS* 1.3 74.2 - - - +
57I LEU* 1.3 66.5 + - - +
59I GLN* 3.0 16.9 + - + -
60I LEU* 3.1 28.8 + - + +
81I CYS 4.5 0.2 - - - +
82I ALA* 3.9 33.0 - - + -
83I PRO* 4.3 8.1 - - + -
86I LEU* 3.3 23.7 - - + +
90I MET* 6.3 0.2 - - + -
93I SER* 3.8 29.6 - - - +
96I ALA* 4.3 4.5 - - + -
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Residues in contact with LEU 57 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29I LEU* 3.6 38.6 - - + +
30I PHE* 4.3 17.3 - - + -
33I LEU* 3.9 29.6 - - + -
53I SER 2.9 19.4 + - - +
54I MET* 3.5 9.6 - - + +
56I LEU* 1.3 72.7 - - - +
58I SER* 1.3 64.4 + - - +
60I LEU* 3.0 18.6 + - + +
61I GLY 3.3 0.3 + - - -
62I ALA* 3.2 23.5 + - + +
64I VAL* 3.8 15.5 - - + -
72I ILE* 3.9 27.4 - - + -
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Residues in contact with SER 58 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54I MET 2.8 20.6 + - - -
55I LYS* 3.7 6.5 - - - -
57I LEU* 1.3 72.8 - - - +
59I GLN* 1.3 57.5 + - - +
61I GLY* 2.9 21.5 + - - -
62I ALA 3.7 16.5 + - - +
64I VAL* 4.3 9.1 - - - +
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Residues in contact with GLN 59 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55I LYS* 3.0 31.2 + - + +
56I LEU* 3.0 12.0 + - + +
58I SER* 1.3 75.8 - - - +
60I LEU* 1.3 54.3 + - + +
61I GLY* 3.1 1.6 + - - -
79I VAL* 2.7 27.3 - - + +
81I CYS 5.2 1.7 - - - +
83I PRO* 3.7 25.3 - - - +
86I LEU* 3.2 28.3 - - - +
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Residues in contact with LEU 60 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30I PHE* 6.0 0.2 - - + -
33I LEU* 3.6 37.5 - - + -
56I LEU* 3.1 32.5 + - + +
57I LEU* 3.0 12.1 + - + +
59I GLN* 1.3 76.4 - - + +
61I GLY* 1.3 58.6 + - - +
62I ALA 3.6 0.9 - - - +
77I VAL* 3.3 11.4 - - + +
78I ASN 3.0 17.7 + - - -
79I VAL* 3.0 42.0 + - + +
80I PHE 4.3 2.0 - - - -
81I CYS 3.7 33.9 - - - +
82I ALA 4.7 0.2 - - - +
96I ALA* 4.5 4.5 - - + -
100I LEU* 4.2 14.4 - - + -
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Residues in contact with GLY 61 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58I SER 2.9 10.8 + - - -
59I GLN 3.1 2.3 - - - -
60I LEU* 1.3 81.1 - - - +
62I ALA* 1.3 63.7 + - - +
63I LYS* 4.0 5.7 + - - +
73I ASP 4.6 0.3 - - - +
76I ASP* 3.3 26.1 + - - +
77I VAL* 4.1 3.6 - - - -
78I ASN* 3.7 15.5 - - - -
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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