Contacts of the helix formed by residues 52 - 64 (chain A) in PDB entry 3F6W
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 ASP 52 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51A LEU* 1.3 74.5 - - - +
53A VAL* 1.3 59.9 + - - +
54A ILE* 2.8 31.6 + - - +
55A GLU* 2.8 23.0 + - - -
56A PHE* 2.9 29.3 + - - +
5B HIS* 2.6 28.0 + - - -
9B TYR* 4.2 13.6 - - + -
50B ARG* 3.0 29.4 + - + +
51B LEU 3.2 22.4 - - - +
53B VAL 4.1 2.7 - - - +
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Residues in contact with VAL 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A ASP* 1.3 75.3 - - + +
54A ILE* 1.3 62.5 + - + +
56A PHE* 3.5 12.9 - - + +
57A MSE 2.9 30.4 + - + +
71A LEU* 5.0 2.7 - - + -
12B LEU* 3.9 36.8 - - + -
51B LEU 4.5 1.0 + - - -
52B ASP 4.6 0.4 + - - -
53B VAL* 4.1 21.5 - - + +
56B PHE* 3.9 29.4 - - + +
71B LEU* 3.9 33.0 - - + -
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Residues in contact with ILE 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A ASP* 2.8 10.9 + - - +
53A VAL* 1.3 86.5 - - + +
55A GLU* 1.3 66.2 + - - +
57A MSE 3.3 18.2 + - + +
58A ASP* 3.2 21.8 + - - +
5B HIS* 3.8 17.7 - - + -
8B ARG* 3.4 46.2 - - + +
9B TYR* 4.1 27.4 - - + +
12B LEU* 4.6 3.8 - - + -
74B LEU* 3.4 32.5 - - + -
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Residues in contact with GLU 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A LEU* 5.9 0.2 - - - +
36A ARG* 4.3 11.1 + - - +
40A PHE* 4.0 18.3 - - + -
49A ARG* 3.0 37.8 + - - -
51A LEU* 3.5 13.4 - - + -
52A ASP* 2.8 39.0 + - - +
54A ILE* 1.3 71.8 - - - +
56A PHE* 1.3 52.3 + - - +
58A ASP* 3.1 9.3 + - - +
59A PHE* 2.8 36.8 + - - +
2B LYS* 5.6 0.7 + - - -
5B HIS* 3.5 21.3 + - + -
50B ARG* 3.0 19.6 + - - -
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Residues in contact with PHE 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A LEU* 3.8 31.4 - - + -
16A LEU* 3.9 21.3 - - + -
51A LEU* 4.3 9.4 - - + +
52A ASP 2.9 18.8 + - - +
53A VAL* 3.5 10.5 - - + +
54A ILE 3.2 0.2 - - - -
55A GLU* 1.3 74.0 - - - +
57A MSE 1.3 73.0 + - + +
59A PHE* 3.2 6.7 + - + +
60A CYS* 3.0 44.9 + - - -
67A PRO* 3.7 22.7 - - + -
70A LEU* 4.1 9.4 - - + -
71A LEU* 3.6 38.4 - - + -
53B VAL* 4.2 15.9 - - + -
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Residues in contact with MSE 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A VAL* 2.9 19.7 + - + +
54A ILE* 3.3 35.2 + - + +
56A PHE* 1.3 79.6 - - + +
58A ASP* 1.3 65.2 + - - +
60A CYS* 3.3 1.9 + - - +
61A ARG* 3.0 40.9 + - - +
67A PRO* 4.1 20.2 - - + -
68A TYR* 4.2 11.0 - - + -
71A LEU* 6.4 0.2 - - + -
8B ARG* 4.2 14.6 - - - +
71B LEU* 4.4 20.9 - - + -
74B LEU* 4.3 9.2 - - + -
75B GLU* 3.9 37.0 - - + +
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Residues in contact with ASP 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A LEU* 3.4 19.3 - - + +
36A ARG* 5.2 10.0 + - - +
54A ILE* 3.2 11.3 + - - +
55A GLU* 3.1 10.5 + - - +
57A MSE 1.3 75.2 - - - +
59A PHE* 1.3 60.7 + - - +
61A ARG* 3.3 10.2 + - - +
62A GLY 2.8 25.1 + - - -
5B HIS* 5.8 0.9 - - - +
8B ARG* 2.9 43.1 + - - -
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Residues in contact with PHE 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A LEU* 3.9 39.9 - - + -
20A ARG* 5.3 0.9 - - + -
30A LEU* 3.5 30.8 - - + +
34A LEU* 4.2 20.1 - - + +
40A PHE* 4.4 9.2 - + - -
41A VAL* 4.2 15.7 - - + -
44A THR* 3.9 25.8 - - + -
45A GLU* 3.9 24.9 - - + -
51A LEU* 4.6 6.5 - - + -
55A GLU 2.8 16.0 + - - +
56A PHE* 3.5 9.9 - - - +
58A ASP* 1.3 77.5 - - - +
60A CYS* 1.3 61.5 - - - +
62A GLY* 3.1 10.0 + - - -
63A ILE* 3.1 25.6 + - + +
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Residues in contact with CYS 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A LEU* 3.9 13.5 - - - -
56A PHE* 3.0 48.2 + - - -
57A MSE 3.5 8.7 - - - +
59A PHE* 1.3 77.3 - - - +
61A ARG* 1.3 57.8 + - - +
63A ILE* 3.0 11.2 + - - +
64A GLY 2.9 23.7 + - - -
65A THR* 3.0 32.7 + - + +
67A PRO* 3.8 17.9 - - + -
70A LEU* 4.1 3.4 - - - -
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Residues in contact with ARG 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A ARG* 5.4 0.2 + - - -
57A MSE 3.0 39.9 + - - +
58A ASP* 3.3 10.3 + - - +
60A CYS* 1.3 75.4 - - - +
62A GLY* 1.3 62.7 + - - +
64A GLY* 3.1 14.1 + - - +
65A THR 4.5 2.0 - - - -
66A ASP* 5.7 0.2 + - - -
67A PRO* 3.5 26.6 - - - +
68A TYR* 3.9 12.9 - - - -
8B ARG* 5.7 1.4 - - - +
75B GLU* 2.9 41.8 + - - -
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Residues in contact with GLY 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A ILE* 3.9 2.1 - - - +
30A LEU* 3.8 17.2 - - - +
33A ARG* 2.9 43.0 + - - -
34A LEU* 4.6 4.9 - - - -
58A ASP 2.8 15.2 + - - -
59A PHE 3.1 5.1 + - - -
60A CYS 3.1 0.2 - - - -
61A ARG* 1.3 78.9 - - - +
63A ILE* 1.3 56.0 + - - +
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Residues in contact with ILE 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A LEU* 4.2 15.9 - - + +
19A ALA* 3.7 20.6 - - + -
20A ARG* 3.9 28.9 - - + +
23A ALA* 3.5 21.2 - - + +
25A ILE* 3.8 14.4 - - + +
30A LEU* 3.8 31.9 - - + -
33A ARG* 4.9 1.3 - - - -
59A PHE* 3.1 12.1 + - + +
60A CYS* 3.1 15.5 - - - +
62A GLY* 1.3 77.6 - - - +
64A GLY* 1.3 59.1 + - - +
65A THR* 3.4 24.7 + - + -
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Residues in contact with GLY 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A ARG* 5.3 0.6 - - - +
60A CYS 2.9 4.3 + - - -
61A ARG* 3.1 13.1 + - - -
63A ILE* 1.3 79.5 - - - +
65A THR* 1.3 59.0 + - - +
66A ASP 4.2 0.7 + - - -
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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
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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