Contacts of the helix formed by residues 47 - 57 (chain A) in PDB entry 1X1M
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 ILE 47 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45A TYR 4.2 0.6 + - - -
46A SER* 1.3 68.7 - - - +
48A SER* 1.3 66.9 + - - +
50A LEU* 2.7 26.8 + - + +
51A LYS* 3.0 26.9 + - + -
70A LEU* 4.5 8.5 - - + -
77A LEU* 3.5 53.2 - - + +
78A LYS 2.9 22.7 - - - +
79A ASP* 4.2 0.8 - - - +
81A GLN* 3.5 19.1 + - + +
82A THR 4.8 1.8 - - - -
83A LEU* 4.3 17.7 - - + -
86A TYR* 4.5 6.5 - - + -
88A ILE* 4.4 9.9 - - + -
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Residues in contact with SER 48 (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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46A SER* 3.1 7.1 - - - -
47A ILE* 1.3 78.0 - - - +
49A PHE* 1.3 66.0 + - - +
51A LYS* 3.1 20.3 + - - +
52A GLN* 3.1 25.4 + - - +
79A ASP* 3.7 31.3 - - - +
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Residues in contact with PHE 49 (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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32A LEU* 4.8 1.3 - - + -
33A PRO* 3.9 24.2 - - + -
45A TYR* 3.6 39.5 - + + -
46A SER* 2.7 22.4 + - - +
48A SER* 1.3 72.3 - - - +
50A LEU* 1.3 55.9 + - + +
52A GLN* 2.7 42.8 + - + +
53A LEU* 2.9 47.0 - - + +
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Residues in contact with LEU 50 (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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15A LEU* 4.3 21.3 - - + -
30A LEU* 3.8 14.1 - - + -
32A LEU* 5.0 15.0 - - + -
45A TYR* 6.2 3.4 - - + -
46A SER 3.8 0.9 + - - +
47A ILE* 2.7 22.7 + - + +
49A PHE* 1.3 77.2 - - + +
51A LYS* 1.3 54.8 + - - +
52A GLN 2.6 11.8 + - - -
53A LEU* 2.9 20.8 + - + -
54A ILE* 3.0 35.0 + - + +
70A LEU* 3.8 23.6 - - + -
83A LEU* 4.3 32.1 - - + -
88A ILE* 5.3 4.3 - - + -
94A VAL* 5.6 1.1 - - + -
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Residues in contact with LYS 51 (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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47A ILE* 3.0 22.6 + - + +
48A SER* 3.1 19.0 + - - +
50A LEU* 1.3 74.5 - - - +
52A GLN* 1.3 56.5 + - + +
54A ILE* 5.0 2.7 - - - -
55A ALA* 3.1 26.0 + - - +
65A PRO* 3.4 12.8 - - + +
68A ILE* 3.6 19.6 - - + +
69A ASP* 3.8 19.6 + - - +
70A LEU* 3.8 27.8 - - + +
76A LYS* 3.1 13.6 - - - +
77A LEU 2.9 28.5 + - - -
78A LYS 3.9 0.2 - - - -
79A ASP* 3.8 23.2 + - + +
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Residues in contact with GLN 52 (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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48A SER* 3.1 27.8 + - - +
49A PHE* 2.7 23.9 + - + +
50A LEU 2.6 4.6 + - - -
51A LYS* 1.3 74.0 - - + +
53A LEU* 1.3 66.1 + - + +
55A ALA* 3.1 3.3 + - - +
56A GLY* 2.8 22.0 + - - -
65A PRO* 3.8 22.1 - - + +
66A GLU* 6.3 0.8 - - - +
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Residues in contact with LEU 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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30A LEU* 3.5 33.1 - - + +
31A GLN 4.8 1.8 - - - +
32A LEU* 3.6 19.5 - - + +
33A PRO* 3.6 29.2 - - + -
49A PHE* 2.9 66.8 + - + +
50A LEU* 2.9 12.7 + - + +
52A GLN* 1.3 74.2 - - + +
54A ILE* 1.3 62.6 + - - +
56A GLY* 3.0 12.4 + - - -
57A LYS* 3.1 10.4 + - - +
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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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15A LEU* 5.4 0.7 - - + -
17A VAL* 3.4 29.4 - - + -
30A LEU* 3.2 24.7 - - + -
50A LEU* 3.0 47.7 + - + +
51A LYS* 4.8 2.0 - - - +
53A LEU* 1.3 77.2 - - - +
55A ALA* 1.3 59.5 + - - +
57A LYS* 2.9 5.1 + - - +
58A LEU* 2.8 43.3 + - + +
68A ILE* 6.1 1.3 - - + -
70A LEU* 4.5 16.4 - - + -
94A VAL* 4.8 2.9 - - + -
96A VAL* 3.2 33.4 - - + -
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Residues in contact with ALA 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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51A LYS 3.1 22.4 + - - +
52A GLN 3.1 3.0 + - - +
54A ILE* 1.3 80.9 - - - +
56A GLY* 1.3 57.3 + - - +
58A LEU 4.0 1.4 - - - -
59A GLN* 3.2 29.2 + - - +
62A VAL* 3.7 24.8 - - + +
64A ASP* 5.8 0.3 - - - -
65A PRO* 3.4 34.4 - - + +
68A ILE* 4.3 3.8 - - + +
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Residues in contact with GLY 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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52A GLN 2.8 13.8 + - - -
53A LEU* 3.0 6.0 + - - -
54A ILE 3.0 0.4 - - - -
55A ALA* 1.3 79.3 - - - +
57A LYS* 1.3 60.5 + - - +
59A GLN* 3.2 25.3 - - - +
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Residues in contact with LYS 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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28A SER* 6.1 2.5 - - - -
29A ILE 5.3 9.8 + - - +
30A LEU* 3.6 28.5 - - + +
31A GLN 6.3 0.4 - - - +
53A LEU 3.1 5.1 + - - +
54A ILE* 2.9 7.6 + - - +
56A GLY* 1.3 78.7 - - - +
58A LEU* 1.3 67.2 + - + +
59A GLN* 3.1 8.3 + - - +
60A GLU* 4.6 5.5 + - - +
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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