Contacts of the helix formed by residues 61 - 71 (chain A) in PDB entry 5LXR
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 VAL 61 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59A HIS* 3.9 17.9 - - + +
60A GLU* 1.3 79.0 - - - +
62A SER* 1.3 62.9 + - - +
63A VAL 3.2 1.1 + - - -
64A PRO* 3.6 12.9 - - + +
65A TYR* 3.8 12.1 + - - +
320B PRO* 3.6 37.2 - - + +
321B GLY* 4.1 8.3 - - - +
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Residues in contact with SER 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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33A ALA* 3.8 13.8 + - - +
34A GLY* 3.7 17.3 - - - -
35A PRO* 4.6 0.9 - - - +
57A PHE* 3.6 25.6 - - - -
59A HIS* 3.1 18.2 + - - +
60A GLU 2.9 1.2 + - - -
61A VAL* 1.3 78.4 - - - +
63A VAL* 1.3 57.4 + - - +
65A TYR* 3.8 4.9 - - - +
66A ALA* 2.8 32.4 + - - +
320B PRO* 4.9 1.6 - - - -
321B GLY* 3.8 15.1 - - - -
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Residues in contact with VAL 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ASP 3.5 23.3 - - - +
10A ARG* 3.6 25.1 - - - +
11A THR 3.9 9.2 - - - +
12A LEU* 3.6 30.0 - - + +
57A PHE* 4.0 11.9 - - + -
59A HIS 4.5 0.9 - - - +
60A GLU* 2.9 11.4 + - + +
62A SER* 1.3 73.5 - - - +
64A PRO* 1.3 73.7 - - + +
66A ALA* 3.3 3.1 + - - +
67A MET* 3.2 20.8 + - - +
84A PHE* 3.7 15.4 - - + -
86A SER* 6.1 1.3 - - - +
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Residues in contact with PRO 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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60A GLU* 3.4 12.6 - - + +
61A VAL* 3.6 10.5 - - + +
63A VAL* 1.3 96.1 - - + +
65A TYR* 1.3 60.0 + - - +
67A MET* 3.4 4.9 + - - +
68A ASN* 3.3 27.6 + - - +
84A PHE* 4.0 19.3 - - + -
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Residues in contact with TYR 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A ALA* 3.8 19.7 - - + -
61A VAL 3.8 11.8 + - - +
62A SER* 3.5 7.4 + - - +
63A VAL 3.2 0.4 - - - -
64A PRO* 1.3 80.9 - - - +
66A ALA* 1.3 58.5 + - - +
68A ASN* 3.1 9.0 + - + +
69A LEU* 2.8 48.2 + - + +
313B MET* 3.4 23.0 - - - +
316B LEU* 3.7 30.0 - - + +
317B GLY 2.6 29.6 + - - -
318B TYR 4.3 1.1 - - - -
319B PRO* 3.7 20.9 - - + +
320B PRO* 3.5 26.2 - - + -
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Residues in contact with ALA 66 (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* 3.6 22.4 - - + -
30A PHE* 4.2 7.9 - - + -
33A ALA* 3.6 24.2 - - + -
57A PHE* 3.8 9.2 - - + -
62A SER 2.8 19.8 + - - +
63A VAL 3.3 0.4 + - - +
65A TYR* 1.3 73.3 - - - +
67A MET* 1.3 66.4 + - - +
69A LEU* 4.3 2.5 - - - -
70A LEU* 2.9 28.9 + - + +
82A ILE* 3.9 3.6 - - - +
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Residues in contact with MET 67 (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* 4.4 1.2 - - - +
63A VAL 3.2 12.5 + - - +
64A PRO 3.4 9.6 - - - +
65A TYR 3.2 0.2 - - - -
66A ALA* 1.3 76.5 - - - +
68A ASN* 1.3 70.4 + - - +
71A ASN* 3.1 55.9 + - - +
82A ILE* 3.4 43.3 - - + +
83A GLN* 4.1 4.7 - - - -
84A PHE* 3.7 42.4 - - + +
312B ARG* 4.6 0.2 + - - -
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Residues in contact with ASN 68 (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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64A PRO* 3.3 14.2 + - - +
65A TYR* 3.1 10.2 + - + +
67A MET* 1.3 85.8 - - - +
69A LEU* 1.3 64.1 + - - +
312B ARG* 3.1 23.4 + - - -
316B LEU* 3.9 30.5 - - + +
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Residues in contact with LEU 69 (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 GLN* 4.2 5.6 - - + -
33A ALA* 3.9 33.9 - - + +
65A TYR* 2.8 27.8 + - + +
66A ALA* 4.0 3.4 - - - +
68A ASN* 1.3 79.2 - - - +
70A LEU* 1.3 71.9 + - + +
73A ILE* 4.1 0.7 - - - +
309B PHE* 3.4 41.8 - - + +
312B ARG* 3.4 19.6 + - + +
313B MET* 3.6 41.3 - - + +
316B LEU* 3.7 10.7 - - + +
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Residues in contact with LEU 70 (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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29A LEU* 3.7 34.3 - - + +
30A PHE* 3.5 49.1 - - + -
33A ALA* 4.6 4.3 - - + -
66A ALA 2.9 12.2 + - - +
69A LEU* 1.3 100.6 - - + +
71A ASN* 1.3 68.3 + - - +
72A GLY 3.2 0.3 + - - -
73A ILE* 3.0 27.7 + - + +
80A ILE* 3.3 12.3 - - + +
82A ILE* 3.8 9.4 - - + -
309B PHE* 3.9 18.8 - - + -
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Residues in contact with ASN 71 (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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67A MET* 3.1 45.1 + - - +
70A LEU* 1.3 75.7 - - - +
72A GLY* 1.3 64.1 + - - +
80A ILE 3.4 3.8 - - - +
81A LYS* 3.7 6.1 - - - +
82A ILE* 3.0 36.1 + - + +
312B ARG* 2.8 31.2 + - - +
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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