Contacts of the helix formed by residues 61 - 71 (chain E) in PDB entry 5LXY
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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311C TYR* 4.5 3.6 - - - -
312C ARG* 4.1 30.3 - - - +
59E HIS* 4.1 11.7 - - + -
60E GLU* 1.3 77.5 - - + +
62E SER* 1.3 63.3 + - - +
64E PRO* 3.1 15.6 - - - +
65E TYR* 3.7 6.4 + - - +
320F PRO* 3.8 22.8 - - + +
321F GLY* 3.6 32.3 - - - +
324F LYS* 4.2 13.9 - - - +
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Residues in contact with SER 62 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33E ALA* 3.5 7.5 + - - +
34E GLY* 3.4 20.1 - - - -
35E PRO* 4.5 0.9 - - - +
57E PHE* 3.6 29.4 - - - -
59E HIS* 3.5 10.0 + - - +
60E GLU 3.0 0.8 + - - -
61E VAL* 1.3 79.8 - - - +
63E VAL* 1.3 55.3 + - - +
64E PRO 3.5 0.2 - - - -
65E TYR* 3.2 7.3 + - - +
66E ALA* 2.7 37.2 + - - +
320F PRO* 4.9 0.9 - - - -
321F GLY* 3.6 17.5 + - - -
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Residues in contact with VAL 63 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9E ASP 3.7 8.1 - - - +
10E ARG* 3.5 36.1 - - + -
11E THR 4.2 7.6 - - - +
12E LEU* 3.8 19.0 - - + +
57E PHE* 4.3 13.5 - - + -
59E HIS 4.3 2.2 - - - +
60E GLU* 2.8 21.4 + - + +
62E SER* 1.3 77.6 - - - +
64E PRO* 1.3 63.0 - - + +
66E ALA* 3.4 3.5 + - - +
67E MET* 3.3 18.5 + - - +
84E PHE* 3.6 29.1 - - + -
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Residues in contact with PRO 64 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311C TYR* 3.0 14.6 - - + +
315C GLN* 4.1 16.2 - - - +
60E GLU 3.3 9.4 - - - +
61E VAL* 3.1 16.4 - - - +
63E VAL* 1.3 91.6 - - + +
65E TYR* 1.3 59.2 + - - +
67E MET* 3.3 2.5 + - + +
68E ASN* 2.8 31.3 + - - +
84E PHE* 4.4 18.4 - - + -
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Residues in contact with TYR 65 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311C TYR* 3.1 30.8 + + + -
33E ALA* 3.4 20.9 - - - -
61E VAL 3.7 9.6 + - - +
62E SER* 3.2 9.7 + - - +
64E PRO* 1.3 79.0 - - - +
66E ALA* 1.3 56.9 + - - +
68E ASN* 3.2 2.3 + - - +
69E LEU* 2.8 56.0 + - + +
313F MET* 3.3 26.2 - - - +
316F LEU* 3.9 19.1 - - + -
317F GLY 2.8 28.1 + - - -
318F TYR 4.1 0.9 - - - -
319F PRO* 3.4 26.4 - - + +
320F PRO* 3.4 20.6 - - + -
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Residues in contact with ALA 66 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12E LEU* 3.5 26.2 - - + -
30E PHE* 4.2 7.4 - - + -
33E ALA* 3.6 16.4 - - + -
57E PHE* 3.6 19.1 - - + -
62E SER 2.7 21.5 + - - +
63E VAL 3.8 0.2 - - - +
65E TYR* 1.3 72.4 - - - +
67E MET* 1.3 56.5 + - - +
69E LEU* 4.6 0.7 - - - -
70E LEU* 2.7 37.6 + - - +
71E ASN 3.8 0.5 + - - -
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Residues in contact with MET 67 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12E LEU* 4.1 8.6 - - + +
63E VAL 3.3 8.9 + - - +
64E PRO 3.3 9.1 + - - +
65E TYR 3.2 0.4 - - - -
66E ALA* 1.3 78.5 - - - +
68E ASN* 1.3 69.8 + - - +
71E ASN* 3.1 49.4 + - + +
82E ILE* 3.3 47.6 - - + +
83E GLN* 3.7 7.4 - - - +
84E PHE* 3.5 41.7 - - + -
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Residues in contact with ASN 68 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311C TYR* 3.6 23.8 + - - +
315C GLN* 5.8 0.4 - - - +
64E PRO* 2.8 19.8 + - - +
65E TYR 3.7 3.6 - - - +
67E MET* 1.3 84.7 - - - +
69E LEU* 1.3 60.3 + - - +
71E ASN 5.0 0.9 + - - +
312F ARG* 3.2 24.3 + - - +
316F LEU* 3.9 23.9 - - + +
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Residues in contact with LEU 69 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32E GLN* 4.3 3.8 - - + -
33E ALA* 4.1 17.5 - - - +
65E TYR* 2.8 40.4 + - + +
66E ALA 4.1 1.3 - - - +
68E ASN* 1.3 81.2 - - - +
70E LEU* 1.3 77.8 + - + +
71E ASN 3.7 1.5 - - - +
73E ILE* 4.5 8.3 - - - +
309F PHE* 4.2 32.1 - - + +
312F ARG* 4.4 17.7 + - + +
313F MET* 4.0 30.1 - - + +
316F LEU* 4.0 15.5 - - + -
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Residues in contact with LEU 70 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29E LEU* 3.8 26.5 - - + +
30E PHE* 3.6 50.5 - - + -
32E GLN* 5.0 0.4 - - + -
33E ALA* 4.5 7.9 - - + -
66E ALA* 2.7 22.0 + - - +
69E LEU* 1.3 94.8 - - + +
71E ASN* 1.3 64.8 + - - +
73E ILE* 3.3 14.6 + - + +
80E ILE* 3.1 26.6 - - + +
82E ILE* 5.7 0.4 - - - -
309F PHE* 3.8 29.6 - - + -
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Residues in contact with ASN 71 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66E ALA 3.8 1.4 + - - -
67E MET* 3.1 43.4 + - - +
68E ASN 5.6 0.7 - - - +
69E LEU 3.7 2.1 - - - +
70E LEU* 1.3 76.9 - - - +
72E GLY* 1.3 68.6 + - - +
73E ILE* 3.5 3.8 + - - +
80E ILE* 3.4 6.5 - - - +
81E LYS* 3.7 1.7 - - - -
82E ILE* 3.0 37.7 + - + +
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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