Contacts of the helix formed by residues 61 - 71 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59I HIS* 3.1 8.3 - - + +
60I GLU* 1.3 78.3 - - - +
62I SER* 1.3 61.8 + - - +
64I PRO* 3.2 18.8 - - - +
65I TYR* 4.1 6.9 + - - +
320J PRO* 4.3 25.8 - - + +
311N TYR* 5.0 2.4 - - - -
315N GLN* 6.1 3.4 - - - +
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Residues in contact with SER 62 (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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33I ALA* 4.2 3.0 + - - +
34I GLY* 3.9 11.3 - - - -
35I PRO* 4.4 1.9 + - - +
57I PHE* 3.4 29.1 - - - -
59I HIS* 2.9 19.3 + - - +
61I VAL* 1.3 77.1 - - - +
63I VAL* 1.3 62.7 + - - +
64I PRO 3.6 0.2 - - - -
65I TYR* 3.3 8.7 + - - +
66I ALA* 3.2 23.0 + - - +
321J GLY* 3.1 31.4 + - - +
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Residues in contact with VAL 63 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9I ASP 4.9 5.6 - - - +
10I ARG 4.7 15.5 - - - -
11I THR 4.8 9.0 - - - +
57I PHE* 4.2 18.3 - - + -
59I HIS 4.0 1.0 + - - +
60I GLU* 3.1 11.9 + - - +
62I SER* 1.3 79.3 - - - +
64I PRO* 1.3 70.0 - - + +
65I TYR 3.3 0.5 + - - -
66I ALA* 3.4 9.4 + - - +
67I MET* 3.5 11.6 + - - +
84I PHE* 4.2 12.9 - - + -
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Residues in contact with PRO 64 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60I GLU 3.3 10.5 - - - +
61I VAL* 3.2 18.6 - - - +
63I VAL* 1.3 91.6 - - + +
65I TYR* 1.3 60.6 + - - +
67I MET* 3.3 4.0 + - - +
68I ASN* 3.3 16.6 + - - +
84I PHE* 4.2 20.5 - - + -
311N TYR* 3.1 18.4 + - + +
315N GLN* 4.5 21.1 - - - +
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Residues in contact with TYR 65 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33I ALA* 3.5 29.8 - - + +
61I VAL 4.3 4.3 - - - +
62I SER* 3.3 12.5 + - - +
63I VAL 3.2 0.8 - - - -
64I PRO* 1.3 82.4 - - - +
66I ALA* 1.3 62.4 + - - +
68I ASN* 3.1 4.0 + - - +
69I LEU* 2.9 36.7 + - + +
313J MET* 3.6 25.1 - - - +
316J LEU* 3.8 22.5 - - + +
317J GLY 2.7 28.2 + - - -
318J TYR 4.4 0.2 - - - -
319J PRO* 3.6 32.3 - - + +
320J PRO 4.7 3.1 - - - -
311N TYR* 3.3 43.0 + + + -
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Residues in contact with ALA 66 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30I PHE* 3.6 18.2 - - + -
33I ALA* 3.6 15.6 - - + +
57I PHE* 3.3 37.5 - - + -
62I SER 3.2 4.9 + - - +
63I VAL 3.9 2.7 - - - +
64I PRO 3.4 0.2 - - - -
65I TYR* 1.3 78.3 - - - +
67I MET* 1.3 57.5 + - - +
69I LEU 4.5 0.4 - - - +
70I LEU* 2.8 36.8 + - - +
71I ASN 3.8 0.7 + - - -
82I ILE* 3.9 4.0 - - + +
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Residues in contact with MET 67 (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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63I VAL 3.5 6.8 + - - +
64I PRO 3.3 9.8 + - - +
65I TYR 3.2 0.4 - - - -
66I ALA* 1.3 78.6 - - - +
68I ASN* 1.3 63.2 + - - +
71I ASN* 3.1 47.1 + - - +
82I ILE* 3.0 50.1 - - + +
83I GLN* 4.1 0.7 - - - -
84I PHE* 3.6 53.6 - - + +
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Residues in contact with ASN 68 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64I PRO 3.3 8.3 + - - +
65I TYR 3.1 7.8 + - - +
67I MET* 1.3 82.2 - - + +
69I LEU* 1.3 62.6 + - - +
71I ASN* 4.7 1.9 + - - +
312J ARG* 3.5 18.9 + - - +
316J LEU* 4.2 21.1 - - + -
311N TYR* 4.1 11.2 - - + +
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Residues in contact with LEU 69 (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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32I GLN* 4.4 18.6 - - + -
33I ALA* 4.4 5.6 - - + +
65I TYR* 2.9 34.2 + - + +
66I ALA* 4.6 0.2 - - - -
68I ASN* 1.3 79.4 - - - +
70I LEU* 1.3 83.9 + - + +
71I ASN 3.8 1.5 - - - +
73I ILE* 4.2 10.7 - - - +
309J PHE* 4.3 14.3 - - + +
312J ARG* 3.7 34.8 + - + +
313J MET* 3.8 25.1 - - + -
316J LEU* 3.9 15.5 - - + -
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Residues in contact with LEU 70 (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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29I LEU* 3.9 37.5 - - + +
30I PHE* 3.5 40.4 - - + -
32I GLN* 5.3 0.7 - - + -
33I ALA* 4.4 7.6 - - + -
66I ALA* 2.8 23.9 + - + +
69I LEU* 1.3 99.7 - - + +
71I ASN* 1.3 65.4 + - - +
72I GLY 3.3 0.9 + - - -
73I ILE* 3.3 27.3 + - + +
80I ILE* 3.4 13.8 - - + +
82I ILE* 3.7 10.1 - - + -
309J PHE* 4.5 10.5 - - + -
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Residues in contact with ASN 71 (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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67I MET* 3.1 41.8 + - - +
68I ASN 4.7 2.1 + - - +
69I LEU 3.8 2.0 - - - +
70I LEU* 1.3 78.4 - - - +
72I GLY* 1.3 68.9 + - - +
73I ILE* 3.2 3.3 + - - +
80I ILE 3.6 3.1 - - - +
81I LYS* 3.7 2.1 - - - -
82I ILE* 2.9 39.6 + - + +
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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