Contacts of the helix formed by residues 51 - 62 (chain A) in PDB entry 1R8E
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 51 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47A ASP 4.5 0.2 + - - -
48A SER 3.6 18.2 + - - +
49A GLN 3.0 0.6 + - - -
50A LEU* 1.3 78.2 - - - +
52A HIS* 1.3 80.1 + - + +
54A ASP* 3.0 43.8 + - + +
55A LEU* 4.2 1.0 + - - +
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Residues in contact with HIS 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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30A LEU 6.0 0.4 - - - +
31A PHE* 3.9 16.8 - + + -
48A SER 4.9 0.8 + - - -
49A GLN* 2.9 38.7 + - + +
51A ILE* 1.3 93.9 - - + +
53A LEU* 1.3 59.8 + - - +
54A ASP 3.3 0.5 + - - -
55A LEU* 3.6 7.9 + - - +
56A ILE* 3.5 25.9 + - + +
73A GLN* 5.3 8.1 + - - +
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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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11A VAL* 4.0 21.1 - - + -
15A ALA* 3.5 28.9 - - + -
17A VAL* 4.6 10.3 - - + -
22A LEU* 4.4 10.5 - - + -
25A TYR* 4.8 5.6 - - + -
31A PHE* 3.8 36.3 - - + -
50A LEU* 3.0 17.4 + - + +
52A HIS* 1.3 76.3 - - - +
54A ASP* 1.3 59.9 + - - +
56A ILE* 3.9 23.3 - - + +
57A LYS* 2.9 43.4 + - + +
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Residues in contact with ASP 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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50A LEU 4.6 2.8 - - - +
51A ILE* 3.0 35.5 + - + +
53A LEU* 1.3 76.7 - - - +
55A LEU* 1.3 67.0 + - - +
57A LYS* 4.0 9.5 + - - +
58A SER* 3.0 28.4 + - - -
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Residues in contact with LEU 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 ILE 4.2 1.2 + - - -
52A HIS* 3.6 9.9 + - - +
54A ASP* 1.3 77.3 - - - +
56A ILE* 1.3 59.3 + - + +
58A SER* 3.2 5.7 + - - -
59A LEU* 2.8 65.9 + - + +
69A MET 5.1 0.4 - - - +
72A ALA* 4.3 6.3 - - + +
73A GLN* 3.9 42.0 - - + +
80A LEU* 5.0 16.2 - - + -
84A TYR* 4.5 12.8 - - - +
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Residues in contact with ILE 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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25A TYR* 4.0 29.4 - - + +
30A LEU* 3.8 32.8 - - + +
31A PHE* 3.7 31.0 - - + -
52A HIS* 3.5 19.4 + - + +
53A LEU* 3.9 16.6 - - + +
54A ASP 3.4 0.4 - - - -
55A LEU* 1.3 81.3 - - + +
57A LYS* 1.3 61.6 + - + +
59A LEU* 5.1 0.7 - - - -
60A LYS* 3.0 28.7 + - + +
69A MET* 3.7 22.3 - - + +
73A GLN* 4.6 8.3 - - - +
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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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15A ALA* 2.6 40.1 + - - +
16A ASN* 5.0 5.5 - - - +
17A VAL* 4.0 19.5 - - + -
53A LEU* 2.9 32.2 + - + +
54A ASP* 4.0 11.1 + - - +
56A ILE* 1.3 76.6 - - + +
58A SER* 1.3 60.8 + - - +
60A LYS* 3.2 11.0 + - + +
61A TYR* 2.9 28.6 + - - +
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Residues in contact with SER 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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54A ASP 3.0 19.4 + - - -
55A LEU* 3.7 5.4 - - - -
57A LYS* 1.3 77.3 - - - +
59A LEU* 1.3 66.7 + - - +
61A TYR* 3.1 16.5 + - - +
62A ILE* 3.2 19.9 + - - +
84A TYR* 5.4 7.9 - - - -
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Residues in contact with LEU 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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55A LEU* 2.8 48.8 + - + +
56A ILE 5.1 0.2 - - - +
58A SER* 1.3 74.8 - - - +
60A LYS* 1.3 63.1 + - - +
62A ILE* 3.2 15.6 - - + +
63A GLY 3.2 3.6 + - - -
64A THR* 2.8 37.1 + - + +
69A MET* 3.7 34.3 - - + -
72A ALA* 3.8 22.7 - - + -
80A LEU* 5.8 0.4 - - + -
83A PHE* 3.6 28.3 - - + -
84A TYR* 4.7 9.2 - - + +
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Residues in contact with LYS 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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17A VAL* 6.3 1.2 - - - +
21A ALA* 5.8 3.8 - - - +
25A TYR* 4.1 21.3 + - - +
56A ILE* 3.0 20.0 + - + +
57A LYS* 3.6 10.5 - - + +
58A SER 3.2 0.2 - - - -
59A LEU* 1.3 74.4 - - - +
61A TYR* 1.3 68.1 + - - +
63A GLY* 3.0 13.9 + - - -
64A THR 4.5 2.5 - - - -
66A LEU* 5.9 2.2 - - + -
69A MET* 3.5 13.7 - - + +
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Residues in contact with TYR 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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57A LYS 2.9 13.6 + - - +
58A SER* 3.1 13.2 + - - +
60A LYS* 1.3 79.3 - - - +
62A ILE* 1.3 70.2 + - + +
63A GLY 3.4 0.7 + - - -
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Residues in contact with ILE 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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58A SER 3.2 12.0 + - - +
59A LEU* 3.2 31.0 - - + +
61A TYR* 1.3 86.8 - - + +
63A GLY* 1.3 58.4 + - - +
64A THR* 3.3 17.9 + - - +
83A PHE* 4.4 0.7 - - + -
84A TYR* 5.0 8.1 - - + -
87A GLN* 3.8 34.3 + - + +
91A ILE* 5.9 9.2 - - + -
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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