Contacts of the helix formed by residues 68 - 77 (chain H) in PDB entry 1R8Y
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 GLY 68 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65H CYS* 3.1 25.9 + - - -
66H GLY 2.9 6.7 + - - -
67H THR* 1.3 78.0 - - - +
69H VAL* 1.3 60.7 + - - +
70H ASP 3.3 2.7 - - - -
71H SER* 3.2 5.4 + - - -
72H ILE* 2.8 37.1 + - - +
94H ALA* 4.1 6.1 - - - -
110H TRP* 4.6 4.5 - - - -
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Residues in contact with VAL 69 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37H THR* 3.7 48.2 - - + +
40H ARG* 2.8 28.0 + - - +
65H CYS 4.7 0.8 + - - -
67H THR* 3.4 15.6 - - - +
68H GLY* 1.3 76.0 - - - +
70H ASP* 1.3 61.8 + - - +
72H ILE* 3.8 12.5 - - + +
73H MET 3.2 7.1 + - - -
194H TYR* 3.3 24.2 - - + +
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Residues in contact with ASP 70 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44H TYR* 2.7 35.4 + - - +
48H LEU* 5.4 0.2 - - + -
62H ASP* 4.1 11.3 + - - +
65H CYS 5.5 1.2 + - - +
68H GLY 3.3 0.4 - - - -
69H VAL* 1.3 73.8 - - - +
71H SER* 1.3 67.6 + - - +
73H MET* 3.1 11.6 + - + +
74H LEU* 3.1 25.1 + - - +
134H ILE* 4.4 13.8 - - + +
136H LEU* 4.7 15.1 - - - +
137H GLY* 5.3 1.0 + - - -
193H TYR* 5.8 1.0 - - - -
194H TYR* 2.6 32.1 + - - -
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Residues in contact with SER 71 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62H ASP* 2.6 32.7 + - - +
65H CYS* 4.7 1.6 - - - -
68H GLY* 3.2 5.8 + - - -
70H ASP* 1.3 75.7 - - - +
72H ILE* 1.3 52.6 + - - +
74H LEU* 2.9 11.2 + - - +
75H VAL* 2.7 37.8 + - - +
81H VAL* 3.8 9.4 - - - +
83H SER* 3.1 28.5 + - - -
110H TRP* 3.7 18.4 - - - -
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Residues in contact with ILE 72 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40H ARG* 5.1 4.0 - - - +
67H THR 4.2 6.3 - - - +
68H GLY 2.8 27.1 + - - +
69H VAL* 3.8 15.7 - - + +
71H SER* 1.3 75.4 - - - +
73H MET* 1.3 62.1 + - - +
75H VAL* 3.9 6.3 - - - +
76H GLU* 3.0 31.0 + - - +
97H GLU* 3.5 30.3 - - + +
101H ARG* 3.9 14.6 - - - +
107H PHE* 3.9 20.2 - - + -
110H TRP* 3.5 24.9 - - + -
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Residues in contact with MET 73 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40H ARG* 3.6 47.5 - - - +
44H TYR* 4.2 13.9 - - + +
45H LYS* 4.2 14.8 - - + -
48H LEU* 3.5 32.3 - - + -
49H LEU* 3.7 29.2 - - - -
69H VAL 3.2 3.6 + - - +
70H ASP* 3.1 13.3 + - - +
72H ILE* 1.3 79.5 - - - +
74H LEU* 1.3 64.5 + - + +
76H GLU* 3.5 10.4 + - - +
77H GLU* 3.1 33.4 + - + +
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Residues in contact with LEU 74 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48H LEU* 4.1 11.7 - - + -
49H LEU* 3.8 22.7 - - + -
52H LEU* 3.6 28.9 - - + -
60H VAL* 3.9 29.2 - - + -
62H ASP* 5.8 0.4 - - + -
70H ASP 3.1 10.4 + - - +
71H SER* 2.9 12.7 + - - +
73H MET* 1.3 76.3 - - + +
75H VAL* 1.3 64.8 + - - +
77H GLU 3.1 11.1 + - - -
78H GLY 3.2 8.0 + - - -
79H PHE* 3.2 22.9 + - + -
81H VAL* 4.1 15.0 - - + -
134H ILE* 4.2 21.3 - - + -
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Residues in contact with VAL 75 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71H SER 2.7 17.9 + - - +
72H ILE* 3.9 3.4 - - - +
74H LEU* 1.3 71.3 - - - +
76H GLU* 1.3 64.1 + - - +
78H GLY* 3.1 14.6 + - - -
79H PHE 4.1 6.3 - - - +
81H VAL* 3.2 26.5 - - + +
106H SER* 3.1 43.3 - - - +
107H PHE* 3.5 27.8 - - + -
110H TRP* 3.5 34.1 - - + -
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Residues in contact with GLU 76 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40H ARG* 5.2 5.2 + - - -
72H ILE* 3.0 23.6 + - - +
73H MET* 3.7 13.0 - - - +
75H VAL* 1.3 80.4 - - - +
77H GLU* 1.3 64.5 + - - +
78H GLY* 3.0 6.2 + - - -
101H ARG* 2.6 45.1 + - - +
106H SER* 5.5 3.7 - - - -
107H PHE* 4.0 5.4 - - + -
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Residues in contact with GLU 77 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49H LEU* 3.3 30.7 - - + +
53H ARG* 3.2 36.0 + - - +
73H MET* 3.1 20.8 + - + +
74H LEU 3.1 4.9 + - - +
76H GLU* 1.3 84.2 - - - +
78H GLY* 1.3 59.7 + - - +
79H PHE* 3.4 17.9 + - + -
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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