Contacts of the helix formed by residues 70 - 83 (chain I) in PDB entry 6RAR
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 LEU 70 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68I ASN* 3.6 37.2 - - - +
69I PHE* 1.3 79.0 - - - +
71I TRP* 1.3 68.1 + - - +
72I GLU* 4.1 26.0 - - + +
73I ASP* 2.8 34.7 + - - +
74I PHE* 3.2 11.4 + - - +
111I TYR* 4.1 4.2 + - - -
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Residues in contact with TRP 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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8I LYS* 4.3 12.0 - - - +
38I ASP* 3.3 49.1 + - + +
41I GLU* 2.9 45.2 + - + -
42I GLY* 3.7 22.2 - - - -
45I MET* 4.3 13.0 - - + -
70I LEU* 1.3 72.9 - - - +
72I GLU* 1.3 60.4 + - + +
74I PHE* 2.8 45.5 + + - +
75I ARG* 2.9 35.8 + - + +
110I PHE* 4.2 9.9 - + - -
111I TYR* 3.5 31.3 + + - +
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Residues in contact with GLU 72 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70I LEU* 4.1 22.9 - - + +
71I TRP* 1.3 79.8 - - - +
73I ASP* 1.3 75.7 + - - +
75I ARG* 3.5 28.3 + - - +
76I LYS* 3.3 38.1 + - + +
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Residues in contact with ASP 73 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68I ASN 3.6 7.4 - - - +
69I PHE* 3.8 18.9 - - + -
70I LEU* 2.8 46.8 + - - +
72I GLU* 1.3 87.1 - - - +
74I PHE* 1.3 60.8 + - - +
76I LYS* 3.7 9.9 + - - +
77I LEU* 3.5 18.7 + - - +
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Residues in contact with PHE 74 (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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45I MET* 4.5 1.3 - - - -
69I PHE* 3.6 20.6 - + + -
70I LEU 3.2 4.7 + - - +
71I TRP* 2.8 33.1 + + + +
73I ASP* 1.3 75.9 - - - +
75I ARG* 1.3 55.0 + - - +
77I LEU* 3.1 14.6 + - + +
78I ALA* 2.7 48.1 + - + -
107I TRP* 4.7 2.7 - + - -
111I TYR* 3.2 64.4 - + + -
114I VAL* 4.0 22.7 - - + -
115I LEU* 3.9 31.2 - - + -
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Residues in contact with ARG 75 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38I ASP* 4.9 1.6 + - - -
41I GLU* 3.0 40.8 + - - +
45I MET* 4.5 8.3 - - + -
71I TRP* 2.9 33.3 + - + +
72I GLU* 3.5 31.8 + - - +
74I PHE* 1.3 79.4 - - - +
76I LYS* 1.3 59.8 + - + +
78I ALA* 3.2 6.4 + - - +
79I ASN* 2.8 50.1 + - - +
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Residues in contact with LYS 76 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72I GLU* 3.3 28.8 + - + +
73I ASP* 4.1 9.9 - - - +
74I PHE 3.2 0.8 - - - -
75I ARG* 1.3 78.1 - - + +
77I LEU* 1.3 65.4 + - - +
79I ASN* 4.0 6.5 - - - +
80I LYS* 3.1 38.7 + - + +
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Residues in contact with LEU 77 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69I PHE* 6.1 0.2 - - + -
73I ASP 3.5 10.6 + - - +
74I PHE* 3.1 26.8 + - + +
76I LYS* 1.3 79.8 - - - +
78I ALA* 1.3 61.7 + - - +
80I LYS* 3.3 11.1 + - - +
81I LEU* 3.0 47.2 + - + +
86I LEU* 4.5 7.6 - - + -
94I ALA* 3.7 37.9 - - + +
95I ILE* 4.3 11.4 - - + +
98I ALA* 3.9 26.0 - - + -
107I TRP* 5.1 0.4 - - + -
115I LEU* 4.7 6.3 - - + -
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Residues in contact with ALA 78 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45I MET* 3.9 30.3 - - + -
53I PHE* 3.9 19.1 - - + -
74I PHE* 2.7 31.0 + - + +
75I ARG* 3.5 5.4 - - - +
77I LEU* 1.3 74.2 - - - +
79I ASN* 1.3 52.4 + - - +
81I LEU* 3.1 6.7 + - - +
82I MET* 2.7 38.9 + - + +
115I LEU* 5.3 1.8 - - - -
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Residues in contact with ASN 79 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45I MET* 4.5 5.2 - - - +
75I ARG* 2.8 44.4 + - - +
76I LYS* 4.1 6.5 - - - +
77I LEU 3.3 0.2 - - - -
78I ALA* 1.3 71.9 - - - +
80I LYS* 1.3 59.2 + - + +
82I MET* 3.4 25.7 - - - +
83I GLN* 2.9 39.3 + - + +
85I GLU* 4.8 1.1 - - - -
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Residues in contact with LYS 80 (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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76I LYS* 3.1 24.4 + - + +
77I LEU* 3.9 10.7 - - - +
79I ASN* 1.3 75.2 - - + +
81I LEU* 1.3 61.6 + - - +
83I GLN 3.7 0.2 - - - -
84I ARG 3.1 4.5 + - - -
85I GLU* 2.8 58.1 + - + +
86I LEU* 3.2 36.6 + - + +
94I ALA* 5.7 1.0 - - - +
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Residues in contact with LEU 81 (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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53I PHE* 3.6 30.1 - - + +
55I VAL* 5.0 1.6 - - + -
77I LEU* 3.0 36.0 + - + +
78I ALA 3.5 4.9 - - - +
80I LYS* 1.3 74.6 - - - +
82I MET* 1.3 66.7 + - - +
84I ARG* 3.0 27.8 + - - +
86I LEU* 3.8 18.1 - - + +
91I ALA* 3.6 32.8 - - + +
95I ILE* 4.1 18.8 - - + -
115I LEU* 3.9 28.7 - - + -
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Residues in contact with MET 82 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45I MET* 4.3 14.4 - - + -
50I LEU 5.7 0.4 - - - +
51I VAL* 3.8 43.1 - - + -
52I THR 3.5 15.2 - - - +
53I PHE* 4.0 10.2 - - + -
78I ALA* 2.7 29.5 + - + +
79I ASN* 3.4 30.7 - - - +
81I LEU* 1.3 75.2 - - - +
83I GLN* 1.3 71.7 + - - +
84I ARG* 3.4 15.1 + - - +
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Residues in contact with GLN 83 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79I ASN* 2.9 22.3 + - + +
82I MET* 1.3 88.6 - - + +
84I ARG* 1.3 70.5 + - - +
85I GLU* 2.9 22.2 + - + +
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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