Contacts of the helix formed by residues 66 - 76 (chain A) in PDB entry 1R1P
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 SER 66 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64A GLY 3.7 1.6 + - - -
65A LEU* 1.3 76.6 - - - +
67A ARG* 1.3 63.9 + - - +
68A HIS* 3.4 6.6 + - - +
69A GLN* 2.8 45.7 + - - +
70A ALA* 3.1 22.7 + - - +
85A ARG* 3.9 2.5 - - - -
88A GLN* 3.3 24.9 - - - -
55C ILE* 5.7 2.5 - - - -
57C PHE* 4.1 20.9 - - - -
58C PRO 5.6 0.2 + - - -
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Residues in contact with ARG 67 (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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66A SER* 1.3 74.9 - - - +
68A HIS* 1.3 77.0 + - + +
70A ALA* 3.3 5.5 + - - +
71A GLU* 3.2 32.8 + - - +
85A ARG* 3.6 25.2 - - - +
88A GLN* 4.5 2.2 + - - -
106A HIS* 3.3 41.1 + - + +
55C ILE* 4.6 12.4 - - + +
556E ASP* 3.4 30.2 + - - -
557E ASP* 2.8 42.0 + - - +
558E PTR 2.7 46.2 + - - +
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Residues in contact with HIS 68 (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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66A SER* 3.3 6.3 + - - +
67A ARG* 1.3 96.5 + - + +
69A GLN* 1.3 61.5 + - + +
71A GLU* 3.3 31.2 + - - +
72A ASN* 2.9 35.9 + - - +
55C ILE* 4.7 13.4 - - + +
57C PHE 4.5 7.2 + - - -
58C PRO 5.1 1.3 - - - +
59C GLU* 3.7 54.6 + - + +
556E ASP* 4.8 4.5 + - - -
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Residues in contact with GLN 69 (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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64A GLY 3.8 3.3 - - - +
65A LEU* 3.5 27.1 - - + +
66A SER* 2.8 39.9 + - - +
68A HIS* 1.3 76.9 - - + +
70A ALA* 1.3 55.9 + - - +
72A ASN* 3.2 2.1 + - - +
73A LEU* 3.0 32.6 + - - +
57C PHE* 2.6 40.0 - - - -
59C GLU 6.0 0.4 - - - +
61C PHE* 3.0 14.6 + - - +
62C HIS* 3.4 36.5 - - + +
63C GLU* 4.7 5.3 + - - +
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Residues in contact with ALA 70 (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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65A LEU* 3.9 19.9 - - + +
66A SER 3.1 14.2 + - - +
67A ARG 3.5 9.4 - - - +
68A HIS 3.2 0.2 - - - -
69A GLN* 1.3 73.6 - - - +
71A GLU* 1.3 60.1 + - - +
73A LEU* 3.3 2.4 + - - +
74A LEU* 2.9 36.1 + - - +
83A ILE* 4.0 9.9 - - + -
85A ARG* 3.9 7.0 - - - +
97A SER* 3.7 27.4 - - - +
104A VAL* 4.9 0.4 - - - -
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Residues in contact with GLU 71 (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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67A ARG* 3.2 11.3 + - - +
68A HIS* 3.3 38.0 + - - +
69A GLN 3.3 0.2 - - - -
70A ALA* 1.3 75.9 - - - +
72A ASN* 1.3 59.9 + - - +
74A LEU 3.3 0.2 + - - -
75A MET* 2.9 40.5 + - + +
104A VAL* 3.8 27.3 - - + +
106A HIS* 2.8 36.8 + - + +
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Residues in contact with ASN 72 (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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68A HIS* 2.9 18.4 + - - +
69A GLN* 3.2 9.8 + - - +
71A GLU* 1.3 81.3 + - - +
73A LEU* 1.3 63.6 + - - +
75A MET* 3.7 10.9 + - - +
76A GLY* 3.9 3.1 + - - -
59C GLU 4.0 12.3 + - - +
62C HIS* 3.1 28.0 + - + +
65C LEU* 4.6 5.8 - - + +
73C LEU* 3.4 40.5 - - + +
77C LYS* 5.3 6.5 - - - +
83C ILE* 3.7 16.4 - - - +
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Residues in contact with LEU 73 (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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62A HIS* 4.5 11.7 - - + +
65A LEU* 4.1 21.5 - - + -
69A GLN 3.0 18.0 + - - +
70A ALA 3.3 5.1 + - - +
72A ASN* 1.3 75.2 - - - +
74A LEU* 1.3 59.1 + - - +
76A GLY* 3.1 19.9 + - - -
77A LYS* 3.9 11.7 - - - +
83A ILE* 4.0 22.4 - - + -
62C HIS* 3.8 19.1 - - + +
64C GLY 6.4 0.2 - - - -
65C LEU* 4.0 13.9 - - + -
69C GLN* 4.4 13.5 - - - +
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Residues in contact with LEU 74 (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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70A ALA 2.9 19.7 + - - +
73A LEU* 1.3 73.5 - - - +
75A MET* 1.3 66.3 + - - +
76A GLY 3.0 2.0 - - - -
77A LYS* 2.9 23.5 + - + +
81A PHE* 3.5 17.3 - - + +
82A PHE* 3.5 30.3 - - - +
83A ILE* 3.8 20.9 - - + -
97A SER* 3.4 43.1 - - - +
98A VAL 4.0 2.5 - - - +
99A ARG* 3.0 20.5 + - + +
104A VAL* 3.6 18.2 - - + -
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Residues in contact with MET 75 (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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71A GLU* 2.9 24.5 + - + +
72A ASN* 3.9 1.3 - - - +
73A LEU 3.4 0.4 - - - -
74A LEU* 1.3 76.3 - - - +
76A GLY* 1.3 56.3 + - - +
77A LYS 3.2 2.4 + - - +
99A ARG* 2.9 44.7 + - - +
102A ASP 3.7 18.2 - - - +
103A ASP* 3.8 13.9 - - + -
104A VAL* 3.8 17.0 - - + +
73C LEU* 3.8 27.6 - - + -
77C LYS* 5.9 6.5 - - - +
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Residues in contact with GLY 76 (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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72A ASN 3.9 3.0 + - - -
73A LEU 3.1 10.7 + - - -
74A LEU 3.0 1.4 - - - -
75A MET* 1.3 76.4 - - - +
77A LYS* 1.3 68.9 + - - +
73C LEU* 5.7 0.2 - - - +
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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