Contacts of the helix formed by residues 77 - 85 (chain A) in PDB entry 1X1R
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 MET 77 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47A GLU* 4.5 16.4 + - - +
49A SER* 3.9 26.2 - - - +
66A LEU* 3.8 24.2 - - + -
75A SER* 3.2 3.4 + - - +
76A ALA* 1.3 89.0 - - + +
78A ARG* 1.3 65.9 + - - +
79A GLU 3.3 2.8 + - - -
80A GLN* 3.4 13.9 + - + +
81A TYR* 3.2 41.7 + - + -
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Residues in contact with ARG 78 (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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47A GLU* 2.8 20.8 + - - -
66A LEU* 4.3 7.6 - - - -
68A THR* 3.7 27.7 - - - +
69A ALA 2.9 31.5 + - - +
70A GLY 3.0 17.2 + - - -
71A GLN 4.1 5.1 + - - -
72A GLU* 3.7 35.7 - - + +
75A SER* 2.9 21.4 + - - +
76A ALA 3.7 1.0 - - - -
77A MET* 1.3 77.4 - - - +
79A GLU* 1.3 63.9 + - - +
81A TYR* 3.3 1.6 + - - +
82A MET* 2.9 47.9 + - + +
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Residues in contact with GLU 79 (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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75A SER 5.3 1.4 + - - +
76A ALA 5.0 3.3 + - - +
77A MET 3.3 0.8 - - - -
78A ARG* 1.3 79.4 - - - +
80A GLN* 1.3 70.2 + - - +
82A MET* 3.8 4.6 - - - +
83A ARG* 2.6 67.9 + - - +
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Residues in contact with GLN 80 (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 LYS* 2.9 30.1 + - - +
64A ASP* 5.6 0.4 + - - -
76A ALA 5.5 1.5 + - - +
77A MET* 3.4 16.8 + - - +
79A GLU* 1.3 85.0 + - - +
81A TYR* 1.3 90.1 + - - +
83A ARG* 3.7 19.1 - - - +
84A THR* 2.7 38.6 + - + +
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Residues in contact with TYR 81 (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 LYS* 3.5 30.7 - - + -
16A LEU 4.7 0.4 - - - -
17A VAL* 3.5 18.1 - - + +
49A SER* 3.5 18.8 + - - -
64A ASP* 2.6 38.8 + - - -
66A LEU* 3.6 47.3 - - + -
77A MET* 3.2 43.5 + - + +
78A ARG 3.9 1.1 - - - +
80A GLN* 1.3 103.7 + - - +
82A MET* 1.3 58.1 + - + +
85A GLY* 2.8 30.7 + - - -
88A PHE* 4.5 0.2 - - - -
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Residues in contact with MET 82 (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* 4.1 14.6 - - + -
19A VAL* 4.3 10.8 - - + -
78A ARG* 2.9 41.8 + - + +
79A GLU* 3.8 4.5 - - - +
81A TYR* 1.3 77.5 - - - +
83A ARG* 1.3 62.9 + - - +
85A GLY 4.0 0.3 + - - -
88A PHE* 3.6 36.0 - - + -
109A LEU* 3.8 34.8 - - + -
110A ILE* 4.3 13.7 - - + -
113A VAL* 3.7 21.0 - - + +
114A LYS* 3.5 18.5 - - - +
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Residues in contact with ARG 83 (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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79A GLU* 2.6 56.6 + - - +
80A GLN* 3.7 16.6 - - - +
82A MET* 1.3 78.5 - - - +
84A THR* 1.3 74.9 + - + +
113A VAL* 3.8 18.9 - - + +
114A LYS* 2.8 26.2 + - - +
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Residues in contact with THR 84 (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 LYS* 2.8 34.7 + - - +
80A GLN* 2.7 25.6 + - + +
83A ARG* 1.3 107.3 - - + +
85A GLY* 1.3 69.2 + - - +
86A ASP* 3.6 9.7 + - - +
114A LYS* 3.7 3.1 + - - +
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Residues in contact with GLY 85 (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 LYS* 3.7 16.4 - - - -
17A VAL* 4.4 7.0 - - - -
81A TYR 2.8 20.6 + - - -
82A MET 4.0 0.8 + - - -
83A ARG 3.6 2.0 - - - -
84A THR* 1.3 77.7 - - - +
86A ASP* 1.3 61.3 + - - +
87A GLY 3.5 2.2 - - - -
88A PHE* 4.7 5.4 - - - -
114A LYS* 2.8 26.5 + - - +
119A PHE* 3.3 9.8 - - - -
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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