Contacts of the helix formed by residues 101 - 110 (chain R) in PDB entry 1XFV
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 101 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95R ASP* 4.8 0.3 + - - -
97R ASN* 4.8 6.6 + - - -
99R TYR* 3.7 1.6 + - - +
100R ILE* 1.3 73.8 - - - +
102R ALA* 1.3 54.8 + - - +
103R ALA* 3.8 10.8 - - - +
104R GLU* 2.5 42.4 + - - +
105R LEU* 2.8 31.2 + - - +
125R ILE* 3.7 0.9 - - - -
134R GLY 5.6 0.4 - - - -
135R GLN* 4.8 12.3 - - - -
808R CA 4.3 0.3 - - - -
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Residues in contact with ALA 102 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101R SER* 1.3 69.9 - - - +
103R ALA* 1.3 70.4 + - - +
105R LEU* 3.6 0.7 - - - -
106R ARG* 3.2 17.7 + - - +
121R VAL* 3.3 18.2 - - + +
122R ASP* 4.0 19.3 - - - +
125R ILE* 3.2 44.2 - - + +
134R GLY 5.1 2.3 + - - +
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Residues in contact with ALA 103 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101R SER* 3.8 12.3 - - - +
102R ALA* 1.3 82.8 - - - +
104R GLU* 1.3 58.3 + - - +
106R ARG* 3.3 16.9 + - - +
107R HIS* 3.0 24.1 + - - +
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Residues in contact with GLU 104 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92R PHE* 3.5 21.5 - - - +
93R ASP* 4.1 1.1 - - - -
94R LYS* 3.2 22.7 + - + +
95R ASP* 2.5 22.8 + - - +
99R TYR 2.9 3.0 - - - +
100R ILE* 3.2 3.0 - - + -
101R SER* 2.5 47.9 + - - +
103R ALA* 1.3 75.5 - - - +
105R LEU* 1.3 67.8 + - - +
106R ARG 3.1 1.8 - - - -
107R HIS* 3.8 9.8 - - + +
108R VAL* 3.0 24.9 + - - +
808R CA 2.0 25.9 - - - -
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Residues in contact with LEU 105 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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526D GLN* 3.3 31.0 - - + +
92R PHE* 4.2 19.0 - - + -
100R ILE* 4.6 6.1 - - + -
101R SER 2.8 12.2 + - - +
102R ALA 3.6 7.4 - - - +
103R ALA 3.3 0.4 - - - -
104R GLU* 1.3 74.8 - - - +
106R ARG* 1.3 58.8 + - - +
108R VAL* 3.9 2.1 - - - +
109R MET* 2.9 44.7 + - + +
121R VAL* 3.8 11.9 - - + -
124R MET* 3.7 31.6 - - + -
125R ILE* 3.4 38.8 - - + +
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Residues in contact with ARG 106 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102R ALA 3.2 7.5 + - - +
103R ALA* 3.5 19.7 + - - +
105R LEU* 1.3 76.8 - - - +
107R HIS* 1.3 64.0 + - - +
108R VAL 2.8 4.4 + - - -
109R MET* 2.7 25.2 + - - -
110R THR* 2.9 28.2 + - + +
116R LEU* 3.9 25.9 + - + +
118R ASP* 3.5 35.4 + - - +
121R VAL* 3.0 29.8 - - + +
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Residues in contact with HIS 107 (chain R).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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623D ASP* 3.1 28.2 + - - -
94R LYS* 4.2 26.2 - - + -
103R ALA 3.0 14.1 + - - +
104R GLU* 3.2 10.0 + - - +
106R ARG* 1.3 84.6 - - - +
108R VAL* 1.3 58.1 + - + +
110R THR* 3.4 17.1 + - - -
111R ASN* 3.7 17.6 - - - +
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Residues in contact with VAL 108 (chain R).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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501D LEU* 4.0 26.0 - - + +
623D ASP* 6.4 0.2 - - - -
91R VAL* 4.3 12.6 - - + +
92R PHE* 3.3 41.3 - - + -
94R LYS* 3.9 30.1 - - + -
104R GLU 3.0 13.2 + - - +
106R ARG 2.8 1.6 + - - -
107R HIS* 1.3 75.0 - - + +
109R MET* 1.3 65.6 + - - +
110R THR 3.0 2.7 + - - -
111R ASN* 3.3 14.6 + - - +
112R LEU* 3.5 20.4 + - + +
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Residues in contact with MET 109 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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513D TRP* 5.7 0.2 - - + -
525D LYS* 4.3 7.6 - - + +
526D GLN* 5.2 8.5 - - - +
529D VAL* 3.9 40.6 - - + -
92R PHE* 4.7 10.5 - - + -
105R LEU* 2.9 36.9 + - + +
106R ARG 2.7 3.8 + - - +
108R VAL* 1.3 78.3 - - - +
110R THR* 1.3 58.2 + - + +
112R LEU* 4.1 6.0 + - + +
114R GLU* 2.9 68.0 + - + +
116R LEU* 3.2 31.9 - - + -
124R MET* 5.2 2.9 - - + -
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Residues in contact with THR 110 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106R ARG* 2.9 35.1 + - + +
107R HIS* 3.4 17.9 + - - -
109R MET* 1.3 79.5 - - + +
111R ASN* 1.3 71.7 + - - +
112R LEU 3.4 0.4 - - - -
113R GLY* 3.5 11.9 + - - -
114R GLU 3.3 15.8 + - - +
115R LYS* 5.0 16.5 - - - +
116R LEU 4.6 8.1 - - - +
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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