Contacts of the helix formed by residues 82 - 95 (chain B) in PDB entry 1XL4
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 82 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69B LEU* 3.8 5.0 - - - +
79B ARG* 3.1 35.9 + - - +
80B PRO 2.8 6.7 + - - -
81B GLY* 1.3 73.6 - - - +
83B PHE* 1.3 65.9 + - - +
84B THR* 3.7 9.2 + - - -
85B ASP* 2.8 27.5 + - - +
86B ALA* 3.4 20.3 + - - +
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Residues in contact with PHE 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B ALA* 3.7 29.6 - - + -
65B ALA* 3.5 24.2 - - + -
66B LEU* 3.6 29.8 - - + -
69B LEU* 4.3 11.9 - - + +
81B GLY 3.7 3.8 + - - -
82B SER* 1.3 69.8 + - - +
84B THR* 1.3 57.8 - - - +
86B ALA* 3.0 3.0 + - - +
87B PHE* 2.6 53.5 + + + +
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Residues in contact with THR 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A PRO* 4.8 11.4 - - + +
79B ARG* 3.8 18.9 + - - +
82B SER* 3.4 4.4 + - - -
83B PHE* 1.3 80.1 - - - +
85B ASP* 1.3 66.2 + - - +
87B PHE* 2.8 25.2 + - - +
88B PHE* 2.8 46.9 + - + -
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Residues in contact with ASP 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B ILE* 4.6 0.9 - - - +
77B ASN 4.7 2.3 - - - +
78B ALA* 3.7 24.2 - - + -
79B ARG* 2.9 49.1 + - - +
82B SER* 2.8 23.9 + - - +
83B PHE 3.5 0.2 - - - -
84B THR* 1.3 75.6 - - - +
86B ALA* 1.3 55.8 + - - +
88B PHE* 4.7 5.4 - - - +
89B PHE* 3.1 26.9 + - - +
102B LEU* 3.9 13.9 - - + +
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Residues in contact with ALA 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B ALA* 3.7 29.6 - - + +
68B TYR* 4.3 3.3 - - - -
69B LEU* 4.0 13.2 - - + -
75B ILE* 4.0 20.4 - - + -
82B SER 3.4 13.7 + - - +
83B PHE* 3.0 9.0 + - - +
85B ASP* 1.3 77.5 - - - +
87B PHE* 1.3 67.1 + - - +
89B PHE* 3.5 2.1 + - - +
90B SER* 3.2 21.3 + - - -
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Residues in contact with PHE 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A THR* 4.3 7.4 - - + -
58B LEU* 3.5 38.8 - - + -
61B ASN* 3.4 38.1 - - + -
62B ALA* 3.8 8.1 - - + -
65B ALA* 3.6 8.9 - - + +
83B PHE* 2.6 35.7 + + + +
84B THR* 3.3 6.3 - - - +
86B ALA* 1.3 73.8 - - - +
88B PHE* 1.3 86.0 + + - +
90B SER* 3.2 5.2 + - - -
91B VAL* 2.9 39.0 + - + +
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Residues in contact with PHE 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A PRO* 4.2 11.4 - - + -
110A ASN* 3.1 55.6 - - + +
111A THR* 3.9 20.4 - - + -
114A THR* 3.7 15.5 - - - -
84B THR* 2.8 42.7 + - + +
85B ASP* 4.4 4.7 - - - +
87B PHE* 1.3 96.8 - + - +
89B PHE* 1.3 64.5 + - - +
91B VAL* 3.7 4.4 - - + +
92B GLN* 3.0 37.7 + - - +
102B LEU* 4.9 3.1 - - + -
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Residues in contact with PHE 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B TYR* 3.4 44.4 - + - -
75B ILE* 3.6 25.6 - - + -
85B ASP 3.1 21.4 + - - +
86B ALA 3.7 4.0 - - - +
87B PHE 3.2 0.2 - - - -
88B PHE* 1.3 73.1 - - - +
90B SER* 1.3 64.0 + - - +
92B GLN* 3.1 8.4 + - + +
93B THR* 2.9 42.0 + - - -
102B LEU* 2.8 50.0 - - + +
103B ILE* 3.9 4.9 - - - -
104B PRO* 3.6 29.6 - - + -
109B ALA* 5.6 0.4 - - + -
113B VAL* 4.1 3.6 - - + -
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Residues in contact with SER 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B ASN* 2.5 27.2 + - - +
64B PHE* 3.4 14.8 - - - +
65B ALA 4.4 0.7 - - - -
68B TYR* 4.3 6.5 - - - -
86B ALA 3.2 11.2 + - - -
87B PHE 3.2 9.4 - - - -
89B PHE* 1.3 78.7 - - - +
91B VAL* 1.3 52.1 + - - +
93B THR* 2.7 24.8 + - - -
94B MET 2.8 15.9 + - - -
116B GLU* 2.3 39.7 + - - +
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Residues in contact with VAL 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A VAL* 5.0 7.4 - - + -
114A THR* 3.4 46.0 - - + +
117A ALA* 4.8 4.9 - - + -
57B TYR* 3.6 15.9 - - - +
61B ASN* 3.0 27.9 + - - +
87B PHE* 2.9 30.5 + - + +
88B PHE* 3.7 8.1 - - + +
90B SER* 1.3 76.6 - - - +
92B GLN* 1.3 59.1 + - + +
94B MET* 4.7 1.1 - - - +
95B ALA* 3.2 28.6 + - - +
97B ILE* 4.7 0.8 - - + +
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Residues in contact with GLN 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A PRO* 5.4 1.4 - - - +
110A ASN* 3.8 20.0 + - - -
113A VAL* 5.0 6.1 - - + +
88B PHE* 3.0 23.6 + - - +
89B PHE* 3.5 9.1 - - + +
90B SER 3.0 0.6 + - - -
91B VAL* 1.3 76.8 - - + +
93B THR* 1.3 58.3 + - - +
96B THR 3.7 0.7 - - - -
97B ILE* 3.0 21.4 + - + -
98B GLY* 2.8 36.6 + - - +
99B TYR* 3.0 50.6 + - + +
100B GLY 4.9 0.9 + - - -
102B LEU* 4.0 27.8 + - - +
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Residues in contact with THR 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89B PHE* 2.9 39.1 + - - -
90B SER 2.7 15.3 + - - -
92B GLN* 1.3 72.5 - - - +
94B MET* 1.3 60.5 + - - +
96B THR* 2.8 24.1 + - - +
98B GLY* 5.6 0.7 - - - -
113B VAL* 3.8 37.2 - - + +
116B GLU* 3.5 24.0 - - + +
117B ALA* 5.0 7.1 - - + +
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Residues in contact with MET 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57B TYR* 3.2 32.3 - - + +
60B THR* 4.4 20.2 - - - -
61B ASN* 3.0 35.7 - - - +
64B PHE* 5.5 0.2 - - - -
90B SER 2.8 17.3 + - - +
91B VAL* 4.4 1.1 - - - +
93B THR* 1.3 75.0 - - - +
95B ALA* 1.3 59.5 + - - +
96B THR* 3.1 12.3 + - - +
116B GLU* 3.7 31.4 - - + +
117B ALA* 5.1 1.7 - - - +
119B CYS* 5.3 3.4 - - - -
120B GLY* 3.6 36.7 - - - +
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Residues in contact with ALA 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A THR* 3.2 17.9 - - + +
117A ALA* 3.8 30.3 - - + +
57B TYR* 4.9 6.3 - - + +
91B VAL 3.2 18.7 + - - +
94B MET* 1.3 78.3 - - - +
96B THR* 1.3 75.6 + - - +
97B ILE* 4.0 9.9 - - + -
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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