Contacts of the helix formed by residues 84 - 97 (chain B) in PDB entry 1XZQ
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 GLY 84 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129A LEU* 5.0 2.0 - - - -
130A ILE* 3.7 22.2 - - - +
82B HIS* 2.7 14.8 + - - +
83B GLY* 1.3 72.8 - - - +
85B PRO* 1.3 71.2 - - - +
86B LEU* 3.3 2.7 - - - -
87B VAL* 3.2 10.6 + - - +
88B VAL* 2.9 27.1 + - - +
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Residues in contact with PRO 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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130A ILE 4.0 10.3 - - - +
132A ALA 5.8 0.4 - - - +
238A ILE* 3.6 27.8 - - + +
239A VAL 4.2 4.3 - - - +
240A THR* 4.1 19.5 - - + -
12B GLY* 3.9 27.8 - - - +
13B LYS* 4.3 4.5 - - - -
83B GLY 3.5 9.2 - - - +
84B GLY* 1.3 82.3 - - - +
86B LEU* 1.3 58.0 + - - +
88B VAL* 3.2 7.8 + - + +
89B LYS* 2.9 30.7 + - - +
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Residues in contact with LEU 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A LEU 5.9 0.4 - - - +
132A ALA* 3.2 33.9 + - + +
133A LYS* 3.8 5.2 - - - +
134A SER 3.6 35.4 - - - +
135A GLU* 4.5 9.2 - - - +
138A LEU* 4.2 15.5 - - + -
238A ILE* 3.6 12.9 - - + +
84B GLY 3.3 0.6 - - - -
85B PRO* 1.3 79.3 - - - +
87B VAL* 1.3 57.6 + - - +
89B LYS* 3.4 28.2 - - + +
90B LYS* 2.9 39.0 + - + +
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Residues in contact with VAL 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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129A LEU* 3.4 33.2 - - + -
138A LEU* 3.7 20.9 - - + -
57B VAL* 4.5 12.8 - - + +
58B ASP* 3.7 28.5 - - + +
81B CYS* 4.6 1.3 - - + -
82B HIS* 4.5 10.3 - - + +
84B GLY* 3.2 12.2 + - - +
86B LEU* 1.3 77.6 - - - +
88B VAL* 1.3 57.7 + - - +
90B LYS* 3.1 6.8 + - + +
91B LEU* 2.8 45.1 + - + +
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Residues in contact with VAL 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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7B VAL* 3.5 41.5 - - + -
17B ALA* 3.7 27.6 - - + -
19B LEU* 4.1 11.0 - - + +
81B CYS* 4.5 6.7 - - - -
82B HIS 4.4 4.0 - - - +
83B GLY 5.1 0.4 - - - -
84B GLY 2.9 29.2 + - - +
85B PRO* 3.5 8.5 - - + +
87B VAL* 1.3 75.2 - - - +
89B LYS* 1.3 54.4 + - - +
91B LEU* 2.9 8.7 + - - +
92B LEU* 2.7 34.1 + - + +
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Residues in contact with LYS 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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135A GLU* 5.5 4.0 + - - -
238A ILE* 4.1 15.8 - - + +
85B PRO 2.9 17.2 + - - +
86B LEU* 3.4 26.8 - - + +
88B VAL* 1.3 80.0 - - - +
90B LYS* 1.3 64.4 + - - +
92B LEU* 3.4 9.0 + - - +
93B ASP* 2.8 49.1 + - - +
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Residues in contact with LYS 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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135A GLU* 3.9 29.9 - - - +
138A LEU* 3.6 28.5 - - + -
52B GLU* 5.6 1.4 - - - +
57B VAL* 5.6 17.7 - - + +
86B LEU* 2.9 32.3 + - + +
87B VAL* 3.1 6.7 + - + +
89B LYS* 1.3 80.3 - - + +
91B LEU* 1.3 64.6 + - + +
93B ASP* 3.7 6.8 + - - +
94B LEU* 3.3 21.0 + - - +
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Residues in contact with LEU 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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19B LEU* 4.0 15.3 - - + -
50B ILE* 3.6 35.0 - - + -
57B VAL* 3.7 17.5 - - + -
58B ASP* 4.7 2.9 - - + +
60B VAL* 4.5 9.2 - - + -
79B VAL* 4.9 3.8 - - + -
81B CYS* 3.7 37.7 - - + -
87B VAL* 2.8 22.0 + - + +
88B VAL 3.4 7.4 - - - +
90B LYS* 1.3 75.1 - - - +
92B LEU* 1.3 66.7 + - - +
94B LEU* 3.3 12.5 + - + +
95B PHE* 2.9 36.5 + - + -
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Residues in contact with LEU 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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5B VAL* 4.5 10.5 - - + +
6B ALA* 4.4 9.9 - - - -
7B VAL* 4.1 37.2 - - + +
19B LEU* 4.0 13.4 - - + +
88B VAL 2.7 16.1 + - - +
89B LYS* 3.6 11.2 - - + +
90B LYS 3.3 0.2 - - - -
91B LEU* 1.3 77.1 - - - +
93B ASP* 1.3 62.9 + - - +
94B LEU 3.2 0.3 + - - -
95B PHE* 3.2 6.9 + - - +
96B LEU* 2.9 38.0 + - + +
102B MET* 3.9 32.5 - - + -
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Residues in contact with ASP 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 LYS* 2.8 37.9 + - - +
90B LYS* 4.1 6.8 - - - +
92B LEU* 1.3 84.6 - - - +
94B LEU* 1.3 56.5 + - - +
96B LEU* 3.6 14.0 - - - +
97B LYS* 3.1 41.8 + - + +
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Residues in contact with LEU 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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33B HIS* 3.4 38.8 - - + +
50B ILE* 3.8 27.4 - - + -
51B HIS 3.9 6.5 - - - +
52B GLU* 3.0 43.5 - - + +
57B VAL* 4.6 8.1 - - + -
90B LYS 3.3 11.8 + - - +
91B LEU* 3.6 13.5 - - + +
92B LEU 3.2 1.0 - - - -
93B ASP* 1.3 78.8 - - - +
95B PHE* 1.3 61.0 + - + +
97B LYS* 3.5 6.6 + - - +
98B SER* 2.7 35.5 + - - +
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Residues in contact with PHE 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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5B VAL* 4.5 15.3 - - + -
19B LEU* 4.3 17.0 - - + -
21B LEU* 4.2 20.0 - - + -
29B ILE* 3.9 26.3 - - + +
30B VAL* 3.9 29.8 - - + -
33B HIS* 5.7 2.5 - - + -
50B ILE* 4.9 13.2 - - + -
79B VAL* 4.4 16.6 - - + -
91B LEU* 2.9 44.2 - - + -
92B LEU* 3.2 6.1 + - - +
94B LEU* 1.3 81.0 - - + +
96B LEU* 1.3 66.2 + - - +
98B SER* 3.2 13.3 + - - +
99B GLY 3.7 0.3 + - - -
100B ALA* 3.3 26.8 + - + +
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Residues in contact with LEU 96 (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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5B VAL* 3.7 26.0 - - + -
92B LEU* 2.9 29.7 + - + +
93B ASP* 3.6 18.4 - - - +
95B PHE* 1.3 77.2 - - - +
97B LYS* 1.3 63.1 - - + +
99B GLY 3.5 5.0 + - - -
100B ALA 3.2 22.7 - - - +
101B ARG* 5.5 0.2 - - - -
102B MET* 3.8 37.7 - - + +
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Residues in contact with LYS 97 (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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52B GLU* 3.7 23.9 + - - +
93B ASP* 3.1 25.0 + - + +
94B LEU* 4.1 5.3 - - - +
95B PHE 3.3 0.2 - - - -
96B LEU* 1.3 76.0 - - + +
98B SER* 1.3 56.4 + - - +
99B GLY 3.3 4.3 + - - -
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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