Contacts of the helix formed by residues 97 - 112 (chain B) in PDB entry 2XWU
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 GLN 97 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93B ILE* 4.2 5.4 - - + -
94B PRO* 3.0 39.6 + - + +
96B ASP* 1.3 90.8 + - - +
98B TYR* 1.3 64.7 + - - +
99B GLU 3.4 1.6 - - - -
100B SER* 3.6 20.6 - - - -
101B LEU* 2.9 26.6 + - + +
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Residues in contact with TYR 98 (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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90B TRP* 3.9 44.7 + + - -
93B ILE* 3.5 27.6 + - + -
94B PRO 3.4 13.9 - - - -
95B THR* 3.3 48.6 + - + +
96B ASP 3.3 0.2 - - - -
97B GLN* 1.3 77.3 - - - +
99B GLU* 1.3 62.8 + - + +
101B LEU* 3.5 5.5 - - + +
102B LYS* 2.7 37.5 + - - +
130B LEU* 4.6 4.6 - - + +
134B MET* 4.7 11.7 - - + -
138B ALA* 4.9 19.5 - - + -
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Residues in contact with GLU 99 (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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95B THR 4.8 0.6 + - - +
96B ASP 4.4 6.3 + - - +
97B GLN 3.4 0.4 - - - -
98B TYR* 1.3 81.3 - - + +
100B SER* 1.3 57.5 + - - +
102B LYS* 3.0 41.0 + - - +
103B ALA* 2.9 30.1 + - - +
134B MET* 4.0 10.7 - - - +
138B ALA 4.7 3.1 - - - +
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Residues in contact with SER 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B ASP 4.8 2.4 + - - -
97B GLN* 3.5 27.2 + - - +
98B TYR 3.3 0.6 - - - -
99B GLU* 1.3 78.8 - - - +
101B LEU* 1.3 57.1 + - - +
103B ALA* 3.3 7.6 + - - +
104B GLN* 3.0 28.5 + - - +
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Residues in contact with LEU 101 (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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59B TRP* 4.9 7.9 - - + -
63B TRP* 3.9 28.0 - - + -
82B LEU* 5.8 0.4 - - + -
86B ILE* 4.2 17.9 - - + -
90B TRP* 4.9 1.6 - - + -
93B ILE* 3.2 37.9 - - + -
97B GLN* 2.9 19.9 + - + +
98B TYR* 3.5 4.3 - - - +
100B SER* 1.3 73.2 - - - +
102B LYS* 1.3 71.3 + - - +
104B GLN* 3.3 5.8 + - + +
105B LEU* 3.2 20.0 + - + +
130B LEU* 3.4 25.1 - - + -
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Residues in contact with LYS 102 (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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98B TYR 2.7 13.6 + - - +
99B GLU* 3.0 45.1 + - - +
101B LEU* 1.3 81.9 - - - +
103B ALA* 1.3 64.4 + - - +
105B LEU* 2.9 12.1 + - - +
106B PHE* 3.0 42.8 + - + -
127B LEU* 4.7 2.7 - - + -
130B LEU* 4.3 14.6 - - + -
134B MET* 3.7 11.3 - - - +
138B ALA 5.1 1.0 + - - -
139B TRP* 3.4 58.3 - - + +
145B ASP* 4.4 3.2 + - - -
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Residues in contact with ALA 103 (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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99B GLU 2.9 10.3 + - - +
100B SER* 3.5 11.2 - - - +
102B LYS* 1.3 75.5 - - - +
104B GLN* 1.3 62.8 + - - +
106B PHE* 3.1 13.2 + - - +
107B THR* 2.9 28.5 + - - +
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Residues in contact with GLN 104 (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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63B TRP* 3.6 25.4 - - + -
100B SER 3.0 14.4 + - - +
101B LEU* 3.6 9.0 - - - +
102B LYS 3.1 0.2 + - - -
103B ALA* 1.3 75.3 - - - +
105B LEU* 1.3 57.2 + - - +
107B THR* 3.3 7.8 + - - -
108B GLN* 3.0 35.2 + - - +
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Residues in contact with LEU 105 (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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63B TRP* 3.5 25.1 - - + -
82B LEU* 4.0 16.2 - - + -
86B ILE* 4.0 24.7 - - + -
101B LEU* 3.2 13.3 + - + +
102B LYS 2.9 9.2 + - - +
104B GLN* 1.3 76.7 - - - +
106B PHE* 1.3 66.4 + - - +
108B GLN* 3.2 4.1 + - + +
109B ILE* 3.0 30.5 + - + +
123B LEU* 4.6 14.1 - - + +
126B ALA* 4.0 6.3 - - + +
127B LEU* 3.6 48.5 - - + +
130B LEU* 4.5 6.5 - - + -
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Residues in contact with PHE 106 (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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102B LYS* 3.0 58.9 + - + -
103B ALA* 3.1 11.5 + - - +
105B LEU* 1.3 76.1 - - - +
107B THR* 1.3 65.5 + - - +
109B ILE* 3.3 8.1 + - - +
110B THR* 2.9 26.3 + - - -
127B LEU* 3.8 25.1 - - + -
139B TRP* 3.3 32.5 - + - -
145B ASP* 5.5 1.8 - - + -
146B MET* 4.5 15.9 - - + -
149B LEU* 3.4 35.2 - - + -
150B PHE* 4.9 10.9 - + - -
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Residues in contact with THR 107 (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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103B ALA* 2.9 17.7 + - - +
104B GLN* 3.4 11.1 - - - -
106B PHE* 1.3 76.3 - - - +
108B GLN* 1.3 63.7 + - - +
110B THR* 3.1 10.5 + - - -
111B ARG* 2.9 37.9 + - + +
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Residues in contact with GLN 108 (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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63B TRP* 3.5 36.8 + - + +
66B LEU* 4.2 16.0 - - + +
104B GLN* 3.0 18.3 + - - +
105B LEU* 3.2 6.7 + - - +
107B THR* 1.3 79.9 - - - +
109B ILE* 1.3 58.1 - - - +
111B ARG* 3.3 29.9 + - - +
112B PHE* 3.1 38.6 + - - +
123B LEU* 4.0 21.1 - - + -
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Residues in contact with ILE 109 (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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105B LEU* 3.0 22.6 + - - +
106B PHE* 3.7 7.0 - - - +
108B GLN* 1.3 73.0 - - - +
110B THR* 1.3 65.2 + - - +
112B PHE 3.4 0.3 + - - -
113B ALA* 3.1 20.8 + - - +
120B LEU* 3.6 25.7 - - + +
123B LEU* 4.1 27.1 - - + +
124B CYS* 4.1 16.4 - - - -
127B LEU* 3.6 40.2 - - + -
150B PHE* 3.9 24.2 - - + -
165B ALA* 4.6 3.6 - - + +
169B LEU* 4.8 3.4 - - + -
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Residues in contact with THR 110 (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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106B PHE* 2.9 15.5 + - - +
107B THR* 3.1 10.5 + - - -
109B ILE* 1.3 75.0 - - - +
111B ARG* 1.3 67.6 + - - +
113B ALA* 3.4 16.9 + - - +
114B SER* 4.2 5.0 + - - -
149B LEU* 5.4 5.2 - - - +
150B PHE* 4.7 13.0 - - + -
156B PRO* 4.5 22.4 - - + -
157B VAL* 5.0 12.6 - - + +
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Residues in contact with ARG 111 (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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66B LEU* 3.3 31.4 + - - +
67B GLN* 4.6 1.6 - - - +
68B PRO* 4.1 24.9 - - - +
75B GLN* 5.6 0.4 - - - +
107B THR* 2.9 22.4 + - + +
108B GLN* 3.3 32.2 + - - +
110B THR* 1.3 78.6 - - - +
112B PHE* 1.3 77.6 + - + +
113B ALA 3.4 0.2 - - - -
114B SER* 3.3 19.2 + - - -
115B GLY* 3.9 4.3 + - - -
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Residues in contact with PHE 112 (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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66B LEU* 3.4 38.6 - - + -
75B GLN* 3.3 26.0 - - - -
108B GLN* 3.1 31.1 + - - +
109B ILE 3.7 4.5 - - - +
110B THR 3.3 0.4 - - - -
111B ARG* 1.3 103.1 - - + +
113B ALA* 1.3 56.7 + - - +
114B SER 3.0 5.8 - - - -
115B GLY* 3.2 18.6 + - - +
116B SER 4.0 17.8 - - - +
119B VAL* 3.9 24.7 - - + -
120B LEU* 3.7 33.0 - - + +
123B LEU* 3.7 11.2 - - + -
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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