Contacts of the helix formed by residues 112 - 123 (chain B) in PDB entry 2XVA
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 THR 112 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87B LEU 3.4 26.2 - - - +
88B ASN* 2.6 38.0 + - - +
108B LEU* 4.4 6.5 - - + -
109B GLU* 2.9 18.3 + - - +
111B LYS* 1.3 82.2 + - - +
113B ILE* 1.3 65.9 + - - +
114B PRO 3.4 0.9 - - - -
115B GLY* 3.4 4.3 + - - -
116B LEU* 3.0 37.8 + - + -
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Residues in contact with ILE 113 (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* 3.8 35.7 - - + +
108B LEU* 4.4 12.8 - - + -
109B GLU 4.1 4.0 - - - +
110B ALA 3.3 5.8 + - - +
112B THR* 1.3 73.8 - - - +
114B PRO* 1.3 74.6 - - + +
116B LEU* 3.2 5.3 + - + -
117B ILE* 3.0 46.8 + - + +
149B PHE* 3.6 57.0 - - + -
151B PHE* 4.5 0.7 - - + -
159B TYR* 3.8 12.1 - - + +
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Residues in contact with PRO 114 (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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110B ALA 3.4 13.7 - - - +
111B LYS 4.0 6.3 - - - +
112B THR 3.7 2.7 - - - -
113B ILE* 1.3 93.2 - - + +
115B GLY* 1.3 61.4 + - - +
117B ILE* 4.1 2.3 - - - +
118B ALA* 3.2 22.2 + - - +
159B TYR* 3.5 28.9 - - + +
158C ARG* 3.5 32.1 - - - +
161C GLU* 3.7 20.9 - - - +
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Residues in contact with GLY 115 (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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111B LYS 5.2 0.4 + - - -
112B THR 3.4 4.5 + - - -
113B ILE 3.3 0.2 - - - -
114B PRO* 1.3 77.6 - - - +
116B LEU* 1.3 59.6 + - - +
118B ALA* 3.5 5.6 + - - +
119B ASN* 3.0 28.6 + - - +
122B ARG* 4.7 2.8 + - - -
158C ARG* 4.3 9.9 - - - +
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Residues in contact with LEU 116 (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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37B LEU* 4.4 14.8 - - + -
87B LEU* 4.5 24.5 - - + +
90B LEU* 5.2 8.1 - - + +
92B PHE* 4.1 23.8 - - + -
105B LEU* 4.1 15.7 - - + -
108B LEU* 3.6 31.0 - - + -
112B THR* 3.0 29.1 + - + +
113B ILE* 3.9 5.8 - - + +
115B GLY* 1.3 72.8 - - - +
117B ILE* 1.3 61.5 + - + +
119B ASN* 3.2 4.7 + - + +
120B MET* 2.8 39.2 + - - +
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Residues in contact with ILE 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B LEU* 4.5 9.6 - - + -
113B ILE* 3.0 34.9 + - + +
114B PRO 4.1 2.5 - - - +
116B LEU* 1.3 77.2 - - + +
118B ALA* 1.3 64.5 + - - +
120B MET* 3.1 16.2 + - - +
121B GLN* 2.9 33.4 + - - +
132B ILE* 4.5 2.5 - - + -
151B PHE* 3.9 16.4 - - + -
156B LEU* 4.4 7.0 - - + -
159B TYR* 3.6 42.4 - - + -
160B TYR* 3.6 28.0 - - + +
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Residues in contact with ALA 118 (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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114B PRO 3.2 18.0 + - - +
115B GLY* 3.9 7.2 - - - +
117B ILE* 1.3 77.8 - - - +
119B ASN* 1.4 56.6 + - - +
121B GLN* 3.4 13.7 + - - +
122B ARG* 2.9 47.2 + - - +
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Residues in contact with ASN 119 (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 LEU 4.3 2.1 - - - +
91B THR* 3.3 17.6 - - - +
92B PHE* 2.9 60.3 + - + -
115B GLY 3.0 19.2 + - - +
116B LEU* 3.5 7.6 - - + +
118B ALA* 1.4 71.8 - - - +
120B MET* 1.3 67.1 + - - +
122B ARG* 3.4 25.8 + - - +
123B CYS* 3.0 29.0 + - - +
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Residues in contact with MET 120 (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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37B LEU* 3.8 28.5 - - + -
92B PHE* 4.0 11.2 - - + -
99B ILE* 3.4 30.3 - - + +
101B SER* 4.7 10.8 - - - +
105B LEU* 5.4 3.8 - - - -
116B LEU* 2.8 28.7 + - + +
117B ILE* 3.4 17.3 - - - +
119B ASN* 1.3 75.9 - - - +
121B GLN* 1.3 57.3 + - - +
123B CYS 3.1 8.5 + - - -
124B THR* 2.8 25.5 + - - -
130B ASN* 3.8 14.6 - - + +
132B ILE* 3.7 35.2 - - + -
160B TYR* 3.9 5.8 - - - +
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Residues in contact with GLN 121 (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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117B ILE* 2.9 26.6 + - - +
118B ALA* 3.6 14.1 - - - +
120B MET* 1.3 71.7 - - - +
122B ARG* 1.3 61.2 + - - +
124B THR* 3.1 12.1 + - - -
159B TYR* 3.0 28.4 + - - +
160B TYR* 3.3 39.0 - - + +
163B TRP* 3.6 33.7 - - + +
196B LYS* 2.9 24.3 + - - +
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Residues in contact with ARG 122 (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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91B THR* 5.9 1.2 - - - -
95B GLN* 3.0 17.2 + - - +
115B GLY 4.7 2.4 + - - -
118B ALA* 2.9 42.7 + - - +
119B ASN* 3.4 38.6 + - - +
121B GLN* 1.3 73.4 - - - +
123B CYS* 1.3 60.8 + - - +
124B THR 3.3 2.1 + - - -
196B LYS* 4.1 9.7 + - - +
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Residues in contact with CYS 123 (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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92B PHE* 3.3 31.0 - - + -
93B ASP* 4.0 7.4 - - - -
94B ARG 3.2 18.2 - - - +
95B GLN* 3.3 11.8 - - - -
96B TYR* 2.8 30.0 + - + +
99B ILE* 3.9 2.4 - - + +
119B ASN* 3.0 38.4 + - - +
120B MET 3.1 4.7 + - - +
121B GLN 3.1 0.4 - - - -
122B ARG* 1.3 81.6 - - - +
124B THR* 1.3 57.7 + - - +
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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