Contacts of the helix formed by residues 105 - 119 (chain B) in PDB entry 2R3B
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 ASP 105 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34B ASN* 4.9 15.8 + - - +
35B ARG* 5.6 4.2 + - - -
102B LEU 5.1 0.6 - - - +
103B GLY 3.8 0.6 - - - -
104B LEU* 1.3 81.8 - - - +
106B ALA* 1.3 59.6 + - - +
107B THR* 3.0 14.4 + - - -
108B ALA* 3.0 21.8 + - - +
109B GLN* 3.0 28.4 + - - +
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Residues in contact with ALA 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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105B ASP* 1.3 76.9 - - - +
107B THR* 1.3 58.5 + - - +
109B GLN* 3.7 15.0 - - - +
110B GLN* 2.9 29.1 + - - +
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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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80B PHE* 4.3 28.9 - - + +
105B ASP* 3.0 12.7 + - - -
106B ALA* 1.3 79.4 - - - +
108B ALA* 1.3 58.0 + - - +
110B GLN* 3.2 10.7 + - - +
111B ILE* 2.9 42.1 + - + +
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Residues in contact with ALA 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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102B LEU* 3.5 43.6 - - + +
103B GLY 3.6 16.2 - - - +
105B ASP* 3.0 22.2 + - - +
107B THR* 1.3 77.7 - - - +
109B GLN* 1.3 61.8 + - - +
111B ILE* 3.4 2.6 + - - +
112B LEU* 3.0 25.3 + - - +
134B LEU* 3.9 7.5 - - + +
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Residues in contact with GLN 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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104B LEU 3.0 21.2 + - - -
105B ASP* 3.0 16.6 + - - +
106B ALA* 3.7 13.7 - - - +
108B ALA* 1.3 75.4 - - - +
110B GLN* 1.3 61.3 + - - +
112B LEU* 3.5 3.5 + - - +
113B LYS* 3.1 39.4 + - - +
134B LEU* 3.8 27.8 - - + +
140B PHE* 5.3 0.7 - - - -
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Residues in contact with GLN 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 ALA 2.9 18.1 + - - +
107B THR* 3.2 10.0 + - - +
109B GLN* 1.3 76.6 - - - +
111B ILE* 1.3 66.1 + - + +
113B LYS* 3.2 12.6 + - + +
114B MSE 3.0 44.6 + - + +
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Residues in contact with ILE 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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31B ILE* 3.8 30.1 - - + -
59B ILE* 5.2 2.2 - - + -
80B PHE* 3.9 35.4 - - + +
86B LEU* 3.8 31.4 - - + -
98B ILE* 4.3 4.9 - - + -
102B LEU* 5.0 2.9 - - + -
107B THR* 2.9 29.2 + - + +
108B ALA* 3.9 5.6 - - - +
110B GLN* 1.3 76.0 - - + +
112B LEU* 1.3 63.2 + - - +
114B MSE 3.2 15.1 + - - +
115B VAL* 2.9 29.5 + - + +
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Residues in contact with LEU 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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98B ILE* 3.8 35.6 - - + +
102B LEU* 5.1 2.0 - - + -
108B ALA 3.0 18.1 + - - +
109B GLN* 3.7 5.6 - - - +
111B ILE* 1.3 77.0 - - - +
113B LYS* 1.3 58.0 + - - +
115B VAL* 3.2 2.1 + - + -
116B LEU* 2.9 55.2 + - + +
127B ILE* 5.2 5.4 - - + -
131B ALA* 3.8 20.4 - - + +
134B LEU* 3.5 34.8 - - + -
135B PHE* 3.8 9.9 - - + +
140B PHE* 4.1 12.8 - - + -
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Residues in contact with LYS 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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109B GLN* 3.1 33.6 + - - +
110B GLN* 3.6 10.6 - - + +
112B LEU* 1.3 77.1 - - - +
114B MSE 1.3 58.1 + - + +
116B LEU* 3.4 2.5 + - - +
117B ALA* 2.9 31.8 + - - +
140B PHE* 3.7 33.2 - - + -
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Residues in contact with MSE 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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83B THR* 3.9 24.2 - - + -
86B LEU* 4.0 19.7 - - + -
87B THR* 3.7 23.1 - - - +
110B GLN* 3.0 42.0 + - + +
111B ILE* 3.6 18.4 - - - +
113B LYS* 1.3 75.0 - - + +
115B VAL* 1.3 58.0 + - + +
117B ALA* 3.3 6.4 + - - +
118B GLN* 2.9 36.5 + - - +
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Residues in contact with VAL 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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31B ILE* 3.6 26.2 - - + -
86B LEU* 5.6 4.0 - - + -
90B VAL* 4.6 13.4 - - + +
96B ILE* 4.1 17.0 - - + -
98B ILE* 4.1 15.7 - - + -
111B ILE* 2.9 24.6 + - + +
112B LEU* 3.7 4.5 - - + +
114B MSE 1.3 75.5 - - + +
116B LEU* 1.3 68.8 + - + +
118B GLN* 3.3 5.8 + - - +
119B HIS* 3.0 23.4 + - - +
125B LEU* 4.0 28.0 - - + -
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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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112B LEU* 2.9 39.5 + - + +
113B LYS* 3.9 3.6 - - - +
115B VAL* 1.3 76.9 - - + +
117B ALA* 1.3 62.5 + - - +
119B HIS* 3.6 14.8 + - - +
125B LEU* 3.9 24.2 - - + -
127B ILE* 4.3 10.8 - - + -
135B PHE* 4.0 6.5 - - + -
140B PHE* 3.6 46.7 - - + -
141B SER 6.1 0.9 - - - +
142B LEU* 4.2 19.5 - - + -
143B THR* 5.2 6.1 + - - -
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Residues in contact with ALA 117 (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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113B LYS 2.9 19.2 + - - +
114B MSE 3.6 6.3 - - - +
116B LEU* 1.3 78.7 - - - +
118B GLN* 1.3 61.4 + - - +
119B HIS 4.4 2.9 - - - +
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Residues in contact with GLN 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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86B LEU* 5.3 2.3 - - - +
87B THR* 2.8 54.7 + - + +
90B VAL* 3.6 20.7 - - + +
91B GLU* 3.2 29.2 - - + +
114B MSE 2.9 21.8 + - - +
115B VAL* 3.9 4.3 - - - +
116B LEU 3.3 0.2 - - - -
117B ALA* 1.3 77.8 - - - +
119B HIS* 1.3 65.8 + - - +
120B GLN* 3.4 15.4 + - - +
123B GLN* 4.4 1.5 - - - +
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Residues in contact with HIS 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 VAL* 6.0 0.2 - - - -
96B ILE* 4.7 7.6 - - + -
115B VAL 3.0 16.6 + - - +
116B LEU* 3.7 10.9 - - + +
117B ALA 3.4 5.5 - - - +
118B GLN* 1.3 76.7 - - - +
120B GLN* 1.3 75.3 + - - +
121B LYS 5.0 1.1 - - - -
123B GLN* 2.7 42.6 + - + -
125B LEU* 3.8 28.2 - - + +
142B LEU* 6.1 0.8 - - - +
143B THR* 5.7 2.4 + - - -
144B TYR* 3.6 54.6 + - + +
147B LYS* 5.0 2.2 - - + -
148B VAL* 4.2 14.6 - - + +
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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