Contacts of the helix formed by residues 108 - 123 (chain B) in PDB entry 2VD0
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 LYS 108 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106B GLU* 2.8 19.5 + - - +
107B LYS* 1.3 74.0 - - + +
109B GLN* 1.3 61.0 + - - +
110B ASP* 2.9 37.5 + - - +
111B VAL* 3.6 21.9 - - + +
112B LYS* 2.9 29.0 + - - +
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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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106B GLU 5.5 0.3 - - - +
107B LYS 3.2 9.1 + - - +
108B LYS* 1.3 71.0 - - - +
110B ASP* 1.3 59.3 + - - +
112B LYS* 3.2 23.6 + - - +
113B GLU* 2.9 66.0 + - - +
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Residues in contact with ASP 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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108B LYS* 2.9 40.0 + - - +
109B GLN* 1.3 77.1 + - - +
111B VAL* 1.3 69.3 + - - +
113B GLU* 3.8 9.7 + - - +
114B GLN* 3.3 22.7 + - - +
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Residues in contact with VAL 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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106B GLU* 4.0 18.4 - - + +
108B LYS* 3.6 37.2 - - + +
109B GLN 3.3 0.2 - - - -
110B ASP* 1.3 84.5 + - - +
112B LYS* 1.3 61.5 + - - +
114B GLN* 3.4 13.2 + - - +
115B MET* 3.0 35.5 + - + +
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Residues in contact with LYS 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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103B PRO* 3.6 17.7 - - - +
104B TRP* 3.1 29.0 + - - +
106B GLU* 3.6 28.6 + - + +
108B LYS 2.9 18.0 + - - +
109B GLN* 3.4 24.4 + - - +
111B VAL* 1.3 74.6 - - - +
113B GLU* 1.3 64.7 + - - +
115B MET* 3.2 6.3 + - - +
116B PHE* 2.9 48.5 + - + -
1200B D27 4.9 6.5 - - - -
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Residues in contact with GLU 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* 2.9 49.1 + - - +
110B ASP* 4.0 9.1 - - - +
112B LYS* 1.3 74.8 - - + +
114B GLN* 1.3 58.3 + - - +
116B PHE* 3.4 6.8 + - - +
117B ASN* 2.9 31.1 + - - +
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Residues in contact with GLN 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 ASP 3.3 16.5 + - - +
111B VAL* 3.5 13.0 - - - +
113B GLU* 1.3 78.4 - - - +
115B MET* 1.3 64.5 + - + +
117B ASN* 3.2 6.5 + - - +
118B GLU* 3.0 52.9 + - - +
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Residues in contact with MET 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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101B CYS 4.5 4.5 - - - +
103B PRO* 3.5 27.8 - - + -
111B VAL* 3.0 21.2 + - + +
112B LYS 3.2 7.4 + - - +
114B GLN* 1.3 75.3 - - + +
116B PHE* 1.3 65.0 + - - +
118B GLU* 3.3 20.9 + - + +
119B LEU* 3.0 55.2 + - + +
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Residues in contact with PHE 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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102B PHE* 3.5 30.3 - + + -
103B PRO* 3.5 39.0 - - + -
104B TRP* 3.6 42.0 - + - -
112B LYS* 2.9 40.6 + - + +
113B GLU* 3.7 7.4 - - - +
115B MET* 1.3 75.3 - - - +
117B ASN* 1.3 63.8 + - - +
119B LEU* 3.9 0.9 - - - +
120B LEU* 3.0 34.8 + - + +
163B PHE* 3.9 36.3 - + + -
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Residues in contact with ASN 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 GLU 2.9 18.7 + - - +
114B GLN* 3.2 7.2 + - - +
116B PHE* 1.3 75.4 - - - +
118B GLU* 1.3 55.8 + - + +
120B LEU* 3.8 6.4 - - - +
121B THR* 2.6 68.3 + - - +
122B TYR* 5.5 2.4 + - - -
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Residues in contact with GLU 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 GLN* 3.0 45.3 + - + +
115B MET* 3.8 19.8 - - + +
117B ASN* 1.3 73.7 - - + +
119B LEU* 1.3 59.2 - - - +
122B TYR* 2.6 72.8 + - + +
123B ASN* 4.1 1.2 - - - +
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Residues in contact with LEU 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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98B PHE* 3.6 10.1 - - + -
101B CYS* 3.4 51.1 - - + +
102B PHE* 3.8 32.1 - - + +
103B PRO* 4.4 1.1 - - + -
115B MET* 3.0 38.8 + - + +
116B PHE 3.9 0.7 - - - +
118B GLU* 1.3 77.3 - - - +
120B LEU* 1.3 57.9 + - - +
123B ASN* 2.9 35.1 + - - +
124B ALA 2.8 26.0 + - - -
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Residues in contact with LEU 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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102B PHE* 3.9 11.9 - - + -
116B PHE* 3.0 35.2 + - + +
117B ASN* 3.9 5.2 - - - +
119B LEU* 1.3 76.0 - - - +
121B THR* 1.3 60.6 + - - +
124B ALA* 3.5 11.1 - - + +
125B PRO* 3.3 16.8 - - - +
160B LEU* 3.8 45.5 - - + +
163B PHE* 3.5 33.7 - - + +
164B LYS* 3.3 33.4 - - + +
167B LEU* 5.4 0.7 - - + -
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Residues in contact with THR 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 ASN* 2.6 44.4 + - - +
120B LEU* 1.3 76.4 - - - +
122B TYR* 1.3 81.2 + - + +
125B PRO* 3.4 17.7 - - - +
164B LYS* 4.7 10.3 - - - +
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Residues in contact with TYR 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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117B ASN* 5.5 2.1 + - - -
118B GLU* 2.6 56.7 + - + +
121B THR* 1.3 102.2 - - + +
123B ASN* 1.3 65.2 + - - +
125B PRO* 4.0 1.9 - - - +
126B HIS* 3.2 25.8 + - - -
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Residues in contact with ASN 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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98B PHE* 3.5 18.5 - - + -
101B CYS* 5.8 2.6 - - - -
118B GLU 4.1 1.7 - - - +
119B LEU* 2.9 35.8 + - - +
122B TYR* 1.3 91.3 - - - +
124B ALA* 1.3 65.4 + - - +
125B PRO* 3.2 3.1 - - - -
126B HIS* 3.0 20.0 + - - +
127B LEU* 3.5 8.1 + - - +
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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