Contacts of the helix formed by residues 98 - 116 (chain B) in PDB entry 2VBO
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 98 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B VAL* 3.3 28.9 - - + +
18B ASP* 2.9 29.5 + - - +
19B GLY 4.9 2.0 - - - -
21B GLY 3.0 29.2 + - - +
22B SER* 4.2 4.9 - - - +
23B ILE* 3.8 18.2 - - + +
95B LEU* 3.7 8.6 - - + +
97B LEU* 1.3 84.0 - - + +
99B GLN* 1.3 65.8 + - - +
100B LYS 3.3 2.5 - - - -
101B GLN* 3.3 22.6 + - + +
102B ALA* 3.0 22.0 + - - +
136B ASN* 5.1 2.4 + - - +
15E A 4.3 3.4 + - - -
16E G 3.1 26.3 + - - -
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Residues in contact with GLN 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B GLN* 2.8 51.4 + - + +
93B PRO* 3.7 13.3 + - - +
95B LEU* 3.4 35.3 + - + +
96B LYS* 4.9 4.3 - - - +
97B LEU 3.5 2.4 - - - -
98B LYS* 1.3 79.0 - - - +
100B LYS* 1.3 61.2 + - + +
102B ALA* 3.1 3.1 + - - +
103B ASN* 2.9 34.9 + - - +
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Residues in contact with LYS 100 (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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97B LEU 5.2 0.4 + - - +
98B LYS 3.3 0.6 - - - -
99B GLN* 1.3 80.4 - - + +
101B GLN* 1.3 68.2 + - - +
103B ASN* 3.3 7.0 + - - +
104B LEU* 3.0 28.4 + - + +
135B LEU* 3.7 37.5 - - + +
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Residues in contact with GLN 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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23B ILE* 4.0 20.9 - - + -
97B LEU 3.4 13.5 + - - +
98B LYS* 3.4 32.7 - - - +
99B GLN 3.3 0.2 - - - -
100B LYS* 1.3 83.4 + - - +
102B ALA* 1.3 62.3 + - - +
104B LEU* 3.2 3.1 + - - +
105B VAL* 3.0 25.8 + - - +
132B ILE* 4.1 21.2 - - + +
135B LEU* 3.5 39.9 + - + +
136B ASN* 2.9 29.4 + - - +
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Residues in contact with ALA 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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23B ILE* 3.9 15.9 - - + +
88B LEU* 4.4 14.7 - - + +
92B GLN* 4.2 15.0 - - + -
95B LEU* 3.8 19.5 - - + -
98B LYS 3.0 13.3 + - - +
99B GLN 3.5 7.6 - - - +
101B GLN* 1.3 76.6 - - - +
103B ASN* 1.3 59.3 + - - +
105B VAL* 3.1 5.7 + - - +
106B LEU* 3.0 31.5 + - - +
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Residues in contact with ASN 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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92B GLN* 2.5 51.1 + - - +
99B GLN* 2.9 18.2 + - - +
100B LYS* 3.9 6.5 - - - +
101B GLN 3.2 0.2 - - - -
102B ALA* 1.3 75.9 - - - +
104B LEU* 1.3 62.4 + - - +
106B LEU* 3.4 18.0 + - - +
107B LYS* 3.0 23.0 + - - +
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Residues in contact with LEU 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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100B LYS* 3.0 21.2 + - + +
101B GLN 3.8 0.2 - - - +
103B ASN* 1.3 73.7 - - - +
105B VAL* 1.3 60.8 + - - +
107B LYS* 3.3 15.8 + - + +
108B ILE* 2.9 34.1 + - + +
128B TRP* 4.1 22.4 - - + +
131B GLN* 3.7 33.2 - - + +
132B ILE* 3.5 28.7 - - + -
135B LEU* 3.8 24.5 - - + -
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Residues in contact with VAL 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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23B ILE* 3.5 21.1 - - + -
24B ILE 5.0 3.1 - - - +
25B ALA* 4.9 2.5 - - + -
41B LEU* 4.2 20.9 - - + -
42B THR 6.1 0.4 - - - +
84B LEU* 4.4 8.3 - - + -
88B LEU* 3.6 23.3 - - + -
101B GLN 3.0 16.8 + - - +
102B ALA 3.1 7.4 + - - +
104B LEU* 1.3 76.8 - - - +
106B LEU* 1.3 57.5 + - - +
108B ILE* 3.3 6.6 + - - +
109B ILE* 2.9 44.5 + - + +
132B ILE* 3.6 18.4 - - + -
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Residues in contact with LEU 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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85B HIS* 3.6 45.9 - - + +
88B LEU* 3.9 15.3 - - + +
89B THR* 3.7 27.8 - - + +
92B GLN* 4.8 1.1 - - + -
102B ALA 3.0 15.2 + - - +
103B ASN* 3.5 30.7 - - - +
104B LEU 3.3 0.2 - - - -
105B VAL* 1.3 78.3 - - - +
107B LYS* 1.3 55.9 + - - +
109B ILE* 3.3 4.4 + - + +
110B GLU* 3.0 44.6 + - - +
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Residues in contact with LYS 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 ASN 3.0 17.4 + - - +
104B LEU* 3.3 17.9 + - + +
106B LEU* 1.3 72.1 - - - +
108B ILE* 1.3 67.8 + - - +
110B GLU* 3.4 10.7 + - - +
111B GLN* 3.1 30.1 + - + +
128B TRP* 3.3 49.9 - - + +
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Residues in contact with ILE 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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39B LEU* 4.6 4.5 - - + -
41B LEU* 4.0 27.1 - - + -
104B LEU 2.9 21.8 + - - +
105B VAL* 3.6 5.2 - - - +
107B LYS* 1.3 76.8 - - - +
109B ILE* 1.3 63.9 + - - +
111B GLN* 3.0 13.2 + - - +
112B LEU* 3.1 22.2 + - + +
125B VAL* 3.6 20.8 - - + +
128B TRP* 3.9 27.4 - - + -
129B VAL* 3.9 28.5 - - + +
132B ILE* 3.7 24.5 - - + -
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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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41B LEU* 3.6 18.2 - - + -
81B ILE* 3.6 33.7 - - + +
82B LYS* 6.1 0.2 - - - -
84B LEU* 4.4 7.2 - - + -
85B HIS* 3.9 46.9 - - + +
105B VAL* 2.9 38.6 + - + +
106B LEU* 3.8 5.8 - - + +
108B ILE* 1.3 75.7 - - - +
110B GLU* 1.3 65.9 + - - +
112B LEU* 3.1 25.0 + - - +
113B PRO* 3.9 4.0 - - - +
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Residues in contact with GLU 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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85B HIS* 2.8 32.0 + - + +
106B LEU* 3.0 28.5 + - - +
107B LYS* 3.8 10.5 - - - +
109B ILE* 1.3 79.9 - - + +
111B GLN* 1.3 72.4 + - - +
112B LEU 3.7 0.3 + - - -
113B PRO* 3.8 9.4 - - - +
114B SER* 5.7 0.3 - - - -
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Residues in contact with GLN 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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107B LYS* 3.1 16.6 + - + +
108B ILE 3.0 7.0 + - - +
110B GLU* 1.3 87.0 + - - +
112B LEU* 1.3 64.1 + - - +
113B PRO* 3.4 3.4 - - - -
114B SER* 3.3 25.5 + - - +
115B ALA* 2.9 22.1 + - - +
125B VAL* 4.0 18.4 - - + -
128B TRP* 3.7 20.9 - - + -
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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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39B LEU* 4.0 32.3 - - + -
41B LEU* 4.9 3.1 - - + -
81B ILE* 4.0 34.1 - - + -
108B ILE* 3.1 24.5 + - + +
109B ILE* 3.1 18.5 + - + +
111B GLN* 1.3 76.2 - - - +
113B PRO* 1.3 73.0 - - + +
115B ALA* 3.1 15.7 + - + +
116B LYS* 3.2 18.0 + - + +
125B VAL* 5.1 0.7 - - + -
3C A 6.0 3.4 - - - +
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Residues in contact with PRO 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 ILE 3.9 4.5 - - - +
110B GLU 3.8 12.1 - - - +
111B GLN 3.4 4.0 - - - -
112B LEU* 1.3 96.2 - - + +
114B SER* 1.3 62.4 + - - +
116B LYS* 3.1 25.3 + - + +
117B GLU* 3.3 16.7 - - - +
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Residues in contact with SER 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 GLU 5.7 0.2 - - - -
111B GLN* 3.3 28.2 + - - +
113B PRO* 1.3 80.6 - - - +
115B ALA* 1.3 60.1 + - - +
116B LYS 3.3 0.5 + - - -
117B GLU* 3.4 21.9 + - - +
118B SER 3.9 1.9 + - - -
121B LYS* 3.5 43.0 + - - +
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Residues in contact with ALA 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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35B PHE* 3.4 17.8 - - - -
39B LEU* 5.2 0.4 - - + -
111B GLN 2.9 18.2 + - - +
112B LEU* 3.1 13.6 + - + +
114B SER* 1.3 73.1 + - - +
116B LYS* 1.3 60.7 + - - +
117B GLU 3.2 0.4 - - - -
118B SER 3.5 6.1 - - - +
121B LYS* 4.2 2.7 - - - -
122B PHE* 3.6 34.0 - - + +
125B VAL* 4.0 26.7 - - + -
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Residues in contact with LYS 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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34B LYS* 3.2 30.0 + - - +
35B PHE* 4.1 3.1 - - - -
112B LEU* 3.2 13.6 + - + +
113B PRO* 3.1 18.2 + - + +
115B ALA* 1.3 78.6 - - - +
117B GLU* 1.3 59.3 + - + +
118B SER 3.6 0.4 - - - -
122B PHE* 5.8 0.2 - - - -
2C T 3.5 56.7 + - - +
3C A 4.4 16.1 + - - +
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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
------------------------------------------------------------
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