Contacts of the strand formed by residues 111 - 117 (chain J) in PDB entry 2VTX
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 LEU 111 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21J CYS 3.8 0.3 - - - +
22J GLU* 3.4 3.1 - - - -
23J LEU* 2.8 50.0 + - + +
50J VAL* 4.2 12.3 - - + -
51J CYS 3.6 6.3 - - - +
52J LEU* 3.8 22.7 - - + -
61J HIS* 4.0 12.1 - - + -
63J VAL* 4.0 30.1 - - + -
81J LEU* 4.3 3.6 - - + -
104J LEU* 3.8 25.1 - - + -
109J GLY* 3.4 2.7 - - - -
110J PRO* 1.3 74.1 - - - +
112J TYR* 1.3 67.4 + - - +
113J ILE* 3.8 26.9 + - + -
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Residues in contact with TYR 112 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21J CYS 3.3 14.8 - - - +
22J GLU* 3.4 32.0 + - + -
49J THR* 5.5 0.2 + - - -
50J VAL* 3.4 5.5 - - - +
51J CYS* 2.7 52.4 + - - +
52J LEU 4.0 2.2 - - - -
53J GLY* 3.6 31.2 - - - -
110J PRO* 4.1 13.1 - - + +
111J LEU* 1.3 76.3 - - - +
113J ILE* 1.3 62.7 + - - +
114J SER 4.2 0.2 - - - -
62K ILE* 4.7 8.1 - - + +
77K PRO* 3.4 41.5 - - + +
80K THR* 5.4 0.4 - - - -
105K LYS* 2.9 32.1 + - - +
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Residues in contact with ILE 113 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19J TRP* 4.1 8.2 - - + -
20J GLY* 3.3 5.2 - - - -
21J CYS* 3.1 44.5 + - - +
23J LEU* 4.2 4.5 - - + -
47J LEU* 4.0 23.6 - - + -
49J THR 3.5 8.1 - - - +
50J VAL* 4.5 8.7 - - + +
63J VAL* 4.0 19.1 - - + -
78J ILE* 6.2 0.7 - - + -
102J PHE* 3.8 35.0 - - + -
111J LEU* 3.8 15.5 - - + +
112J TYR* 1.3 78.6 - - - +
114J SER* 1.3 69.2 + - - +
76K VAL* 4.7 1.0 - - - +
77K PRO 5.1 0.7 - - - -
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Residues in contact with SER 114 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18J ILE* 5.3 1.8 - - - -
19J TRP* 3.4 10.1 - - - -
47J LEU* 3.8 5.4 - - - +
48J ARG* 3.1 18.6 + - - +
49J THR* 2.6 50.0 + - - +
112J TYR 4.2 0.4 - - - -
113J ILE* 1.3 78.7 - - - +
115J GLY* 1.3 59.3 + - - +
76K VAL* 3.8 11.9 - - - -
77K PRO 3.8 15.0 + - - -
78K ILE* 4.2 9.0 - - - -
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Residues in contact with GLY 115 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18J ILE* 3.5 4.4 - - - +
19J TRP* 2.8 45.1 + - - +
45J LEU* 4.0 6.1 - - - -
46J ALA 3.0 13.5 - - - -
47J LEU* 4.1 0.7 - - - -
48J ARG* 3.8 9.9 - - - +
114J SER* 1.3 77.7 + - - +
116J GLN* 1.3 62.2 + - - +
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Residues in contact with GLN 116 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17J LEU* 3.9 15.4 - - - +
18J ILE* 4.1 11.4 - - + +
19J TRP 4.6 0.7 - - - +
45J LEU* 3.3 9.6 - - - +
46J ALA* 2.7 36.5 + - - +
48J ARG* 3.0 45.8 + - + +
115J GLY* 1.3 77.0 - - - +
117J HIS* 1.3 69.3 + - - +
118J VAL* 4.9 0.9 - - + -
93K GLY 3.6 7.3 - - - +
94K ILE* 3.7 10.1 - - - -
95K GLU 3.0 29.4 + - - +
96K LEU* 3.9 16.2 - - - +
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Residues in contact with HIS 117 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17J LEU* 3.5 36.2 + - + +
19J TRP* 4.2 15.0 - - + +
32J PHE* 3.5 37.0 - + - -
43J HIS* 3.8 30.5 - + + +
44J GLN 3.5 11.4 + - - +
45J LEU* 5.0 4.2 - - + -
116J GLN* 1.3 75.0 + - - +
118J VAL* 1.3 70.3 + - - +
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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