Contacts of the strand formed by residues 18 - 23 (chain I) 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 ILE 18 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17I LEU* 1.4 88.2 - - - +
19I TRP* 1.3 64.2 + - - +
48I ARG* 5.4 3.4 - - + -
114I SER* 5.2 2.0 - - - -
115I GLY 3.2 22.0 - - - +
116I GLN* 4.0 16.3 - - + +
117I HIS* 4.7 2.5 - - - -
65J ILE* 3.6 46.2 - - + +
67J ASP* 3.9 22.3 + - - +
69J GLU* 5.6 1.2 - - - +
74J LYS* 5.5 7.8 - - + +
76J VAL* 4.3 23.2 - - + +
78J ILE* 4.9 6.7 - - + -
94J ILE* 4.8 6.7 - - + -
96J LEU* 4.5 12.2 - - + +
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Residues in contact with TRP 19 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17I LEU 3.6 0.6 + - - +
18I ILE* 1.3 73.4 - - - +
20I GLY* 1.3 72.7 + - - +
21I CYS* 3.5 31.9 - - + -
30I PHE* 3.8 24.5 - + - -
32I PHE* 3.6 27.8 - + + -
45I LEU* 3.8 21.3 - - + -
47I LEU* 4.1 10.8 - - + -
102I PHE* 3.5 18.8 - + - -
113I ILE* 3.7 26.5 - - + -
114I SER* 3.3 3.9 - - - -
115I GLY* 2.8 51.2 + - - +
116I GLN 4.6 0.2 - - - +
117I HIS* 3.9 27.6 - + + +
76J VAL* 3.5 10.4 - - - +
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Residues in contact with GLY 20 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19I TRP* 1.3 96.4 + - - +
21I CYS* 1.3 61.9 + - - +
30I PHE* 4.8 4.5 - - - -
113I ILE 3.2 11.4 - - - -
76J VAL* 3.7 19.1 - - - +
77J PRO* 6.2 0.7 - - - -
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Residues in contact with CYS 21 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19I TRP* 3.5 25.1 - - + -
20I GLY* 1.3 76.2 - - - +
22I GLU* 1.3 58.9 + - - +
23I LEU* 4.2 4.0 - - - -
30I PHE* 3.6 45.8 - - + -
102I PHE* 4.7 2.2 - - - -
111I LEU 3.9 0.2 - - - +
112I TYR* 3.3 8.1 - - - +
113I ILE* 2.9 54.4 + - - -
77J PRO* 6.1 0.2 - - - +
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Residues in contact with GLU 22 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21I CYS* 1.3 72.8 - - - +
23I LEU* 1.3 82.8 + - - +
24I ASN* 2.5 31.0 + - - +
27I ASN* 4.1 7.8 - - - +
30I PHE* 4.9 5.0 - - - +
110I PRO* 3.6 23.0 - - + +
111I LEU 3.4 7.2 - - - +
112I TYR* 3.5 26.9 + - + -
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Residues in contact with LEU 23 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21I CYS* 4.2 5.6 - - - -
22I GLU* 1.3 86.4 - - - +
24I ASN* 1.3 66.3 + - - +
27I ASN 3.2 11.0 - - - +
28I LYS 4.0 4.5 - - - +
29I THR 4.6 0.2 - - - +
30I PHE* 3.4 37.2 - - + +
63I VAL* 4.3 7.2 - - + -
102I PHE* 4.1 10.5 - - + +
103I ARG 4.1 2.9 - - - -
104I LEU* 3.9 41.4 - - + +
109I GLY* 4.1 1.0 - - - -
110I PRO* 3.5 0.2 - - - +
111I LEU* 2.9 41.1 + - + +
113I ILE* 4.0 23.3 - - + -
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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