Contacts of the helix formed by residues 19 - 23 (chain L) in PDB entry 1T6V
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 ASN 19 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18L ASP* 1.3 94.6 + - - +
20L TYR* 1.3 65.2 + - - +
21L ARG 3.2 0.7 + - - -
22L GLY* 3.0 18.6 + - - +
23L TYR 2.8 20.0 + - - +
24L SER* 3.5 20.8 + - - -
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Residues in contact with TYR 20 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16L GLY 3.8 19.1 - - - +
17L LEU* 3.0 23.6 + - + +
18L ASP 3.2 1.8 - - - -
19L ASN* 1.3 76.2 - - - +
21L ARG* 1.3 82.1 + - + +
23L TYR* 3.1 19.5 + - - +
28L TRP* 4.2 5.2 - + + -
96L LYS* 3.6 53.6 + - + +
99L VAL* 3.7 11.0 - - + -
100L SER* 3.5 27.3 + - - -
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Residues in contact with ARG 21 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19L ASN 3.2 1.6 + - - -
20L TYR* 1.3 94.4 - - + +
22L GLY* 1.3 58.5 + - - +
23L TYR* 3.3 20.9 - - + -
99L VAL* 4.1 11.9 + - + +
100L SER* 3.4 50.9 + - - +
29N TYR* 5.9 2.4 - - - +
30N ALA* 4.4 27.1 + - - +
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Residues in contact with GLY 22 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19L ASN* 3.0 17.3 + - - +
20L TYR 3.0 1.4 - - - -
21L ARG* 1.3 76.2 - - - +
23L TYR* 1.3 62.6 + - - +
24L SER 3.7 2.9 + - - -
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Residues in contact with TYR 23 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17L LEU 3.3 0.3 - - - +
19L ASN* 2.8 20.2 + - - -
20L TYR 3.1 11.6 + - - +
21L ARG* 3.5 19.1 - - + -
22L GLY* 1.3 78.0 - - - +
24L SER* 1.3 65.2 + - - +
27L ASN* 4.2 10.1 - - - +
28L TRP* 3.2 25.7 + + - +
99L VAL* 3.7 22.7 - - + -
103L ASN 4.5 0.2 + - - -
104L GLY* 3.6 9.0 - - - -
105L MET* 3.1 52.8 + - + -
106L ASN* 5.0 0.7 + - - -
111L TRP* 3.9 21.2 - + - -
28N SER 5.7 1.0 - - - -
29N TYR* 4.1 19.4 - - + +
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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