Contacts of the helix formed by residues 52 - 57 (chain Y) in PDB entry 1T6B
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 SER 52 (chain Y).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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683X ASP* 2.9 13.8 + - - -
50Y ASP* 2.6 21.8 + - - -
51Y LYS* 1.3 85.3 - - - +
53Y GLY* 1.3 63.5 + - - +
54Y SER* 3.1 3.1 + - - -
55Y VAL* 3.2 15.1 + - - +
56Y ALA 3.6 4.0 + - - -
85Y PHE 3.9 2.2 + - - -
86Y SER* 4.0 4.3 - - - -
114Y PRO* 3.7 2.1 - - - +
115Y VAL 3.8 1.6 - - - -
116Y GLY 3.2 12.1 - - - -
117Y GLU 3.3 17.0 - - - -
118Y THR* 3.3 3.3 + - - -
303Y MN 2.3 27.1 + - - -
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Residues in contact with GLY 53 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
682X ASN* 3.4 29.2 + - - -
683X ASP* 4.3 1.1 - - - -
685X LEU* 3.6 15.5 - - - +
52Y SER* 1.3 74.3 - - - +
54Y SER* 1.3 61.2 + - - +
55Y VAL 3.2 0.9 + - - -
56Y ALA* 3.3 14.2 + - - +
114Y PRO 4.2 5.6 - - - -
115Y VAL* 4.0 5.6 - - - -
116Y GLY 3.1 16.4 + - - +
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Residues in contact with SER 54 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
683X ASP* 2.9 23.5 + - - +
685X LEU* 3.8 17.8 - - - +
52Y SER* 3.1 1.2 + - - -
53Y GLY* 1.3 76.7 - - - +
55Y VAL* 1.3 57.4 + - - +
56Y ALA 3.6 0.2 - - - -
148Y ASP* 2.8 25.0 + - - +
150Y LYS* 5.1 11.4 + - - +
179Y LEU* 4.0 10.4 - - - +
303Y MN 2.1 29.4 + - - -
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Residues in contact with VAL 55 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50Y ASP* 3.2 44.4 - - + +
51Y LYS* 4.3 2.7 - - - -
52Y SER 3.5 11.7 - - - +
53Y GLY 3.2 0.2 - - - -
54Y SER* 1.3 77.6 + - - +
56Y ALA* 1.3 64.8 + - - +
57Y ASN 3.3 2.9 - - - -
58Y ASN* 2.9 14.2 + - - -
59Y TRP* 3.3 10.0 + - + -
62Y ILE* 4.0 13.9 - - + -
114Y PRO* 4.8 1.6 - - + -
148Y ASP* 3.3 37.0 - - + +
178Y VAL* 4.4 8.5 - - + -
179Y LEU* 4.3 14.8 - - + -
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Residues in contact with ALA 56 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
688X TYR* 4.0 36.3 - - + -
52Y SER 3.6 1.4 + - - -
53Y GLY* 3.3 16.1 + - - +
54Y SER 3.6 0.6 - - - -
55Y VAL* 1.3 77.3 - - - +
57Y ASN* 1.3 57.6 + - - +
58Y ASN 3.0 4.2 + - - -
59Y TRP* 3.5 13.5 + - - +
60Y ILE* 6.1 0.7 - - - +
114Y PRO* 3.4 40.8 - - + +
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Residues in contact with ASN 57 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
688X TYR* 4.0 30.4 + - + -
55Y VAL 3.3 0.8 - - - -
56Y ALA* 1.3 76.7 - - - +
58Y ASN* 1.3 70.4 + - - +
59Y TRP 3.7 0.7 - - - -
60Y ILE* 5.4 4.1 + - - +
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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