Contacts of the helix formed by residues 105 - 114 (chain T) in PDB entry 1S72
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 ASP 105 (chain T).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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800 A 4.4 7.8 + - - +
950 A 3.9 21.0 + - - +
970 G 2.7 44.1 + - - +
102T ASP* 5.0 0.8 + - - +
103T LEU 3.0 4.1 - - - +
104T GLU* 1.3 78.9 - - - +
106T GLU* 1.3 66.5 + - - +
107T LYS* 2.7 24.1 + - - +
108T ARG* 3.6 27.5 + - + +
109T GLU* 3.1 22.9 + - - +
111T ARG* 4.6 0.2 + - - -
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Residues in contact with GLU 106 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
970 G 4.1 14.9 + - - +
104T GLU 3.8 4.9 + - - +
105T ASP* 1.3 74.8 + - - +
107T LYS* 1.3 56.7 + - + +
109T GLU* 3.7 9.8 - - - +
110T ALA* 2.8 37.5 + - - +
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Residues in contact with LYS 107 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
790 G 3.0 35.7 + - + +
970 G 3.5 54.5 + - + +
105T ASP* 2.7 15.2 + - - +
106T GLU* 1.3 76.6 - - + +
108T ARG* 1.3 64.8 + - - +
110T ALA* 3.3 6.2 + - - +
111T ARG* 2.9 39.8 + - - +
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Residues in contact with ARG 108 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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800 A 4.2 16.0 + - - +
40T VAL* 3.7 14.2 - - - +
41T ARG 3.1 8.7 + - - -
43T ASN* 2.9 38.1 - - - +
46T ASP* 2.8 43.0 + - - -
101T LEU* 3.4 19.7 - - - +
102T ASP 2.9 28.6 + - - +
103T LEU* 4.1 9.4 - - + +
105T ASP* 3.3 22.7 + - + +
107T LYS* 1.3 76.9 - - - +
109T GLU* 1.3 65.0 + - - +
111T ARG* 3.1 21.8 + - - +
112T LEU* 2.9 24.1 + - + +
119T ALA* 3.9 7.8 + - + +
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Residues in contact with GLU 109 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35T TYR* 5.6 0.2 - - + -
103T LEU* 4.1 41.0 - - + +
105T ASP 3.1 14.6 + - - +
106T GLU* 3.8 8.8 - - - +
108T ARG* 1.3 78.8 - - - +
110T ALA* 1.3 63.0 + - - +
112T LEU* 3.2 8.1 + - + +
113T GLU* 3.0 47.0 + - - +
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Residues in contact with ALA 110 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106T GLU 2.8 23.4 + - - +
107T LYS* 3.5 8.3 - - - +
109T GLU* 1.3 73.3 + - - +
111T ARG* 1.3 63.3 + - - +
113T GLU* 3.3 6.1 + - - +
114T SER* 3.0 25.6 + - - -
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Residues in contact with ARG 111 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
790 G 3.6 56.6 + - - +
800 A 2.9 33.5 + - - -
970 G 5.2 0.4 - - - +
37T GLN* 3.9 0.2 - - - +
105T ASP* 4.6 2.2 + - - -
107T LYS* 2.9 21.4 + - - +
108T ARG* 3.3 30.9 - - - +
110T ALA* 1.3 77.1 - - - +
112T LEU* 1.3 57.7 + - - +
114T SER* 3.1 10.3 + - - -
117T ASP* 2.9 34.6 - - + +
118T SER 4.4 6.1 - - - -
119T ALA* 3.6 31.5 + - + +
8073T MG 2.8 18.9 - - - -
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Residues in contact with LEU 112 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27T LEU* 5.1 3.4 - - + -
35T TYR* 3.6 46.0 - - + +
37T GLN* 3.7 28.9 - - - +
40T VAL* 4.3 13.9 - - + -
101T LEU* 3.7 21.5 - - + -
103T LEU* 3.4 38.8 - - + -
108T ARG* 2.9 17.7 + - - +
109T GLU* 3.2 8.5 + - - +
111T ARG* 1.3 76.3 - - - +
113T GLU* 1.3 58.5 + - - +
119T ALA* 3.9 8.5 - - + +
8073T MG 2.6 18.2 - - - -
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Residues in contact with GLU 113 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35T TYR* 3.8 30.6 + - + +
109T GLU* 3.0 42.0 + - - +
110T ALA* 3.9 5.0 - - - +
112T LEU* 1.3 76.8 - - - +
114T SER* 1.3 70.8 + - - +
115T GLU* 3.5 2.8 + - - +
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Residues in contact with SER 114 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35T TYR 4.8 1.4 - - - +
110T ALA 3.0 14.7 + - - -
111T ARG* 3.1 15.9 + - - -
113T GLU* 1.3 81.6 - - - +
115T GLU* 1.3 57.4 + - - +
116T ASP* 4.2 5.4 - - - -
117T ASP* 3.4 21.4 + - - +
8073T MG 2.3 30.8 - - - -
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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