Contacts of the helix formed by residues 96 - 104 (chain B) in PDB entry 1ATH
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 96 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B CYS* 4.3 6.0 + - - +
23B TYR* 4.6 14.4 - - - +
95B CYS* 1.3 87.6 - - - +
97B ASP* 1.3 68.7 + - + +
99B LEU* 4.1 2.7 - - - +
100B GLN* 3.6 20.2 + - - +
350B LYS* 3.7 29.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 97 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B CYS 3.0 0.4 + - - -
96B ASN* 1.3 81.8 - - + +
98B THR* 1.3 66.1 + - - +
100B GLN* 3.3 20.7 + - - +
101B GLN* 3.0 30.8 + - - +
342B ASP* 3.6 21.7 - - - +
348B LYS 5.7 1.1 - - - +
350B LYS* 4.6 2.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 98 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B ALA* 3.8 12.6 - - + -
95B CYS 3.0 7.0 + - - -
97B ASP* 1.3 74.9 - - - +
99B LEU* 1.3 63.7 + - - +
101B GLN* 3.1 5.4 + - - +
102B LEU* 3.0 25.7 + - + +
340B LEU* 4.7 0.6 - - + +
342B ASP* 3.9 11.1 + - - +
343B LEU* 3.6 44.9 - - + +
348B LYS 3.7 3.5 + - - -
349B SER* 3.6 5.0 - - - -
350B LYS* 2.8 34.6 + - - +
351B LEU* 4.9 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 99 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B MET 5.3 1.1 - - - +
21B CYS 3.1 26.0 - - - +
22B ILE* 4.1 4.7 - - + -
23B TYR 3.4 22.0 - - - +
91B LYS* 3.3 47.8 - - + +
94B ALA* 3.9 16.2 - - + +
95B CYS 3.0 23.8 + - - +
96B ASN 4.1 2.9 - - - +
98B THR* 1.3 75.9 - - - +
100B GLN* 1.3 62.9 + - - +
102B LEU* 3.4 4.0 + - - +
103B MET* 3.0 24.7 + - + +
116B SER* 4.1 12.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 100 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B TYR* 4.9 15.4 + - - +
96B ASN 3.6 13.5 + - - +
97B ASP* 3.3 24.3 + - - +
99B LEU* 1.3 79.2 - - - +
101B GLN* 1.3 67.3 + - - +
103B MET* 2.9 19.2 + - - +
104B GLU* 2.9 31.3 + - + +
109B ASP* 5.9 2.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 101 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B ASP* 3.0 19.5 + - + +
98B THR* 3.6 8.1 - - - +
100B GLN* 1.3 77.8 - - + +
102B LEU* 1.3 61.4 + - - +
104B GLU* 3.3 15.4 + - - +
105B VAL* 3.1 29.7 + - - +
339B GLY 3.4 16.8 + - - +
340B LEU* 3.6 13.2 - - + +
341B VAL* 2.8 18.0 + - - +
342B ASP* 2.8 54.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 102 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B PHE* 3.8 33.0 - - + +
90B THR* 5.1 2.2 - - - -
91B LYS* 3.5 35.0 - - + +
94B ALA* 3.7 22.9 - - + -
98B THR* 3.0 25.9 + - + +
99B LEU* 3.7 2.5 - - - +
101B GLN* 1.3 74.1 - - - +
103B MET* 1.3 63.1 + - - +
104B GLU 3.2 1.0 + - - -
105B VAL* 4.4 2.0 - - - -
106B PHE* 3.3 32.3 + - + +
108B PHE* 4.0 1.3 - - + -
340B LEU* 3.8 16.8 - - + -
343B LEU* 3.8 25.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 103 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B TYR 5.2 3.8 - - - +
91B LYS* 3.5 27.6 - - - -
99B LEU* 3.0 19.3 + - + +
100B GLN* 2.9 13.1 + - + +
102B LEU* 1.3 75.0 - - - +
104B GLU* 1.3 57.5 + - - +
107B LYS 3.7 0.2 + - - -
108B PHE* 2.9 53.0 + - + +
109B ASP* 2.8 36.4 + - + +
116B SER* 4.1 34.3 - - - +
119B ILE* 4.2 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 104 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B GLN* 2.9 36.2 + - + +
101B GLN* 3.7 15.6 - - - +
103B MET* 1.3 79.7 - - - +
105B VAL* 1.3 66.3 + - + +
107B LYS* 3.8 17.9 + - - +
109B ASP* 4.0 22.5 - - - +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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