Contacts of the helix formed by residues 79 - 92 (chain a) in PDB entry 5XTD
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 GLY 79 (chain a).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75a ILE* 2.9 21.2 + - - -
76a ALA* 2.8 7.5 + - - -
78a THR* 1.3 78.5 - - - +
80a ILE* 1.3 64.9 + - - -
82a VAL* 3.1 14.4 + - - +
83a ALA* 3.2 11.6 + - - +
201b PLX 5.4 6.2 - - - +
100e VAL* 4.2 10.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 80 (chain a).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76a ALA* 2.9 27.8 + - + +
79a GLY* 1.3 74.7 - - - +
81a PRO* 1.3 68.9 - - + +
83a ALA* 2.9 19.0 + - + +
84a ILE* 3.0 31.7 + - + +
201b PLX 4.7 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 81 (chain a).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76a ALA 3.7 1.1 - - - +
77a LEU* 3.3 27.1 - - - +
78a THR* 3.8 6.5 - - - +
79a GLY 3.6 3.6 - - - -
80a ILE* 1.3 95.7 - - + +
82a VAL* 1.3 57.3 + - + +
84a ILE* 3.3 10.8 + - + +
85a PHE* 2.9 46.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 82 (chain a).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78a THR 3.1 19.5 - - - +
79a GLY* 3.1 8.0 + - - +
80a ILE 3.1 0.8 - - - -
81a PRO* 1.3 76.0 - - + +
83a ALA* 1.3 66.8 + - - +
85a PHE* 3.3 6.9 + - + +
86a ILE* 2.9 46.3 + - + +
100e VAL* 4.5 4.5 - - + -
101e LEU* 3.5 26.5 - - + -
104e THR* 3.8 23.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 83 (chain a).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79a GLY 3.2 7.8 + - - +
80a ILE* 2.9 12.4 + - + +
82a VAL* 1.3 79.9 - - - +
84a ILE* 1.3 59.5 + - + +
86a ILE* 3.9 4.4 - - - +
87a THR* 2.9 36.5 + - + +
201b PLX 3.9 44.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 84 (chain a).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80a ILE* 3.0 34.8 + - + +
81a PRO* 3.5 11.0 - - + +
83a ALA* 1.3 75.6 - - + +
85a PHE* 1.3 75.4 + - + +
87a THR* 2.5 22.1 + - - +
88a LEU* 2.9 35.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 85 (chain a).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81a PRO* 2.9 34.4 + - + +
82a VAL* 3.3 6.5 + - + +
84a ILE* 1.3 84.3 - - + +
86a ILE* 1.3 59.6 + - + +
88a LEU* 4.0 10.9 - - + +
89a VAL* 2.9 40.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 86 (chain a).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82a VAL* 2.9 40.7 + - + +
83a ALA* 4.0 3.8 - - - +
85a PHE* 1.3 78.3 - - + +
87a THR* 1.3 66.3 + - - +
89a VAL* 3.9 3.7 - - - +
90a ASN* 2.9 48.7 + - - +
117a ILE* 4.4 16.2 - - + -
201b PLX 4.3 28.7 - - + -
104e THR* 5.0 2.0 - - - -
108e TYR* 3.4 39.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 87 (chain a).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83a ALA* 2.9 20.6 + - + +
84a ILE* 2.5 26.0 + - - +
86a ILE* 1.3 74.5 - - - +
88a LEU* 1.3 63.2 + - - +
90a ASN* 3.8 1.0 - - - +
91a VAL* 2.9 38.8 + - - +
201b PLX 2.9 44.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 88 (chain a).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84a ILE* 2.9 39.7 + - + +
85a PHE* 4.0 13.2 - - + +
87a THR* 1.3 80.7 - - - +
89a VAL* 1.3 67.9 + - + +
91a VAL* 3.1 5.3 + - + -
92a PHE* 2.9 53.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 89 (chain a).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85a PHE* 2.9 31.5 + - + +
86a ILE* 4.0 3.8 - - - +
88a LEU* 1.3 77.2 - - + +
90a ASN* 1.3 60.2 + - - +
93a ILE* 3.1 43.3 + - + +
94a GLY 3.4 5.9 + - - -
116a PRO* 3.7 28.2 - - + +
117a ILE* 4.3 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 90 (chain a).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86a ILE* 2.9 31.2 + - - +
87a THR 3.8 0.2 - - - +
89a VAL* 1.3 81.2 - - - +
91a VAL* 1.3 65.1 + - - +
92a PHE 3.3 0.7 + - - -
94a GLY* 3.6 17.5 + - - +
95a GLN* 4.8 5.4 + - - +
115a HIS* 3.6 22.9 + - - -
116a PRO* 5.2 1.3 - - - +
117a ILE* 5.8 0.2 - - - +
201b PLX 3.1 83.3 + - + +
50d HIS* 3.8 3.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 91 (chain a).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87a THR* 2.9 29.0 + - - +
88a LEU* 3.1 8.3 + - + +
90a ASN* 1.3 75.5 - - - +
92a PHE* 1.3 82.8 + - + +
201b PLX 4.1 24.0 - - + -
45d PHE* 5.2 11.7 - - + -
46d ILE* 3.7 37.0 - - + +
49d GLN* 4.0 8.8 - - + +
50d HIS* 3.8 1.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 92 (chain a).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88a LEU* 2.9 38.5 + - + +
89a VAL* 5.2 0.2 - - - -
91a VAL* 1.3 102.7 - - + +
93a ILE* 1.3 75.2 + - + +
94a GLY 3.2 2.2 + - - -
45d PHE* 6.4 1.3 - + - -
49d GLN* 4.0 34.3 - - + +
50d HIS* 3.8 15.6 + - - -
53d ASN* 4.6 1.3 - - - +
----------------------------------------------------------
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