Contacts of the helix formed by residues 82 - 90 (chain D) in PDB entry 1XHU
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 82 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80D PHE* 2.4 18.7 + - - +
81D ASN* 1.3 76.8 - - - +
83D PRO* 1.3 66.0 - - - +
84D THR* 3.9 1.0 - - - -
85D LEU* 3.1 34.7 + - - +
86D LEU* 2.8 31.1 + - - +
160D GLU* 2.6 22.1 + - - -
163D LEU* 3.8 16.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 83 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81D ASN 4.5 1.6 - - - +
82D SER* 1.3 85.2 - - - +
84D THR* 1.3 60.0 + - - +
86D LEU* 3.6 12.3 + - + +
87D PHE* 3.1 20.3 + - - +
154D LYS* 4.6 6.3 - - + +
158D ASN* 3.7 28.5 - - + +
160D GLU* 3.6 14.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 84 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82D SER* 3.1 3.7 + - - +
83D PRO* 1.3 75.4 - - - +
85D LEU* 1.3 58.9 + - - +
87D PHE* 2.6 34.5 + - + +
88D LEU* 3.1 13.3 + - + +
151D THR* 4.2 6.5 - - + -
154D LYS* 3.1 40.1 + - + +
155D MET* 3.4 10.1 + - + -
158D ASN* 4.7 0.2 - - - +
160D GLU* 3.1 15.1 + - + -
163D LEU* 6.2 0.2 - - - -
164D PHE* 3.4 36.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 85 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80D PHE* 4.5 15.7 - - + -
81D ASN 5.7 0.9 - - - +
82D SER* 3.1 27.7 + - - +
84D THR* 1.3 78.4 - - - +
86D LEU* 1.3 56.7 + - - +
88D LEU* 2.7 29.9 + - + +
89D LEU* 2.8 38.6 + - + +
123D TYR* 3.3 55.6 - - + +
125D LEU* 5.1 4.0 - - + -
163D LEU* 4.0 14.6 - - + -
164D PHE* 4.6 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 86 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77D TYR* 2.9 50.5 - - + +
80D PHE* 3.8 23.6 - - + +
82D SER 2.8 17.0 + - - +
83D PRO* 3.7 10.8 - - + +
85D LEU* 1.3 77.2 - - - +
87D PHE* 1.3 62.1 + - - +
90D SER* 2.8 56.7 + - - +
13L G 4.1 33.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 87 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83D PRO 3.1 13.4 + - - +
84D THR 2.6 20.4 + - - +
86D LEU* 1.3 75.3 - - - +
88D LEU* 1.3 71.2 + - + +
90D SER 5.1 0.3 + - - -
147D LYS* 3.3 41.4 - - + -
150D GLN* 3.4 46.2 - - + -
151D THR* 3.4 12.1 - - + -
154D LYS* 3.7 27.6 - - + +
6I T 5.5 1.3 - - - -
13L G 4.8 10.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 88 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56D GLN* 4.0 2.4 + - - -
84D THR* 3.1 20.3 + - + +
85D LEU* 2.7 17.0 + - + +
87D PHE* 1.3 91.0 - - + +
89D LEU* 1.3 63.2 + - + +
90D SER 3.7 2.5 - - - +
112D THR* 2.8 31.4 + - + +
125D LEU* 4.1 27.4 - - + -
147D LYS* 4.2 18.6 - - + -
151D THR* 3.5 23.6 - - + +
164D PHE* 4.1 33.7 - - + -
166D ILE* 6.0 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 89 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56D GLN* 3.0 34.8 - - - +
59D TYR* 4.1 17.0 - - + -
60D LEU* 3.3 27.9 - - + +
80D PHE* 4.2 13.9 - - + -
85D LEU* 2.8 45.5 + - + +
88D LEU* 1.3 80.1 - - + +
90D SER* 1.3 64.8 + - - +
116D LEU* 3.5 28.0 - - + -
123D TYR* 4.2 5.4 - - + -
125D LEU* 4.1 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 90 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60D LEU* 4.7 1.1 - - - -
77D TYR* 3.2 19.6 - - - -
80D PHE* 4.0 10.1 - - - -
86D LEU* 2.8 46.3 + - - +
87D PHE 4.9 0.6 + - - -
88D LEU 3.7 2.9 - - - +
89D LEU* 1.3 81.8 - - - +
91D ARG* 1.3 67.4 + - - +
92D GLY 3.9 0.7 - - - -
13L G 3.3 20.8 - - - +
----------------------------------------------------------
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