Contacts of the helix formed by residues 92 - 100 (chain W) in PDB entry 1XDM
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 LEU 92 (chain W).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83W LEU 4.1 10.8 - - - +
84W TYR* 3.9 20.0 - - + +
85W GLN 3.2 18.8 - - - +
86W LYS* 3.9 21.1 - - + +
90W GLY 3.9 2.2 + - - +
91W LYS* 1.3 72.7 - - - +
93W PHE* 1.3 64.7 + - - +
94W ARG* 3.5 30.5 - - + +
95W ASN* 2.9 41.8 + - - +
96W ILE* 3.0 13.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 93 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56W ARG* 3.2 29.2 - - + -
59W ARG* 3.4 7.4 - - + -
60W GLU* 3.1 41.1 - - + -
63W PHE* 3.1 35.3 - + + -
78W LEU* 5.6 1.8 - - + -
82W THR* 4.5 13.5 - - + +
85W GLN* 3.1 24.9 + - + +
86W LYS* 3.0 32.3 - - - -
87W ASP* 3.2 11.4 - - + -
91W LYS 4.1 0.2 - - - -
92W LEU* 1.3 70.1 - - - +
94W ARG* 1.3 65.6 + - - +
96W ILE* 3.3 17.7 + - + +
97W LEU* 3.2 22.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 94 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78W LEU* 5.0 5.7 - - - +
83W LEU* 3.9 40.4 + - + +
84W TYR* 4.2 20.4 - - - -
85W GLN 4.7 0.4 + - - -
92W LEU* 3.5 31.6 - - + +
93W PHE* 1.3 81.7 - - - +
95W ASN* 1.3 67.3 + - - +
97W LEU* 3.3 7.9 + - - +
98W LYS* 3.1 23.9 + - + +
104W VAL* 3.7 16.3 - - + +
139W LYS 5.0 0.4 + - - -
140W ASP* 2.7 53.9 + - - +
141W GLY* 4.4 12.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 95 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91W LYS* 4.2 18.1 - - - +
92W LEU* 2.9 45.2 + - - +
94W ARG* 1.3 78.8 + - - +
96W ILE* 1.3 55.6 + - - +
97W LEU 2.8 5.6 - - - -
98W LYS* 4.0 20.1 - - + +
99W GLU* 2.6 37.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 96 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60W GLU* 5.5 1.8 - - + -
63W PHE* 3.2 28.5 - - + +
64W SER* 4.4 11.0 - - - +
87W ASP* 3.1 38.8 - - + +
91W LYS* 3.5 20.6 - - + +
92W LEU 3.0 16.3 + - - +
93W PHE* 3.5 19.5 - - + +
95W ASN* 1.3 76.1 - - - +
97W LEU* 1.3 57.9 + - - +
99W GLU* 3.7 5.5 - - - +
100W LYS* 3.1 46.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 97 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63W PHE* 3.8 48.7 - - + +
76W VAL* 4.1 25.8 - - + -
78W LEU* 4.7 5.8 - - + -
93W PHE 3.2 16.6 - - - +
94W ARG 3.3 4.9 - - - +
95W ASN 2.8 0.2 - - - -
96W ILE* 1.3 77.2 - - - +
98W LYS* 1.3 68.5 + - - +
99W GLU 3.0 1.3 - - - -
100W LYS* 3.0 15.8 + - + -
101W GLY 3.1 8.5 + - - -
102W ILE* 3.1 36.7 + - + +
104W VAL* 3.7 25.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 98 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94W ARG* 3.1 13.7 + - + +
95W ASN* 2.9 24.1 + - + +
97W LEU* 1.3 78.5 - - - +
99W GLU* 1.3 67.6 + - - +
101W GLY* 3.1 11.6 + - - -
102W ILE 4.0 7.2 + - - -
104W VAL* 4.7 3.3 - - + +
141W GLY* 5.2 19.2 + - - -
143W ASP* 5.6 3.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 99 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91W LYS* 5.0 13.7 - - - +
95W ASN 2.6 20.1 + - - +
96W ILE* 3.7 9.4 - - - +
98W LYS* 1.3 76.5 - - - +
100W LYS* 1.3 58.2 + - + +
101W GLY* 2.7 12.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 100 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63W PHE 3.1 23.7 + - - +
64W SER* 4.3 5.1 + - - +
65W VAL 2.8 29.8 - - - +
66W ASP 4.2 4.7 - - - +
67W SER* 4.1 28.0 - - - +
69W ILE* 4.4 9.2 - - + -
70W ASN* 3.1 28.1 + - + +
96W ILE* 3.1 26.3 + - - +
97W LEU* 3.0 9.4 + - + +
99W GLU* 1.3 81.1 - - + +
101W GLY* 1.3 63.0 + - - +
102W ILE* 3.0 14.4 + - + -
----------------------------------------------------------
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