Contacts of the helix formed by residues 73 - 82 (chain A) in PDB entry 1XXE
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 GLU 73 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A SER* 3.8 0.2 - - - -
60A THR* 3.1 32.6 + - + +
71A THR* 4.6 3.1 - - - -
72A VAL* 1.3 82.0 - - - +
74A HIS* 1.3 71.1 + - + +
76A LEU* 3.2 10.4 + - - +
77A SER* 2.7 31.3 + - - -
230A ASP* 2.3 38.5 - - - +
233A GLY* 3.5 9.2 - - - +
234A ASP* 3.7 13.0 - - - +
253A HIS* 2.6 33.6 + - - -
320A TUX 3.2 11.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 74 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A THR* 4.5 13.3 - - + +
72A VAL 3.3 0.8 - - - +
73A GLU* 1.3 97.8 - - + +
75A ILE* 1.3 65.7 + - - +
77A SER* 2.9 18.6 + - - -
78A VAL* 3.2 6.4 + - - +
96A ILE* 6.0 2.9 - - + -
98A ILE* 4.2 21.0 - - + +
101A GLY 3.8 14.4 + - - -
102A SER 5.0 7.2 + - - +
103A GLY* 6.0 1.3 - - - -
106A PHE* 5.7 7.2 - - + -
179A THR* 4.3 0.4 - - - -
226A HIS* 3.1 25.1 + + - -
229A PHE* 3.7 17.1 - + + -
230A ASP* 3.5 7.9 - - - -
319A ZN 2.5 28.6 - - - -
320A TUX 3.4 10.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 75 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A LEU* 5.0 8.1 - - + -
28A ILE* 5.3 7.9 - - + -
39A PHE* 4.4 19.5 - - + -
72A VAL* 3.3 18.7 + - - +
74A HIS* 1.3 78.7 - - - +
76A LEU* 1.3 82.4 + - + +
77A SER 3.1 0.3 + - - -
78A VAL* 3.1 6.9 + - + +
79A LEU* 3.0 41.8 + - + +
89A ILE* 4.3 12.8 - - + -
96A ILE* 4.7 13.3 - - + +
106A PHE* 3.4 54.8 - - + -
110A ILE* 5.1 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 76 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ILE* 4.3 8.7 - - + -
39A PHE* 4.5 5.2 - - + -
48A ALA* 4.1 22.0 - - + +
60A THR* 6.2 0.4 - - + -
62A LEU* 4.6 5.8 - - + -
72A VAL* 2.9 41.9 + - + +
73A GLU* 3.5 8.1 - - - +
74A HIS 3.2 0.4 - - - -
75A ILE* 1.3 85.0 - - + +
77A SER* 1.3 58.1 + - - +
79A LEU* 3.4 19.9 + - + +
80A HIS* 2.8 29.5 + - - +
233A GLY* 3.8 13.9 - - - +
236A TYR* 3.7 20.1 - - + +
237A LEU* 4.1 24.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A GLU 2.7 15.6 + - - -
74A HIS* 2.9 5.8 + - - -
76A LEU* 1.3 73.3 - - - +
78A VAL* 1.3 66.1 + - - +
80A HIS* 3.1 13.9 + - - +
81A LEU* 3.1 15.2 + - - +
229A PHE* 2.6 65.7 + - - -
230A ASP* 5.2 0.4 - - - -
232A ILE* 4.4 3.7 - - - +
233A GLY* 3.5 13.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A HIS 3.2 4.0 + - - +
75A ILE* 3.1 8.6 + - + +
77A SER* 1.3 77.2 - - - +
79A LEU* 1.3 68.3 + - + +
81A LEU* 3.0 9.0 + - - +
82A LEU* 2.9 35.3 + - + +
103A GLY* 3.6 29.4 - - - +
106A PHE* 4.2 13.7 - - + -
107A TYR* 3.9 30.7 - - + +
110A ILE* 4.5 7.2 - - + -
175A VAL* 4.8 1.8 - - + -
229A PHE* 3.7 22.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A ILE* 5.9 3.6 - - + -
37A ILE* 3.9 26.7 - - + -
75A ILE* 3.0 23.5 + - + +
76A LEU* 3.5 17.7 - - + +
78A VAL* 1.3 76.7 - - + +
80A HIS* 1.3 64.1 + - - +
82A LEU 3.1 1.2 + - - -
83A GLU 2.8 19.6 + - - -
84A ILE* 3.2 43.6 + - + -
87A VAL* 4.7 5.8 - - + -
89A ILE* 4.0 18.2 - - + -
110A ILE* 4.9 19.5 - - + -
236A TYR* 4.1 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A LEU 2.8 13.8 + - - +
77A SER* 3.1 10.5 + - - +
79A LEU* 1.3 77.5 - - - +
81A LEU* 1.3 62.9 + - + +
83A GLU* 3.1 14.9 + - - +
147A LEU* 4.0 16.4 - - + +
232A ILE* 2.8 33.2 + - + +
235A LEU* 4.6 2.9 - - + -
236A TYR* 3.0 46.2 - + + +
241A PRO* 3.3 8.9 - - + +
242A VAL* 3.0 44.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A SER* 3.3 9.9 - - - +
78A VAL* 3.0 6.4 + - - +
80A HIS* 1.3 78.9 - - + +
82A LEU* 1.3 64.9 + - + +
83A GLU* 3.4 8.8 + - - +
107A TYR* 5.2 6.7 - - + -
147A LEU* 5.8 2.9 - - + -
166A PHE* 4.5 5.8 - - + -
171A GLU* 3.9 39.2 - - + +
174A ILE* 4.3 6.5 - - + -
175A VAL* 3.6 30.5 - - + -
229A PHE* 3.8 20.9 - - + -
232A ILE* 4.0 28.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A LYS* 3.7 9.2 + - - -
78A VAL* 2.9 35.6 + - + +
81A LEU* 1.3 74.7 - - - +
83A GLU* 1.3 78.5 + - - +
84A ILE* 3.5 20.6 - - + +
107A TYR* 4.0 31.6 - - + +
110A ILE* 4.0 17.9 - - + -
111A ARG* 4.3 17.3 - - + +
114A ILE* 3.3 28.4 - - + +
----------------------------------------------------------
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