Contacts of the helix formed by residues 75 - 92 (chain C) in PDB entry 1XK4
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 75 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B ASP* 5.2 0.3 - - - +
19C PHE* 3.8 2.2 - - - -
30C ASP 4.4 1.1 - - - -
31C THR* 4.2 17.6 - - - +
73C GLN 4.0 1.0 - - - -
74C LEU* 1.3 75.5 - - - +
76C PHE* 1.3 66.4 + - - +
77C GLU* 3.5 15.9 + - - +
78C GLU* 3.0 35.9 + - - +
79C PHE* 2.9 21.3 + - - +
3501C CA 4.5 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 76 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A GLY* 3.3 22.9 - - - -
80A VAL* 4.3 7.9 - - + -
83A HIS* 3.5 44.5 - + + +
12C ILE* 5.9 0.2 - - + -
15C ILE* 3.7 31.6 - - + -
16C ILE* 3.8 26.2 - - + -
19C PHE* 3.5 39.0 - + + -
30C ASP 4.4 2.2 + - - -
75C SER* 1.3 76.3 - - - +
77C GLU* 1.3 62.2 + - - +
79C PHE* 3.1 6.6 + + - +
80C ILE* 2.8 54.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 77 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A VAL* 3.8 23.1 - - + +
83A HIS* 4.9 8.8 + - - -
84A LYS* 5.3 6.8 - - - +
61B ASN* 2.8 44.5 + - - +
62B THR* 3.8 19.6 + - - +
63B ASP* 4.1 7.6 - - + -
75C SER* 3.2 13.5 - - - +
76C PHE* 1.3 86.2 + - - +
78C GLU* 1.3 60.5 + - - +
80C ILE* 3.2 19.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 78 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B ASN* 4.1 5.6 - - - +
63B ASP* 4.1 10.6 - - + +
66C LEU* 3.4 36.4 - - - +
67C ASP* 4.0 0.4 - - - -
68C THR* 3.0 25.4 + - - +
69C ASN* 3.0 14.9 + - - +
73C GLN 3.0 5.2 - - - +
74C LEU* 3.1 8.0 - - + +
75C SER* 3.0 33.3 + - - +
77C GLU* 1.3 76.0 - - - +
79C PHE* 1.3 62.4 + - - +
81C MET* 3.4 18.4 + - - +
3501C CA 2.4 31.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 79 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A LEU* 5.0 2.7 - - + -
15C ILE* 4.2 12.3 - - + -
18C THR* 5.9 0.9 - - + -
19C PHE* 3.7 29.2 - + + -
32C LEU* 3.7 15.7 - - + -
37C PHE* 4.4 18.8 - + - -
40C LEU* 3.7 38.4 - - + -
66C LEU* 5.2 0.2 - - - -
74C LEU* 4.5 11.2 - - + +
75C SER 2.9 16.3 + - - +
76C PHE* 3.6 13.0 - + - +
78C GLU* 1.3 73.3 - - - +
80C ILE* 1.3 66.3 + - - +
81C MET 3.1 2.5 - - - -
82C LEU* 2.9 27.7 + - + +
83C MET* 3.3 45.9 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 80 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A VAL* 4.6 6.5 - - + +
76A ILE* 3.9 38.8 - - + +
79A GLY* 3.9 19.1 - - - -
80A VAL* 4.1 11.4 - - + -
61B ASN* 4.1 1.6 - - + -
12C ILE* 6.1 1.3 - - + -
15C ILE* 4.8 12.6 - - + -
76C PHE* 2.8 44.4 + - + +
77C GLU 3.2 18.6 - - - +
79C PHE* 1.3 78.6 - - - +
81C MET* 1.3 57.5 + - - +
83C MET* 3.2 13.1 + - + +
84C ALA* 2.9 27.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 81 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A ILE* 4.2 19.1 - - + -
60B ILE* 4.9 1.8 - - + -
61B ASN* 3.4 44.4 - - + +
67B ASN* 3.4 28.7 - - - +
69B GLN* 3.8 23.6 - - - -
70B GLU* 3.7 16.8 - - + +
66C LEU* 4.4 4.9 - - + -
78C GLU 3.4 13.5 - - - +
79C PHE 3.0 0.6 + - - -
80C ILE* 1.3 79.8 - - - +
82C LEU* 1.3 57.2 + - - +
84C ALA* 3.3 4.8 + - - +
85C ARG* 3.0 47.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 82 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C PHE* 3.8 34.1 - - + -
41C VAL* 4.9 1.6 - - + -
45C LEU* 4.4 11.4 - - + -
49C LEU* 5.0 6.1 - - + -
62C ILE* 4.5 13.0 - - + -
66C LEU* 3.8 26.5 - - + +
79C PHE* 2.9 15.3 + - + +
81C MET* 1.3 75.9 - - - +
83C MET* 1.3 84.1 + - + +
85C ARG* 3.3 11.6 + - + +
86C LEU* 3.0 42.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 83 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A LEU* 4.0 27.6 - - + -
9A LEU* 4.0 18.5 - - + +
15C ILE* 4.1 17.9 - - + -
45C LEU* 3.9 27.6 - - + -
79C PHE* 3.6 48.7 - - + +
80C ILE* 3.2 15.1 + - + +
82C LEU* 1.3 88.6 - - + +
84C ALA* 1.3 62.9 + - - +
86C LEU* 3.3 8.6 + - + +
87C THR* 2.9 29.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 84 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A LEU* 3.7 20.2 - - + +
75A VAL* 6.2 1.6 - - + -
76A ILE* 3.7 34.5 - - + -
69B GLN* 5.7 2.9 - - - +
80C ILE* 2.9 13.4 + - + +
81C MET* 3.8 6.5 - - - +
83C MET* 1.3 77.6 - - - +
85C ARG* 1.3 61.5 + - - +
87C THR* 3.4 7.0 + - - -
88C TRP* 3.0 24.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 85 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B ASN* 3.2 33.3 - - - +
69B GLN* 2.7 29.1 + - - +
65C ASP* 5.2 12.3 + - - +
66C LEU* 3.6 23.6 - - - +
81C MET* 3.0 30.6 + - - +
82C LEU* 3.3 12.9 + - + +
84C ALA* 1.3 75.0 - - - +
86C LEU* 1.3 62.7 + - + +
88C TRP* 3.4 9.0 + - - +
89C ALA* 2.9 27.7 + - - +
88D TRP* 4.5 19.2 - - + -
92D GLU* 5.9 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 86 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A LEU* 3.9 13.5 - - + -
45C LEU* 3.5 42.4 - - + -
48C PHE* 4.3 19.0 - - + +
49C LEU* 4.2 24.0 - - + -
82C LEU* 3.0 35.5 + - + +
83C MET* 3.8 11.4 - - + +
85C ARG* 1.3 77.6 - - + +
87C THR* 1.3 60.2 + - - +
89C ALA* 3.4 8.9 + - + +
90C SER* 2.9 30.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 87 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A LEU* 3.5 42.5 - - - +
12A ILE* 4.2 11.0 - - + +
13A ILE* 3.8 6.1 - - + +
68A PHE* 3.6 25.4 - - + -
72A LEU* 4.2 10.9 - - + +
83C MET 2.9 21.2 + - - -
84C ALA* 3.6 6.1 - - - -
86C LEU* 1.3 73.3 - - - +
88C TRP* 1.3 61.4 + - - +
90C SER* 3.2 7.5 + - - -
91C HIS* 2.8 30.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 88 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A PHE* 3.7 26.9 - + + -
69A GLN* 3.6 54.5 - - + -
72A LEU* 4.1 7.6 - - + -
84C ALA 3.0 17.1 + - - +
85C ARG* 3.6 8.7 - - - +
87C THR* 1.3 77.2 - - - +
89C ALA* 1.3 60.7 + - + +
91C HIS* 3.1 17.6 + + - +
92C GLU* 2.8 63.3 + - + +
85D ARG* 4.3 19.7 - - + -
88D TRP* 4.7 22.7 - + - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 89 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C ARG 2.9 17.6 + - - +
86C LEU* 3.7 12.6 - - + +
87C THR 3.3 0.2 - - - -
88C TRP* 1.3 80.5 - - + +
90C SER* 1.3 62.3 + - - +
92C GLU* 3.4 20.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 90 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A LEU* 5.9 0.2 - - - -
10A ASN* 2.6 30.3 + - - -
13A ILE* 4.1 6.7 - - - +
48C PHE* 4.1 16.9 - - - -
86C LEU 2.9 17.4 + - - -
87C THR* 3.6 6.7 - - - -
89C ALA* 1.3 73.2 - - - +
91C HIS* 1.3 66.0 + - - +
92C GLU 3.4 4.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 91 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ILE* 3.6 31.5 - - + +
16A TYR* 5.9 0.8 - - - -
17A HIS* 4.7 12.1 + + - -
27A HIS* 5.2 13.7 + + - -
68A PHE* 3.7 43.0 - + + +
87C THR 2.8 16.9 + - - +
88C TRP* 3.2 19.2 - + - +
90C SER* 1.3 72.6 - - - +
92C GLU* 1.3 90.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 92 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88C TRP* 2.8 55.5 + - + +
89C ALA* 3.8 17.0 - - - +
90C SER 3.3 4.8 - - - -
91C HIS* 1.3 112.8 + - - +
85D ARG* 6.1 0.5 - - - -
----------------------------------------------------------
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