Contacts of the helix formed by residues 108 - 132 (chain Z) in PDB entry 5K0Y
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 ASP 108 (chain Z).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
930A G 5.5 0.3 + - - -
931A G 3.2 25.5 + - - +
932A G 3.0 28.6 - - - +
101Z HIS* 3.1 26.9 + - + +
102Z LEU* 4.2 1.4 - - - +
105Z ASN* 3.9 21.2 + - + +
106Z ARG 3.5 2.4 - - - -
107Z LYS* 1.4 73.4 - - - +
109Z LYS* 1.4 60.3 + - - +
110Z ASP* 3.4 4.3 - - - +
111Z ALA* 3.0 42.8 + - + +
112Z LYS* 3.3 14.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 109 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
931A G 4.4 2.6 + - - +
992A A 5.4 2.4 + - - +
993A A 6.2 1.6 - - - +
1028A C 3.9 38.4 + - - +
1029A G 3.7 34.2 + - - +
1073A A 5.8 1.8 + - - -
106Z ARG 5.4 1.6 + - - -
107Z LYS* 3.2 14.9 + - - +
108Z ASP* 1.4 68.2 + - - +
110Z ASP* 1.4 64.2 + - - +
112Z LYS* 3.3 28.2 + - - +
113Z PHE* 3.2 22.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 110 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
930A G 3.2 31.3 + - - +
931A G 3.7 24.2 + - - +
991A G 4.3 10.4 + - - +
992A A 6.0 1.6 - - - +
1005A A 4.7 0.3 + - - -
108Z ASP* 3.4 9.9 - - - +
109Z LYS* 1.4 77.2 - - - +
111Z ALA* 1.4 56.3 + - - +
113Z PHE* 3.3 8.0 + - - +
114Z ARG* 2.9 63.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 111 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98Z VAL* 3.5 13.6 - - + +
101Z HIS* 3.9 21.5 - - + -
102Z LEU* 4.2 15.8 - - + +
108Z ASP* 3.0 32.2 + - + +
109Z LYS 3.3 0.4 - - - -
110Z ASP* 1.4 76.1 + - - +
112Z LYS* 1.4 55.3 + - - +
114Z ARG* 3.9 6.2 - - - +
115Z LEU* 3.0 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 112 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1027A A 4.7 9.4 - - - +
1028A C 4.2 19.5 - - - +
102Z LEU* 3.7 24.8 - - + +
106Z ARG* 3.2 30.9 + - - +
107Z LYS 3.9 1.6 - - - -
108Z ASP 3.3 26.7 + - - +
109Z LYS* 3.3 30.0 + - + +
111Z ALA* 1.4 73.9 - - - +
113Z PHE* 1.4 63.1 + - - +
115Z LEU* 3.5 6.4 + - - +
116Z ILE* 3.3 31.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 113 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
665A U 3.3 28.3 - - - -
666A C 5.3 1.8 - - - -
992A A 3.4 71.8 - + - +
1027A A 3.7 38.9 + + + +
1028A C 4.9 0.9 - - - +
109Z LYS 3.2 8.7 + - - +
110Z ASP* 3.5 10.8 - - - +
112Z LYS* 1.4 79.1 - - - +
114Z ARG* 1.4 78.6 + - - +
116Z ILE* 3.5 7.8 + - + +
117Z LEU* 3.3 25.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 114 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
930A G 5.0 5.3 + - - +
991A G 3.3 28.9 + - - -
992A A 3.5 21.9 + - - -
1005A A 3.3 25.3 + - - +
1006A G 3.5 39.7 + - - -
98Z VAL* 4.8 6.3 - - + -
110Z ASP* 2.9 50.7 + - - +
111Z ALA* 3.9 7.2 - - - +
113Z PHE* 1.4 93.5 - - - +
115Z LEU* 1.4 65.3 + - - +
117Z LEU* 3.3 17.0 + - - +
118Z ILE* 3.1 33.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 115 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95Z ALA* 3.4 34.1 - - + +
98Z VAL* 3.8 18.1 - - + +
99Z ARG* 4.1 27.8 - - + +
102Z LEU* 3.9 24.9 - - + -
111Z ALA 3.0 19.6 + - - +
112Z LYS* 3.7 6.5 - - - +
113Z PHE 3.4 0.2 - - - -
114Z ARG* 1.4 74.0 - - - +
116Z ILE* 1.4 58.2 + - + +
118Z ILE* 3.3 6.3 + - - +
119Z GLU* 2.9 48.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 116 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
666A C 3.8 23.8 - - + +
1026A A 5.3 6.3 - - + +
1027A A 3.4 46.4 - - - +
112Z LYS* 3.3 17.0 + - + +
113Z PHE* 3.5 9.2 - - + +
115Z LEU* 1.4 76.9 - - + +
117Z LEU* 1.4 56.7 + - - +
119Z GLU* 3.3 14.7 + - - +
120Z SER* 3.0 35.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 117 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
666A C 4.1 37.9 - - - +
667A G 5.1 1.3 - - - +
1006A G 6.1 4.0 - - - -
4Z MET 4.5 1.6 - - - +
5Z HIS* 4.0 32.1 - - - +
6Z ALA* 4.8 6.5 - - - -
7Z PRO* 4.9 8.1 - - + -
113Z PHE* 3.3 16.5 + - + +
114Z ARG* 3.3 24.0 + - - +
116Z ILE* 1.4 77.7 - - - +
118Z ILE* 1.4 63.7 + - + +
120Z SER* 3.3 7.0 + - - -
121Z ARG* 3.1 33.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 118 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1005A A 4.3 13.0 - - - +
1006A G 4.5 4.5 - - - +
91Z LEU* 3.6 26.9 - - + +
94Z LYS* 4.1 15.0 - - + +
95Z ALA* 3.9 16.8 - - + +
98Z VAL* 3.7 31.0 - - + -
114Z ARG* 3.1 20.5 + - + +
115Z LEU* 3.7 5.6 - - - +
117Z LEU* 1.4 74.7 - - + +
119Z GLU* 1.4 56.5 + - - +
121Z ARG* 3.2 33.0 + - - +
122Z ILE* 3.0 27.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 119 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95Z ALA* 4.6 2.5 - - + -
99Z ARG* 3.2 25.3 + - - +
115Z LEU* 2.9 41.3 + - + +
116Z ILE* 3.6 13.4 - - - +
118Z ILE* 1.4 74.1 - - - +
120Z SER* 1.4 60.3 + - - +
122Z ILE* 3.3 11.5 + - - +
123Z HIS* 2.9 41.3 + - + +
141Z TYR* 4.0 19.6 - - + +
143Z SER* 5.0 2.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 120 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
666A C 3.3 17.6 + - - -
667A G 3.7 34.0 - - - -
116Z ILE* 3.0 17.7 + - - +
117Z LEU 3.3 8.9 + - - -
119Z GLU* 1.4 73.7 - - - +
121Z ARG* 1.4 61.6 + - - +
123Z HIS* 3.2 13.2 + - - +
124Z ARG* 3.1 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 121 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
667A G 5.4 0.4 - - - -
920A G 3.6 20.9 - - - +
921A G 3.1 19.1 + - - -
1006A G 4.1 7.9 + - - -
1007A A 5.2 4.2 + - - -
5Z HIS* 3.2 55.7 + - + -
6Z ALA* 5.0 4.9 - - - +
91Z LEU* 3.3 29.7 - - + +
94Z LYS* 3.7 18.4 - - - +
117Z LEU* 3.1 27.3 + - + +
118Z ILE* 3.3 35.5 - - - +
120Z SER* 1.4 74.0 - - - +
122Z ILE* 1.4 62.2 + - - +
124Z ARG* 3.7 1.4 + - - +
125Z LEU* 3.3 33.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 122 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88Z LEU* 3.8 15.8 - - + +
91Z LEU* 3.7 36.3 - - + +
92Z ILE* 3.8 9.2 - - + +
95Z ALA* 3.7 29.8 - - + -
118Z ILE 3.0 18.8 + - - +
119Z GLU* 3.3 10.5 + - - +
121Z ARG* 1.4 73.1 - - - +
123Z HIS* 1.4 58.0 + - - +
125Z LEU* 3.4 3.5 + - - +
126Z ALA* 2.8 30.3 + - + +
139Z TRP* 5.3 1.1 - - + -
141Z TYR* 3.8 46.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 123 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119Z GLU* 2.9 32.5 + - + +
120Z SER* 3.2 12.3 + - - +
122Z ILE* 1.4 75.8 - - - +
124Z ARG* 1.4 57.9 + - + +
126Z ALA* 3.7 5.3 - - - +
127Z ARG* 2.9 30.4 + - - +
140Z LYS* 3.5 32.1 + - - +
141Z TYR* 3.5 41.2 - + + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 124 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
667A G 3.4 41.5 + - - +
668A U 3.6 31.2 + - - +
1018A U 4.4 2.0 + - - +
1019A A 3.1 34.2 + - - +
1020A A 3.2 26.5 + - - -
1021A U 4.5 11.5 + - - -
1022A C 5.6 0.4 - - - +
4Z MET* 4.5 8.7 - - - +
5Z HIS* 3.4 28.0 + - - +
120Z SER 3.1 13.9 + - - +
121Z ARG 4.1 4.0 - - - +
122Z ILE 3.4 0.2 - - - -
123Z HIS* 1.4 73.4 - - + +
125Z LEU* 1.4 64.9 + - + +
127Z ARG* 3.6 25.1 + - - +
128Z TYR* 3.3 21.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 125 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
919A G 4.9 9.4 - - - +
920A G 3.9 22.7 - - - +
1018A U 3.5 26.7 - - + +
1019A A 3.7 12.6 - - - +
5Z HIS* 5.3 1.8 - - + -
87Z ASP* 3.6 20.2 - - - +
88Z LEU* 4.2 12.3 - - + -
91Z LEU* 4.1 14.8 - - + -
121Z ARG* 3.3 26.7 + - + +
122Z ILE 3.7 3.6 - - - +
124Z ARG* 1.4 77.9 - - + +
126Z ALA* 1.4 57.1 + - - +
128Z TYR* 3.4 7.2 + - + +
129Z TYR* 3.0 49.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 126 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88Z LEU* 4.2 8.0 - - + +
122Z ILE* 2.8 22.4 + - + +
123Z HIS* 3.7 7.2 - - - +
125Z LEU* 1.4 72.3 - - - +
127Z ARG* 1.4 55.9 + - - +
129Z TYR* 3.1 6.0 + - - +
130Z LYS* 2.8 57.1 + - - +
135Z LEU* 3.6 15.9 - - + +
139Z TRP* 4.4 7.4 - - + -
140Z LYS* 5.4 2.9 - - + +
141Z TYR* 5.9 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 127 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
668A U 3.4 48.1 + - - -
669A A 4.3 9.0 + - - -
1019A A 4.3 4.8 + - - -
123Z HIS 2.9 17.7 + - - +
124Z ARG* 3.6 36.3 + - - +
126Z ALA* 1.4 73.4 - - - +
128Z TYR* 1.4 60.9 + - - +
130Z LYS* 3.4 13.0 + - - +
131Z THR* 3.1 33.4 + - + +
140Z LYS* 5.8 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 128 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1015A C 5.3 1.3 - - - -
1016A A 3.5 21.8 - - - -
1017A U 3.3 33.8 + - - -
1018A U 3.3 59.2 - + - +
124Z ARG 3.3 9.7 + - - +
125Z LEU* 3.4 14.1 - - + +
126Z ALA 3.2 0.6 - - - -
127Z ARG* 1.4 78.5 - - - +
129Z TYR* 1.4 91.6 + + - +
131Z THR* 2.9 21.5 + - - -
132Z LYS* 3.6 36.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 129 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1015A C 3.8 17.4 + - - -
1016A A 6.2 0.7 - - - -
1018A U 5.8 0.9 - - - -
85Z PRO* 3.7 29.4 - - + +
87Z ASP* 3.1 37.1 + - - -
88Z LEU* 4.3 14.8 - - + -
125Z LEU* 3.0 35.3 + - + +
126Z ALA* 3.1 10.1 + - - +
128Z TYR* 1.4 99.4 - + - +
130Z LYS* 1.4 62.4 + - - +
132Z LYS 3.4 1.6 + - - -
133Z ARG 3.2 4.7 + - - -
134Z VAL* 2.9 50.5 + - + +
135Z LEU* 3.7 19.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 130 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126Z ALA* 2.8 31.0 + - - +
127Z ARG* 3.6 10.5 - - - +
128Z TYR 3.4 0.2 - - - -
129Z TYR* 1.4 76.4 - - - +
131Z THR* 1.4 64.3 + - + +
132Z LYS 3.2 1.0 + - - -
133Z ARG* 3.3 12.5 + - - +
135Z LEU* 3.7 19.1 - - + +
136Z PRO 3.9 15.5 - - - +
137Z PRO* 4.2 25.9 - - + +
139Z TRP* 3.2 52.9 + - - -
140Z LYS* 4.3 20.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 131 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127Z ARG* 3.1 20.4 + - + +
128Z TYR* 2.9 25.3 + - - -
130Z LYS* 1.4 78.8 - - + +
132Z LYS* 1.4 65.0 + - - +
133Z ARG* 3.4 7.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 132 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1017A U 3.3 41.1 + - - +
1018A U 3.9 14.4 + - - -
128Z TYR* 3.6 38.7 + - + +
129Z TYR* 3.4 4.4 + - + +
130Z LYS 3.2 0.6 - - - -
131Z THR* 1.4 82.9 + - - +
133Z ARG* 1.4 73.3 + - - +
134Z VAL* 3.4 15.5 - - + +
----------------------------------------------------------
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