Contacts of the helix formed by residues 134 - 157 (chain G) in PDB entry 5XS0
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 134 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103G PHE* 4.1 0.7 - - - -
132G LEU* 3.4 0.9 - - - +
133G LYS* 1.3 71.9 - - - +
135G LYS* 1.3 64.3 + - - +
136G ALA* 3.5 3.8 + - - +
137G LEU* 3.2 37.4 + - - +
138G SER* 3.0 24.8 + - - -
130H GLU* 3.7 20.0 + - - -
10Y C 2.6 25.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 135 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96G VAL* 4.0 17.7 - - + -
103G PHE* 3.6 52.0 - - + -
133G LYS 3.6 1.0 + - - -
134G SER* 1.3 72.5 + - - +
136G ALA* 1.3 57.4 + - - +
138G SER* 3.2 4.0 + - - -
139G LEU* 2.9 36.2 + - + +
95H PHE* 3.5 39.1 - - + +
97H ASP* 2.8 34.0 + - - -
130H GLU* 5.3 0.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 136 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134G SER* 3.2 7.0 + - - +
135G LYS* 1.3 78.9 - - - +
137G LEU* 1.3 57.9 + - + +
139G LEU 3.4 0.2 + - - -
140G GLU* 2.9 31.3 + - - +
95H PHE* 3.6 26.4 - - + -
105H VAL 4.8 1.1 - - - +
126H TYR* 3.6 9.1 - - + -
128H VAL* 3.6 37.9 - - + -
130H GLU* 4.2 6.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 137 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132G LEU* 4.3 15.7 - - + +
134G SER* 3.2 22.4 + - - +
136G ALA* 1.3 81.3 - - + +
138G SER* 1.3 60.7 + - - +
140G GLU* 3.9 16.4 - - - +
141G LYS* 2.9 33.1 + - - +
128H VAL* 5.3 7.2 - - + -
130H GLU* 5.3 4.9 - - - +
10Y C 3.3 43.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 138 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103G PHE* 3.7 15.8 + - - +
105G VAL* 3.8 22.0 - - - -
129G SER* 3.2 28.4 + - - -
132G LEU* 3.5 13.8 - - - +
134G SER 3.0 15.2 + - - -
135G LYS 3.2 9.2 + - - -
137G LEU* 1.3 76.8 - - - +
139G LEU* 1.3 58.2 + - - +
142G ALA* 2.9 32.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 139 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93G VAL* 4.3 12.1 - - + -
96G VAL* 3.8 28.5 - - + -
105G VAL* 3.9 14.4 - - + -
107G VAL* 4.7 1.1 - - + -
135G LYS* 2.9 22.1 + - + +
136G ALA 3.9 0.4 - - - +
138G SER* 1.3 75.8 - - - +
140G GLU* 1.3 63.1 + - - +
142G ALA* 3.9 0.3 - - - +
143G ARG* 2.9 39.2 + - + +
94H ASP* 3.6 24.9 - - + +
95H PHE* 3.6 20.0 - - + -
126H TYR* 3.3 28.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 140 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136G ALA 2.9 17.2 + - - +
137G LEU* 3.9 20.1 - - - +
139G LEU* 1.3 75.9 - - - +
141G LYS* 1.3 65.4 + - - +
143G ARG* 4.0 0.8 - - - +
144G LYS* 2.7 66.7 + - + +
126H TYR* 3.6 34.0 - - + +
128H VAL* 4.6 8.7 - - - +
149H ASP* 4.7 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 141 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128G VAL 3.1 23.5 + - - +
129G SER* 3.8 16.1 - - - +
132G LEU* 4.7 11.4 - - + -
137G LEU 2.9 18.6 + - - +
138G SER 3.8 2.7 - - - +
140G GLU* 1.3 77.1 - - - +
142G ALA* 1.3 57.8 + - - +
144G LYS* 4.2 2.4 - - - +
145G GLU* 2.4 71.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 142 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105G VAL* 3.8 15.5 - - + +
107G VAL* 3.7 20.4 - - + -
127G GLY* 3.2 35.2 - - - +
128G VAL 4.1 5.4 - - - +
129G SER* 4.7 0.2 - - - -
138G SER 2.9 17.9 + - - +
139G LEU 3.9 1.1 - - - +
141G LYS* 1.3 77.8 - - - +
143G ARG* 1.3 56.8 + - - +
146G ALA* 2.9 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 143 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91G GLN* 2.4 58.6 + - - +
93G VAL* 3.3 29.3 - - + +
107G VAL* 4.0 13.2 - - + -
139G LEU* 2.9 24.2 + - - +
140G GLU* 4.0 2.5 - - - +
142G ALA* 1.3 76.0 - - - +
144G LYS* 1.3 63.5 + - + +
146G ALA 3.2 1.2 + - - -
147G VAL* 3.0 21.7 + - - +
90H GLN* 6.2 0.2 - - - +
92H ASN* 4.2 10.7 - - - +
94H ASP* 2.7 38.2 + - - -
108H CYS* 3.4 38.4 - - - +
110H PHE* 4.1 5.7 - - - -
124H VAL* 4.5 10.8 - - + -
126H TYR* 4.0 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 144 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140G GLU* 2.7 55.2 + - + +
141G LYS* 4.2 2.9 - - - +
143G ARG* 1.3 75.8 - - + +
145G GLU* 1.3 62.5 + - + +
147G VAL* 3.3 4.5 + - - -
148G THR* 3.0 28.0 + - - -
124H VAL* 4.2 11.0 - - + +
126H TYR* 4.2 10.7 - - + +
149H ASP* 2.8 33.2 + - - -
153H ARG* 3.5 44.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 145 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126G TYR 3.8 3.7 - - - +
127G GLY* 3.9 8.7 - - - -
128G VAL* 3.5 17.1 + - - +
141G LYS* 2.4 64.2 + - + +
144G LYS* 1.3 76.9 - - - +
146G ALA* 1.3 58.2 + - - +
148G THR* 4.0 4.2 - - - +
149G ASP* 2.9 34.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 146 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91G GLN* 4.2 0.2 - - - +
107G VAL* 3.3 31.0 - - + +
109G ALA* 3.8 18.8 - - + +
125G GLY* 3.5 10.2 - - - +
126G TYR 3.4 13.2 - - - +
127G GLY* 3.5 1.3 - - - +
142G ALA 2.9 19.8 + - - +
143G ARG 3.2 4.9 + - - +
145G GLU* 1.3 76.1 - - - +
147G VAL* 1.3 57.7 + - - +
150G GLY* 2.9 25.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 147 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86G HIS* 5.4 4.7 - - + +
88G ILE* 3.7 22.9 - - + -
91G GLN* 3.6 12.1 - - - +
109G ALA* 4.0 11.7 - - + -
111G VAL* 3.6 8.6 - - + +
143G ARG 3.0 16.3 + - - +
144G LYS* 3.8 4.5 - - - +
146G ALA* 1.3 76.2 - - - +
148G THR* 1.3 65.5 + - - +
150G GLY 3.3 1.2 + - - -
151G LEU* 3.0 21.9 + - + +
122H GLU 4.8 2.0 - - - +
123H ASP* 3.5 33.2 - - - +
124H VAL* 3.5 28.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 148 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68G GLY* 4.6 17.5 - - - -
144G LYS 3.0 17.0 + - - -
145G GLU* 4.0 4.7 - - - -
147G VAL* 1.3 78.3 - - - +
149G ASP* 1.3 58.7 + - - +
151G LEU* 3.2 10.9 + - + +
152G LYS* 2.9 42.4 + - + +
123H ASP* 5.1 2.9 + - - -
153H ARG* 3.6 15.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 149 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144F LYS* 2.9 37.3 + - - -
125G GLY* 3.6 0.3 - - - -
126G TYR 3.4 19.2 + - - +
145G GLU 2.9 18.6 + - - +
146G ALA 3.9 1.6 - - - +
148G THR* 1.3 77.0 - - - +
150G GLY* 1.3 58.1 + - - +
152G LYS* 3.2 23.2 + - - +
153G ARG* 2.9 34.8 + - - +
156G ARG* 4.2 10.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 150 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111G VAL* 3.6 17.0 - - - +
123G ASP* 4.6 2.8 - - - +
124G VAL 4.0 4.5 - - - -
125G GLY* 3.3 24.3 - - - -
146G ALA 2.9 14.4 + - - -
147G VAL 3.3 2.2 + - - -
149G ASP* 1.3 75.4 - - - +
151G LEU* 1.3 58.2 + - - +
153G ARG* 3.4 1.3 + - - +
154G ALA* 2.9 30.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 151 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71G VAL* 6.0 0.7 - - + -
72G ILE* 4.6 18.4 - - + -
84G TRP* 3.8 14.1 - - + -
86G HIS* 3.7 39.0 - - + +
111G VAL* 3.7 11.3 - - + +
113G VAL* 3.6 24.0 - - + -
147G VAL* 3.0 14.5 + - + +
148G THR* 3.2 13.2 + - + +
150G GLY* 1.3 77.2 - - - +
152G LYS* 1.3 60.1 + - + +
154G ALA* 3.3 0.9 + - - +
155G LEU* 2.9 42.5 + - + +
123H ASP* 5.7 2.5 - - - +
157H SER* 4.9 3.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 152 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65G TYR* 4.8 14.8 - - - +
66G ILE* 3.6 27.0 + - + +
67G GLU* 5.6 0.2 - - - +
68G GLY* 4.5 11.9 - - - +
71G VAL* 4.2 27.3 - - + +
148G THR* 2.9 23.4 + - + +
149G ASP* 3.2 32.2 + - - +
151G LEU* 1.3 77.8 - - + +
153G ARG* 1.3 56.8 + - - +
155G LEU* 3.3 6.0 + - - +
156G ARG* 2.9 46.1 + - - +
162G LEU 4.9 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 153 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144F LYS* 3.4 48.1 + - - +
147F VAL* 5.2 0.8 - - - +
148F THR* 3.7 19.8 + - - -
123G ASP* 2.9 34.7 + - + +
124G VAL 2.8 26.0 + - - +
149G ASP* 2.9 34.4 + - - +
150G GLY 4.0 2.7 - - - +
152G LYS* 1.3 76.0 - - - +
154G ALA* 1.3 61.6 + - - +
156G ARG* 3.3 51.4 + - - +
157G SER* 3.7 12.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 154 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86F HIS* 6.0 0.2 - - - -
111G VAL 3.7 14.8 - - - +
113G VAL* 3.6 22.0 - - + -
121G HIS* 3.6 36.1 - - - +
122G GLU 4.9 0.2 - - - -
123G ASP* 3.8 10.9 - - - +
150G GLY 2.9 18.1 + - - +
151G LEU* 3.8 1.8 - - - +
153G ARG* 1.3 78.1 - - - +
155G LEU* 1.3 62.1 + - - +
157G SER* 3.5 10.1 + - - -
158G PHE* 4.3 2.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 155 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71G VAL* 3.8 30.7 - - + +
72G ILE* 5.4 0.7 - - + +
75G ALA* 4.1 20.2 - - + -
79G PHE* 4.9 3.1 - - + -
84G TRP* 4.1 15.0 - - + -
113G VAL* 3.6 31.2 - - + -
151G LEU* 2.9 36.2 + - + +
152G LYS 3.9 2.9 - - - +
154G ALA* 1.3 72.1 - - - +
156G ARG* 1.3 65.5 + - - +
157G SER 3.1 3.7 + - - -
158G PHE* 3.2 27.1 + - + -
162G LEU* 3.5 29.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 156 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72F ILE* 5.0 4.3 - - + -
144F LYS* 5.9 0.4 - - - +
149G ASP* 4.2 10.3 + - - -
152G LYS* 2.9 32.3 + - + +
153G ARG* 3.3 55.3 - - - +
154G ALA 3.3 0.2 - - - -
155G LEU* 1.3 77.6 - - - +
157G SER* 1.3 56.8 + - - +
158G PHE 3.0 6.3 + - - -
159G GLY 3.3 17.3 + - - +
162G LEU 3.9 8.7 + - - +
163G GLY* 3.4 34.3 - - - +
164G ASN* 3.6 16.2 - - - +
166G ILE* 4.5 10.8 - - - +
167G LEU* 4.4 28.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 157 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72F ILE* 3.4 30.8 - - - +
76F ASN* 3.2 15.8 + - - +
84F TRP* 3.7 12.8 - - - -
86F HIS* 3.9 13.3 + - - -
151F LEU* 5.0 2.1 - - - +
121G HIS* 3.6 28.4 + - - -
123G ASP* 4.8 3.6 + - - -
153G ARG 3.7 12.5 + - - -
154G ALA* 3.8 8.8 + - - -
155G LEU 3.1 2.2 - - - -
156G ARG* 1.3 75.4 - - - +
158G PHE* 1.3 58.3 + - - +
159G GLY 3.4 0.4 - - - -
----------------------------------------------------------
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