Contacts of the helix formed by residues 130 - 152 (chain G) in PDB entry 1SMK
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 ARG 130 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129G THR* 1.3 99.5 - - + +
131G ASP* 1.3 61.9 + - + +
132G ASP 3.5 0.4 - - - -
133G LEU* 3.8 13.5 - - - +
134G PHE* 3.7 16.1 + - - +
163G PRO* 6.2 0.5 - - - +
255G THR* 5.1 14.3 - - - +
349G LYS* 4.7 5.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 131 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129G THR 3.3 1.8 + - - -
130G ARG* 1.3 78.3 - - + +
132G ASP* 1.3 68.5 + - - +
133G LEU 3.1 2.0 - - - -
134G PHE* 3.3 15.2 + - - +
135G LYS* 3.4 24.0 + - - +
349G LYS* 3.3 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 132 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124G ARG* 3.6 20.8 + - - +
128G MET* 3.0 48.2 - - + +
129G THR 3.4 15.8 + - - +
130G ARG 3.5 0.2 - - - -
131G ASP* 1.3 79.2 - - - +
133G LEU* 1.3 62.3 + - - +
135G LYS* 3.7 9.7 + - - +
136G ILE* 3.4 26.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 133 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122G VAL* 3.3 27.1 - - + +
123G PRO 4.6 5.8 - - - +
124G ARG* 3.8 24.8 - - + +
129G THR* 4.8 5.8 - - + +
130G ARG* 3.8 23.1 - - - +
131G ASP 3.1 0.4 - - - -
132G ASP* 1.3 78.6 - - - +
134G PHE* 1.3 66.1 + - - +
136G ILE* 3.0 14.4 + - + +
137G ASN* 3.0 39.7 + - - +
162G ASN* 3.7 28.3 - - + +
163G PRO* 5.0 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 134 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130G ARG 3.7 10.0 + - - +
131G ASP* 3.3 18.3 + - - +
133G LEU* 1.3 80.3 - - - +
135G LYS* 1.3 58.9 + - + +
138G ALA* 2.7 49.9 + - + +
163G PRO* 4.1 26.2 - - + -
166G SER* 3.8 24.2 - - - -
167G THR* 5.8 0.4 - - + -
170G ILE* 3.9 23.6 - - + -
349G LYS* 3.3 52.3 - - + +
353G PHE* 4.2 17.0 - + + -
----------------------------------------------------------
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
----------------------------------------------------------
131G ASP* 3.4 18.8 + - - +
132G ASP* 3.8 12.3 - - - +
133G LEU 3.3 0.4 - - - -
134G PHE* 1.3 85.3 - - + +
136G ILE* 1.3 67.1 + - + +
138G ALA* 3.5 4.9 - - - +
139G GLY* 3.3 12.6 + - - -
353G PHE* 5.0 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 136 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122G VAL* 3.3 32.1 - - + -
124G ARG* 3.2 50.3 - - + +
132G ASP 3.4 16.8 - - - +
133G LEU* 3.0 5.1 + - - +
135G LYS* 1.3 72.7 - - + +
137G ASN* 1.3 66.8 + - - +
138G ALA 2.8 5.7 + - - -
139G GLY* 2.9 14.4 + - - -
140G ILE* 3.1 21.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 137 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120G ALA 4.5 1.8 + - - -
121G GLY* 3.6 19.8 - - - -
122G VAL 3.1 23.7 + - - +
133G LEU* 3.0 33.2 + - + +
134G PHE 4.4 0.7 - - - +
136G ILE* 1.3 83.1 - - - +
138G ALA* 1.3 55.5 + - - +
140G ILE* 3.8 9.0 - - - -
141G VAL* 2.8 41.4 + - + +
161G SER* 4.7 0.8 - - - -
162G ASN* 2.7 38.1 + - - +
163G PRO* 4.9 3.8 - - + -
167G THR* 5.2 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 138 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134G PHE* 2.7 40.5 + - + +
135G LYS* 3.5 5.6 - - - +
136G ILE 2.8 1.0 + - - -
137G ASN* 1.3 74.6 - - - +
139G GLY* 1.3 57.1 + - - +
141G VAL* 3.2 2.6 + - - +
142G LYS* 2.8 29.3 + - - +
167G THR* 5.6 0.9 - - - +
170G ILE* 4.2 16.8 - - + +
353G PHE* 3.3 30.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 139 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135G LYS 3.3 6.4 + - - -
136G ILE 2.9 7.0 + - - -
138G ALA* 1.3 77.3 - - - +
140G ILE* 1.3 53.7 + - - +
142G LYS* 2.9 13.7 + - - +
143G THR* 2.6 42.3 + - - +
353G PHE* 3.9 9.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 140 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120G ALA* 4.2 19.3 - - + +
121G GLY* 4.5 7.0 - - - +
122G VAL* 3.9 14.8 - - + -
136G ILE* 3.1 34.4 + - + +
137G ASN* 3.6 14.6 - - - +
139G GLY* 1.3 74.1 - - - +
141G VAL* 1.3 64.0 + - + +
143G THR* 2.9 20.7 + - - +
144G LEU* 3.0 36.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 141 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118G VAL* 5.8 1.1 - - + -
120G ALA 5.3 0.4 - - - +
137G ASN* 2.8 29.7 + - - +
138G ALA* 3.6 4.9 - - - +
140G ILE* 1.3 74.5 - - + +
142G LYS* 1.3 58.0 + - - +
144G LEU* 3.3 6.3 + - - +
145G CYS* 2.9 50.4 + - - -
159G LEU* 4.0 10.8 - - + -
161G SER* 3.5 35.4 - - - +
167G THR* 3.8 35.2 - - + +
170G ILE* 4.4 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 142 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138G ALA 2.8 14.1 + - - +
139G GLY* 2.9 16.1 + - - +
141G VAL* 1.3 77.5 - - - +
143G THR* 1.3 63.9 + - + +
145G CYS* 3.1 4.3 + - - +
146G GLU* 2.9 59.4 + - + +
170G ILE* 4.7 1.1 - - - +
174G VAL* 4.0 14.2 - - + +
353G PHE* 4.5 11.9 - - + -
354G ILE* 4.3 22.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 143 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103G GLN* 4.7 16.5 + - - +
106G LEU* 4.3 9.1 - - - +
139G GLY* 2.6 21.3 + - - +
140G ILE* 2.9 24.6 + - - +
142G LYS* 1.3 82.4 - - + +
144G LEU* 1.3 65.2 + - - +
146G GLU* 3.1 31.8 - - - +
147G GLY 3.4 4.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 144 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50G LEU* 3.8 30.9 - - + +
76G TYR* 4.0 26.7 - - + +
103G GLN* 5.7 1.8 - - - +
106G LEU* 4.3 15.2 - - + +
110G LEU* 4.6 2.3 - - - +
118G VAL* 3.9 10.3 - - + -
120G ALA* 3.6 30.5 - - + -
140G ILE* 3.0 31.1 + - + +
141G VAL* 3.9 4.9 - - - +
143G THR* 1.3 78.4 - - - +
145G CYS* 1.3 66.6 + - - +
146G GLU 3.0 1.8 - - - -
147G GLY* 3.1 3.3 + - - -
148G ILE* 3.0 26.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 145 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141G VAL* 2.9 32.7 + - - +
142G LYS 3.6 4.0 - - - +
144G LEU* 1.3 78.2 - - - +
146G GLU* 1.3 56.0 + - - +
148G ILE* 3.8 10.1 - - - -
149G ALA* 2.9 26.3 + - - +
157G VAL* 6.1 2.9 - - - -
159G LEU* 5.0 4.5 - - - -
171G ALA* 3.3 33.9 - - - -
174G VAL* 3.8 19.3 - - + -
175G PHE* 3.1 25.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 146 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142G LYS* 2.9 50.1 + - + +
143G THR* 3.1 32.4 - - - +
145G CYS* 1.3 75.7 - - - +
147G GLY* 1.3 66.7 + - - +
149G ALA* 3.9 4.6 - - - +
150G LYS* 3.3 21.1 + - - +
174G VAL* 3.9 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 147 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106G LEU* 4.6 7.4 - - - -
107G GLU* 5.8 2.2 - - - -
110G LEU* 3.2 20.4 - - - -
143G THR 3.4 6.6 + - - -
144G LEU 3.1 5.5 + - - -
146G GLU* 1.3 79.1 - - - +
148G ILE* 1.3 49.0 + - - +
150G LYS* 2.8 12.8 + - - +
151G CYS* 2.6 38.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 148 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50G LEU* 4.3 8.3 - - + -
110G LEU* 3.4 13.7 - - + +
116G ILE* 3.4 46.7 - - + -
118G VAL* 4.6 2.5 - - + -
144G LEU* 3.0 16.5 + - + +
145G CYS* 3.7 16.8 - - - +
147G GLY* 1.3 74.7 - - - +
149G ALA* 1.3 65.3 + - - +
150G LYS 2.9 1.2 + - - -
152G CYS* 3.0 34.5 + - - +
153G PRO* 3.1 10.4 - - + -
155G ALA 5.5 0.4 - - - +
157G VAL* 4.1 25.8 - - + -
175G PHE* 3.9 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 149 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145G CYS 2.9 22.5 + - - +
146G GLU* 3.9 5.2 - - - +
148G ILE* 1.3 73.9 - - - +
150G LYS* 1.3 55.7 + - - +
153G PRO* 3.4 12.4 - - - +
174G VAL 4.7 0.7 - - - +
175G PHE* 3.5 15.9 - - + -
178G ALA* 3.7 20.6 - - + -
180G THR* 3.2 43.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 150 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107G GLU* 2.8 33.0 + - - +
146G GLU 3.3 12.8 + - - +
147G GLY* 2.8 11.8 + - - +
149G ALA* 1.3 80.6 - - - +
151G CYS* 1.3 64.1 + - - +
152G CYS 3.8 0.2 - - - -
153G PRO* 4.1 5.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 151 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107G GLU* 3.5 48.5 - - - -
110G LEU* 3.5 24.9 - - + -
111G THR* 3.8 27.9 + - - +
112G GLY 4.4 2.3 + - - -
147G GLY* 2.6 20.0 + - - +
150G LYS* 1.3 82.2 - - - +
152G CYS* 1.3 60.5 + - - +
153G PRO* 3.4 4.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 152 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110G LEU* 3.4 33.7 - - - +
112G GLY 4.9 1.1 - - - +
113G MET* 4.0 9.6 - - - +
116G ILE* 3.1 35.7 - - - -
148G ILE* 3.0 22.2 + - - +
151G CYS* 1.3 79.5 - - - +
153G PRO* 1.3 53.5 - - - +
154G ARG 2.8 6.3 + - - -
155G ALA* 2.8 37.4 + - + +
----------------------------------------------------------
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