Contacts of the helix formed by residues 140 - 156 (chain G) in PDB entry 3EXG
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 ALA 140 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135G ASN* 5.8 2.7 - - + +
137G ILE* 3.0 21.6 + - + +
138G VAL 3.3 2.6 + - - -
139G GLY* 1.3 76.0 - - - +
141G GLN* 1.3 61.5 + - - +
143G PRO* 3.2 11.6 - - - +
144G LEU* 3.5 12.8 - - + +
174G GLN* 3.5 13.6 - - - +
91H ASP* 3.6 24.2 - - - +
92H GLN* 3.3 20.4 + - - +
96H SER* 4.5 7.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 141 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86G ILE* 3.7 17.1 - - + +
87G THR* 3.8 17.9 - - - +
88G ALA* 3.3 30.2 - - - +
135G ASN* 3.8 11.3 - - - +
137G ILE 4.0 3.9 + - - +
139G GLY* 3.1 23.0 + - - +
140G ALA* 1.3 72.4 + - - +
142G VAL* 1.3 61.1 + - + +
143G PRO 3.5 0.2 - - - -
144G LEU* 3.3 12.4 + - - +
145G GLY* 2.8 27.9 + - - -
163G THR* 3.7 5.1 - - + +
164G LEU 3.0 28.2 + - - +
165G TYR* 3.5 15.4 - - - +
169G ALA* 5.7 0.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 142 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139G GLY 2.8 14.0 + - - +
141G GLN* 1.3 79.7 - - + +
143G PRO* 1.4 70.8 - - + +
145G GLY* 3.4 1.4 + - - -
146G ALA* 3.1 21.3 + - - +
163G THR* 3.6 9.0 - - + +
165G TYR* 3.7 32.3 - - + -
175G ILE* 3.6 33.2 - - + -
178G ALA* 4.0 10.4 - - + +
191G PHE* 3.8 30.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 143 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139G GLY 3.3 9.9 - - - +
140G ALA 3.2 8.1 - - - +
142G VAL* 1.4 91.6 - - + +
144G LEU* 1.3 62.3 + - - +
146G ALA 3.1 2.6 + - - -
147G GLY 3.0 16.5 + - - -
174G GLN* 3.4 39.5 - - + +
178G ALA* 4.3 9.8 - - + -
61H GLY* 3.7 15.7 - - - +
64H GLY* 3.6 27.1 - - - -
65H ILE* 3.4 15.1 - - + +
92H GLN* 3.7 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
----------------------------------------------------------
86G ILE* 3.6 12.6 - - + -
135G ASN* 3.7 23.3 - - - +
140G ALA* 3.5 17.5 + - + +
141G GLN* 3.3 11.2 + - - +
143G PRO* 1.3 77.6 - - - +
145G GLY* 1.3 54.9 + - - +
147G GLY* 2.8 2.1 + - - -
148G ILE* 2.7 41.1 + - + +
64H GLY 3.6 9.9 - - - +
67H VAL* 3.6 21.1 - - + -
68H GLY* 3.5 24.9 - - - +
71H MET* 4.4 13.2 - - + -
92H GLN* 4.2 4.3 - - - +
96H SER* 3.8 20.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 145 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86G ILE* 3.7 13.6 - - - +
141G GLN 2.8 16.6 + - - -
142G VAL 3.7 1.1 - - - -
143G PRO 3.2 0.2 - - - -
144G LEU* 1.3 75.9 - - - +
146G ALA* 1.3 52.3 + - - +
147G GLY 2.7 10.0 + - - -
148G ILE* 3.1 5.2 + - - +
149G ALA* 2.8 22.2 + - - +
161G CYS* 3.6 6.6 - - - -
163G THR* 3.3 24.2 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
142G VAL 3.1 11.1 + - - +
143G PRO 3.1 10.5 + - - +
145G GLY* 1.3 72.4 - - - +
147G GLY* 1.3 56.8 + - - +
149G ALA* 3.6 13.2 - - - +
150G LEU* 2.9 22.0 + - - +
163G THR* 4.1 1.6 + - - -
178G ALA* 4.2 17.3 - - + +
182G ALA* 4.7 1.3 - - + -
187G LEU* 3.6 14.2 - - + +
189G CYS* 4.1 13.0 - - - -
191G PHE* 4.5 4.0 - - + -
65H ILE* 4.0 18.9 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
143G PRO 3.0 6.0 + - - -
144G LEU 2.8 7.2 + - - -
146G ALA* 1.3 78.2 - - - +
148G ILE* 1.3 66.7 - - - +
149G ALA 3.2 0.4 - - - -
150G LEU* 3.1 5.5 + - - +
151G ALA 3.1 16.6 + - - -
65H ILE* 3.3 29.8 - - - -
69H ALA* 3.5 16.0 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
84G HIS* 3.5 37.9 - - + +
86G ILE* 4.2 14.1 - - + -
132G TYR* 3.5 48.5 - - + +
144G LEU* 2.7 26.2 + - + +
145G GLY* 3.4 8.1 - - - +
147G GLY* 1.3 74.0 - - - +
149G ALA* 1.3 57.0 + - - +
151G ALA* 2.9 5.2 + - - +
152G CYS* 2.8 27.3 + - - -
161G CYS* 3.9 8.5 - - + -
68H GLY* 3.7 16.9 - - - +
71H MET* 5.4 1.1 - - + -
72H ALA* 4.3 12.7 - - + +
----------------------------------------------------------
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 GLY 2.8 19.4 + - - +
146G ALA* 3.6 7.4 - - - +
148G ILE* 1.3 73.2 - - - +
150G LEU* 1.3 63.3 + - - +
151G ALA 3.0 1.0 + - - -
152G CYS* 3.0 13.5 + - - +
153G LYS* 3.2 10.6 + - - +
161G CYS* 4.0 10.4 - - + +
187G LEU* 3.9 7.9 - - + -
188G PRO* 3.6 21.7 - - - +
189G CYS* 3.6 30.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 150 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146G ALA 2.9 17.6 + - - +
147G GLY* 3.1 11.8 + - - +
149G ALA* 1.3 75.0 - - - +
151G ALA* 1.3 56.8 + - - +
153G LYS* 3.7 6.8 + - + +
154G TYR* 3.1 32.7 + - + +
185G TRP* 4.4 16.2 - - + -
187G LEU* 3.5 24.4 - - + +
24H PHE* 3.7 36.6 - - + -
26H LEU* 5.2 1.6 - - + -
53H ILE* 4.5 15.5 - - + -
65H ILE* 4.2 16.8 - - + -
69H ALA* 4.2 10.1 - - + -
74H LEU* 5.6 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 151 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147G GLY 3.1 10.3 + - - +
148G ILE 2.9 9.7 + - - +
150G LEU* 1.3 75.6 - - - +
152G CYS* 1.3 69.2 + - - +
154G TYR* 3.3 1.6 - - - +
155G ASN* 2.8 31.5 + - - +
69H ALA* 4.3 3.4 - - - -
72H ALA* 3.8 24.2 - - + +
74H LEU* 3.2 32.1 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
84G HIS* 3.4 35.0 - - - -
148G ILE* 2.8 21.0 + - - -
149G ALA* 3.0 8.3 + - - +
151G ALA* 1.3 78.8 - - - +
153G LYS* 1.3 64.5 + - - +
155G ASN* 3.0 13.2 + - - +
156G GLY* 3.1 10.9 + - - -
157G LYS 4.2 4.0 + - - -
158G ASP 5.2 0.3 + - - -
159G GLU* 3.3 43.0 + - + +
160G VAL 4.0 9.2 - - - -
161G CYS 4.5 0.2 - - - -
188G PRO* 3.9 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 153 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A GLU* 6.5 1.3 - - - -
149G ALA 3.2 3.6 + - - +
150G LEU* 3.9 10.7 - - + +
152G CYS* 1.3 78.1 - - - +
154G TYR* 1.3 58.8 + - - +
156G GLY* 3.0 20.5 + - - +
185G TRP* 2.9 33.9 + - - +
186G LYS* 4.1 13.2 - - - +
187G LEU* 4.3 10.1 - - + -
188G PRO* 4.0 19.7 - - + +
50H LYS* 5.5 0.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 154 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150G LEU* 3.1 27.0 + - + +
151G ALA* 3.3 9.9 - - - +
153G LYS* 1.3 81.8 - - - +
155G ASN* 1.3 67.7 + - - +
156G GLY 3.6 0.2 + - - -
21H GLU* 3.2 21.1 + - + -
22H LYS* 4.2 3.5 - - - -
23H VAL 3.9 5.7 + - - -
24H PHE* 3.9 21.9 - + - +
50H LYS* 3.3 69.8 + - + +
51H ARG* 3.1 28.4 + - - -
53H ILE* 5.8 0.4 - - + -
74H LEU* 3.7 27.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 155 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151G ALA* 2.8 21.7 + - - +
152G CYS* 3.8 5.5 - - - +
154G TYR* 1.3 92.3 - - - +
156G GLY* 1.3 66.7 + - - +
157G LYS* 3.5 24.4 + - + +
159G GLU* 5.2 6.2 + - - +
22H LYS* 5.9 0.3 - - - +
72H ALA* 4.8 8.9 + - - +
74H LEU* 3.8 17.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 156 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A GLU* 6.0 6.3 - - - -
152G CYS 3.1 4.5 + - - -
153G LYS* 3.0 17.7 + - - -
154G TYR 3.3 0.2 - - - -
155G ASN* 1.3 78.5 - - - +
157G LYS* 1.3 65.0 + - - +
158G ASP* 3.5 3.8 - - - -
----------------------------------------------------------
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