Contacts of the helix formed by residues 140 - 159 (chain E) in PDB entry 1APM
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 GLU 140 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138E PHE 3.7 1.6 + - - +
139E ALA* 1.3 71.1 - - - +
141E PRO* 1.3 62.0 - - + +
143E ALA* 3.3 5.2 + - - +
144E ARG* 2.7 41.3 + - - +
232E ALA* 4.8 7.6 - - + -
260E HIS* 3.7 8.1 + - - +
261E PHE* 3.5 11.3 - - + -
262E SER* 2.8 48.1 + - - -
265E LEU* 3.7 20.1 - - + +
296E TRP* 3.1 23.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 141 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139E ALA* 3.4 11.0 - - + -
140E GLU* 1.3 96.0 - - + +
142E HIS* 1.3 65.4 + - - +
144E ARG* 4.0 24.6 - - - +
145E PHE* 3.1 22.3 + - - +
313E PRO* 5.1 1.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 142 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135E ILE* 5.3 5.2 - - + -
138E PHE* 4.0 30.2 - + + +
139E ALA* 2.7 25.4 + - + +
141E PRO* 1.3 81.6 - - - +
143E ALA* 1.3 60.3 + - - +
145E PHE* 3.1 18.4 + - - +
146E TYR* 2.8 49.5 + + - -
313E PRO* 3.2 36.2 - - + +
314E PHE* 3.8 23.7 - + + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 143 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138E PHE* 4.2 7.5 - - + +
139E ALA 2.8 11.4 + - - +
140E GLU* 3.8 9.2 - - - +
142E HIS* 1.3 77.0 - - - +
144E ARG* 1.3 63.4 + - - +
146E TYR* 3.0 5.3 + - - +
147E ALA* 2.8 24.9 + - - +
228E ILE* 5.0 2.2 - - + +
231E MET* 3.7 37.6 - - + +
232E ALA* 4.6 11.9 - - + +
296E TRP* 3.9 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 144 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140E GLU* 2.7 23.8 + - - +
141E PRO* 4.0 27.3 - - - +
143E ALA* 1.3 73.3 - - - +
145E PHE* 1.3 58.9 + - - +
147E ALA* 3.8 0.9 - - - +
148E ALA* 2.9 28.5 + - + +
296E TRP* 2.8 80.1 + - + +
297E PHE* 4.3 3.7 - - + -
299E THR* 3.9 26.9 - - - +
300E THR* 3.6 26.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 145 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141E PRO 3.1 13.6 + - - +
142E HIS 3.1 9.8 + - - +
144E ARG* 1.3 80.4 - - - +
146E TYR* 1.3 75.6 + + - +
148E ALA* 3.7 6.2 + - - +
149E GLN* 2.8 37.3 + - - +
178E GLY 3.6 18.2 - - - -
179E TYR* 3.7 28.7 - + - -
305E ILE* 4.2 12.5 - - + +
310E VAL* 3.6 37.2 - - + -
311E GLU 4.3 0.9 - - - -
312E ALA* 3.8 14.8 - - + -
313E PRO* 3.3 30.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 146 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128E MET* 3.8 18.2 - - + -
138E PHE* 3.7 20.3 - + - -
142E HIS* 2.8 48.4 + + - -
143E ALA 3.0 5.0 + - - +
145E PHE* 1.3 97.2 - + - +
147E ALA* 1.3 68.0 + - - +
148E ALA 3.1 1.6 - - - -
149E GLN* 3.0 24.2 + - - +
150E ILE* 3.2 16.4 + - + +
174E ILE* 4.3 18.4 - - + +
178E GLY 3.9 12.5 + - - -
180E ILE* 4.0 14.3 - - + +
227E LEU* 6.0 0.4 - - + -
231E MET* 3.8 23.1 - - - -
313E PRO* 4.9 1.0 - - - +
314E PHE* 4.0 18.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 147 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143E ALA 2.8 15.4 + - - +
144E ARG* 3.8 7.6 - - - +
146E TYR* 1.3 77.5 - - - +
148E ALA* 1.3 63.9 + - - +
150E ILE* 3.0 12.4 + - - +
151E VAL* 2.9 26.6 + - - +
224E LEU* 4.5 2.8 - - + +
228E ILE* 3.8 34.1 - - + -
231E MET* 4.2 5.1 - - + +
296E TRP* 4.3 6.7 - - + -
297E PHE* 4.3 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 148 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144E ARG 2.9 17.2 + - - +
145E PHE* 3.8 8.5 - - - +
146E TYR 3.1 0.4 - - - -
147E ALA* 1.3 77.7 - - - +
149E GLN* 1.3 62.6 + - - +
151E VAL 3.3 1.0 + - - -
152E LEU* 3.2 21.3 + - - +
297E PHE* 4.2 4.0 - - + -
300E THR* 4.0 19.5 - - + -
302E TRP* 3.4 31.2 - - + -
305E ILE* 4.2 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 149 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102E PHE* 3.7 27.7 - - + -
145E PHE* 2.8 49.2 + - - +
146E TYR* 3.0 17.9 + - - +
148E ALA* 1.3 78.7 - - - +
150E ILE* 1.3 55.7 - - - +
152E LEU* 3.6 0.5 + - - +
153E THR* 2.7 37.4 + - - -
179E TYR* 2.9 27.5 - - - +
180E ILE* 3.1 31.4 + - + +
305E ILE* 3.8 19.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 150 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146E TYR* 3.6 13.2 - - + +
147E ALA* 3.0 7.9 + - - +
149E GLN* 1.3 76.2 - - - +
151E VAL* 1.3 60.1 + - - +
153E THR* 3.3 3.8 + - - +
154E PHE* 2.9 55.8 + - + +
167E LEU* 4.1 11.7 - - + -
172E LEU* 4.0 28.7 - - + -
180E ILE* 4.1 17.3 - - + -
182E VAL* 4.4 8.5 - - + -
224E LEU* 3.5 22.7 - - + -
227E LEU* 4.0 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 151 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147E ALA 2.9 15.7 + - - +
148E ALA 3.3 7.8 + - - +
150E ILE* 1.3 76.4 - - - +
152E LEU* 1.3 57.9 + - - +
154E PHE* 3.3 3.1 + - - +
155E GLU* 2.9 26.0 + - - +
221E TRP* 3.9 9.7 - - + -
224E LEU* 3.7 23.1 - - + -
288E VAL* 4.0 12.6 - - + -
291E ILE* 3.9 17.9 - - + -
292E LYS* 3.7 22.2 - - + -
297E PHE* 4.2 7.6 - - + -
302E TRP* 3.6 26.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 152 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100E PHE* 3.5 21.9 - - + -
102E PHE* 4.1 5.2 - - + -
148E ALA 3.2 8.8 + - - +
149E GLN 3.9 6.5 - - - +
151E VAL* 1.3 74.0 - - - +
153E THR* 1.3 60.0 + - - +
155E GLU* 3.3 10.6 + - - +
156E TYR* 2.9 22.0 + - - +
292E LYS* 4.0 20.6 - - - +
302E TRP* 3.7 45.8 - - + +
303E ILE* 6.1 1.3 - - + -
305E ILE* 3.8 22.9 - - + -
306E TYR* 3.9 17.9 - - + +
354E OCT 4.0 13.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 153 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100E PHE* 3.6 10.6 - - + -
102E PHE* 3.4 24.9 - - - +
103E LEU* 3.7 33.0 - - + -
149E GLN 2.7 22.1 + - - -
150E ILE* 3.7 8.4 - - + +
151E VAL 3.2 0.4 - - - -
152E LEU* 1.3 74.0 - - - +
154E PHE* 1.3 66.6 + - + +
156E TYR* 3.1 2.9 + - - +
157E LEU* 2.8 39.6 + - + +
182E VAL* 4.4 14.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 154 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150E ILE* 2.9 37.1 + - + +
153E THR* 1.3 79.4 - - + +
155E GLU* 1.3 61.9 + - - +
157E LEU* 4.2 12.6 - - + +
158E HIS* 2.8 43.0 + + - +
164E TYR* 3.9 26.0 - + + -
167E LEU* 4.1 22.4 - - + -
182E VAL* 6.5 1.3 - - + -
220E ASP* 3.4 46.0 - - + -
221E TRP* 3.5 37.7 - + + -
224E LEU* 4.2 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 155 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15E VAL* 3.6 19.3 - - - +
19E LEU* 4.3 10.7 - - + +
151E VAL 2.9 18.2 + - - +
152E LEU* 3.6 14.7 - - - +
154E PHE* 1.3 80.4 - - - +
156E TYR* 1.3 64.2 + - - +
158E HIS* 4.3 2.5 - - - +
159E SER* 3.3 18.9 + - - -
221E TRP* 4.6 1.7 - - - -
288E VAL* 3.6 33.3 - - + +
289E ASN* 5.3 1.4 + - - +
292E LYS* 2.8 32.4 + - - +
354E OCT 4.2 14.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 156 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18E PHE* 4.9 2.0 - + - -
19E LEU* 4.4 14.4 - - + -
22E ALA* 4.0 29.6 + - + +
26E PHE* 4.9 4.5 - - - +
97E ALA 4.8 1.4 + - - -
98E VAL* 3.7 9.6 - - + -
99E ASN* 3.0 37.0 + - - +
100E PHE* 3.7 40.8 - + + -
103E LEU* 3.9 12.8 - - + -
152E LEU 2.9 13.6 + - - +
153E THR 3.4 7.2 - - - +
155E GLU* 1.3 76.9 - - - +
157E LEU* 1.3 85.5 + - + +
159E SER* 2.7 24.9 + - - -
160E LEU* 3.5 33.0 + - + +
354E OCT 4.5 1.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 157 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98E VAL* 4.7 1.8 - - + -
103E LEU* 4.0 16.4 - - + -
153E THR* 2.8 33.8 + - + +
154E PHE* 4.1 13.2 - - + +
156E TYR* 1.3 91.9 - - + +
158E HIS* 1.3 66.3 + - - +
160E LEU* 3.0 13.7 + - - +
162E LEU* 3.1 47.0 + - + +
164E TYR* 4.0 35.2 - - + -
182E VAL* 6.2 0.7 - - + -
185E PHE* 4.3 16.8 - - + -
220E ASP* 5.6 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 158 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154E PHE* 2.8 34.2 + + + +
155E GLU* 4.3 2.9 - - - +
157E LEU* 1.3 77.4 - - + +
159E SER* 1.3 61.5 + - - +
160E LEU 3.0 0.2 - - - -
161E ASP* 2.9 16.8 + - - +
162E LEU 3.1 17.4 + - - -
163E ILE* 4.6 0.2 - - - -
164E TYR 4.8 0.2 - - - -
217E LYS* 3.3 38.2 + - + +
220E ASP* 2.8 38.4 - - + +
221E TRP* 3.6 31.6 + + - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 159 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19E LEU* 3.6 32.9 + - - +
23E LYS* 3.3 21.5 + - - +
155E GLU 3.3 11.0 + - - -
156E TYR 2.7 18.6 + - - -
158E HIS* 1.3 78.7 - - - +
160E LEU* 1.3 65.4 + - - +
161E ASP* 3.2 2.7 + - - +
----------------------------------------------------------
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