Contacts of the helix formed by residues 141 - 164 (chain B) in PDB entry 1PA6
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 141 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A ASP* 3.8 19.1 - - - +
282A SER* 4.4 1.0 + - - -
287A VAL* 5.4 2.1 - - - +
289A ILE* 6.1 0.7 - - - +
15B LYS* 3.1 22.8 + - - +
57B PHE* 3.6 31.9 - - + -
136B VAL* 5.8 1.1 - - + -
137B ASN 3.6 2.5 + - - +
138B LEU* 3.2 14.0 + - + +
139B PHE 3.6 0.2 - - - -
140B ARG* 1.3 77.9 - - - +
142B ASP* 1.3 61.1 + - - +
143B GLU 3.4 3.6 + - - -
144B PHE* 3.0 26.8 + - + +
145B LYS* 2.8 34.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 142 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A LEU* 4.9 4.9 - - - +
242A GLU* 2.5 25.2 - - - +
254A TYR* 4.5 5.0 - - - +
255A THR 4.8 1.9 + - - +
256A LEU* 3.2 40.3 - - + +
285A LYS* 3.0 29.1 + - - -
287A VAL* 4.6 19.4 - - + +
140B ARG 3.6 3.6 + - - -
141B ASP* 1.3 73.8 + - - +
143B GLU* 1.3 64.1 + - - +
145B LYS* 3.5 4.5 + - - +
146B THR* 2.9 30.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 143 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A THR 3.6 0.5 - - - +
282A SER* 3.4 20.7 + - - +
283A THR* 3.3 9.5 + - - +
284A GLN* 2.6 42.8 + - - +
285A LYS* 3.3 23.0 + - + +
287A VAL* 5.1 0.7 - - + -
330A LEU* 4.1 17.4 - - + +
15B LYS* 2.7 41.6 + - - +
141B ASP* 3.4 3.6 + - - -
142B ASP* 1.3 79.0 - - - +
144B PHE* 1.3 58.0 + - - +
146B THR* 3.2 8.7 + - - -
147B THR* 2.9 30.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 144 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B LYS* 4.6 3.3 - - + +
18B TYR* 3.7 42.6 - - + -
19B THR* 3.8 17.7 - - - -
22B PHE* 3.7 25.4 - + - -
138B LEU* 3.2 48.5 - - + +
139B PHE* 3.5 34.3 - + - -
141B ASP* 3.0 18.1 + - + +
143B GLU* 1.3 72.3 - - - +
145B LYS* 1.3 67.4 + - - +
147B THR* 2.9 19.3 + - + -
148B ILE* 2.9 22.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 145 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A LEU* 3.7 16.1 - - + +
237A ASP* 3.1 8.5 + - - +
240A THR* 3.1 33.3 + - - +
256A LEU* 4.7 1.9 - - + +
109B TYR* 3.3 52.6 - - + +
139B PHE 3.6 22.2 - - - +
140B ARG* 3.9 19.7 + - - +
141B ASP 2.8 21.9 + - - +
142B ASP 3.8 3.6 - - - +
144B PHE* 1.3 72.1 - - - +
146B THR* 1.3 59.2 + - - +
148B ILE* 2.9 8.3 + - + +
149B GLN* 2.8 31.5 + - - +
10D A 3.9 14.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 146 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A LEU* 4.1 13.2 - - - +
285A LYS* 4.3 1.0 + - - -
330A LEU* 3.6 27.0 + - + +
471A PHE* 3.3 11.3 - - + -
472A ASN* 3.4 30.7 - - - +
142B ASP* 2.9 28.0 + - - -
143B GLU* 3.4 11.4 - - - -
144B PHE 3.1 0.2 - - - -
145B LYS* 1.3 76.6 - - - +
147B THR* 1.3 57.6 + - - +
149B GLN* 3.5 11.6 + - - +
150B HIS* 3.0 22.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 147 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A LEU* 4.1 18.8 - - - +
19B THR* 4.1 27.9 + - + +
22B PHE* 4.1 19.2 - - + +
23B ASN* 3.9 21.6 + - - +
143B GLU 2.9 15.4 + - - -
144B PHE* 2.9 17.3 + - + -
146B THR* 1.3 73.8 - - - +
148B ILE* 1.3 65.9 + - - +
150B HIS* 3.3 8.5 + - - +
151B PHE* 3.1 19.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 148 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B PHE* 3.8 28.9 - - + -
109B TYR* 3.9 49.6 - - + +
110B ALA* 4.1 9.6 - - + -
112B LEU* 4.2 18.4 - - + +
139B PHE* 4.0 7.2 - - + -
144B PHE* 2.9 40.6 + - + +
145B LYS* 2.9 8.1 + - - +
147B THR* 1.3 74.7 - - - +
149B GLN* 1.3 56.7 + - - +
151B PHE* 2.6 35.6 + - - +
152B ARG* 3.0 7.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 149 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A HIS* 5.4 0.8 + - - -
236A LEU* 3.1 40.3 + - - +
423A GLN* 5.7 14.2 + - + +
471A PHE* 3.6 12.5 - - + -
472A ASN* 5.2 1.4 + - - -
474A TYR* 3.9 19.6 + - - -
109B TYR* 3.0 30.1 + - + +
145B LYS 2.8 16.7 + - - +
146B THR* 3.7 10.5 + - - +
148B ILE* 1.3 78.5 - - - +
150B HIS* 1.3 56.1 + - - +
152B ARG* 3.9 9.7 - - - +
153B HIS* 2.9 30.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 150 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A VAL* 3.5 41.5 - - + +
330A LEU* 5.4 1.7 - - + +
471A PHE* 3.5 45.8 - + + +
23B ASN* 4.2 15.6 + - - -
146B THR 3.0 14.2 + - - +
147B THR* 3.4 12.3 - - - +
148B ILE 3.0 0.4 - - - -
149B GLN* 1.3 76.1 - - - +
151B PHE* 1.3 62.9 + - - +
153B HIS* 3.3 1.9 + - - +
154B THR* 2.9 43.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 151 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B PHE* 3.5 36.8 - + + +
25B GLU* 4.0 18.2 - - + -
97B LEU* 3.6 20.0 - - + -
112B LEU* 3.5 34.3 - - + -
147B THR 3.1 9.0 + - - +
148B ILE* 2.6 20.3 + - - +
150B HIS* 1.3 74.3 - - - +
152B ARG* 1.3 59.5 + - - -
154B THR* 3.3 8.5 + - - -
155B ALA* 3.1 20.3 + - - +
203B PHE* 3.9 18.2 - + - -
205B PHE* 3.4 27.6 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 152 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418A LYS* 5.6 1.0 - - - +
423A GLN* 3.7 35.0 + - - +
424A LEU* 3.5 36.6 + - - +
110B ALA* 3.5 37.9 + - - +
111B ASN* 5.8 1.0 - - - +
112B LEU* 4.0 18.1 - - + +
148B ILE* 3.0 12.1 + - - +
149B GLN* 4.1 10.5 - - - +
151B PHE* 1.3 73.4 - - - +
153B HIS* 1.3 60.3 + - - +
155B ALA* 3.5 6.7 - - - +
156B LEU* 2.7 38.8 + - - +
199B GLU* 5.6 2.0 + - - +
200B PHE* 4.5 20.8 + - + +
203B PHE* 4.1 24.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 153 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A TYR* 4.1 33.2 - + + -
375A VAL 4.6 2.6 + - - -
376A THR* 5.5 2.0 - - + -
423A GLN* 6.0 1.5 - - - +
469A THR 3.5 25.8 + - - -
470A LYS 4.0 2.8 + - - -
471A PHE* 3.5 47.6 - + + +
472A ASN 5.0 1.6 - - - -
149B GLN 2.9 19.9 + - - +
150B HIS* 3.3 2.6 + - - +
152B ARG* 1.3 75.8 - - - +
154B THR* 1.3 63.1 + - - +
156B LEU* 3.8 7.5 - - + +
157B GLN* 2.9 58.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 154 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B HIS* 2.9 32.0 + - - -
151B PHE* 3.6 10.3 - - - -
152B ARG 3.1 0.2 - - - -
153B HIS* 1.3 79.2 + - - +
155B ALA* 1.3 63.3 + - - +
157B GLN* 4.1 4.1 - - - +
158B ALA* 3.2 24.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 155 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B PHE* 3.1 12.0 + - + +
152B ARG 3.5 7.0 - - - +
154B THR* 1.3 76.2 - - - +
156B LEU* 1.3 57.9 + - - +
158B ALA* 3.3 4.9 + - - +
159B ALA* 2.9 29.8 + - - +
200B PHE* 3.8 9.7 - - + -
202B ASP 4.3 7.9 - - - +
203B PHE* 3.7 36.1 - - + -
204B SER 5.7 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 156 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A TYR* 3.9 14.6 - - + +
376A THR* 4.1 16.4 - - + -
418A LYS* 3.3 39.7 - - + -
423A GLN* 5.0 2.2 - - - +
152B ARG* 2.7 25.7 + - - +
153B HIS* 3.8 5.4 - - + +
155B ALA* 1.3 74.1 - - - +
157B GLN* 1.3 57.9 + - - +
159B ALA* 3.1 1.7 + - - +
160B ILE* 2.8 51.0 + - + +
192B ALA* 4.0 9.9 - - + -
200B PHE* 3.6 39.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 157 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376A THR* 3.2 35.8 + - - +
469A THR* 2.9 33.5 + - - +
153B HIS* 2.9 42.8 + - + +
154B THR* 4.3 4.0 - - - +
156B LEU* 1.3 78.8 - - + +
158B ALA* 1.3 58.7 + - - +
160B ILE* 3.9 6.7 - - - -
161B ASN* 2.5 42.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 158 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B THR* 3.2 21.1 + - + +
155B ALA* 3.7 4.5 - - - +
156B LEU 3.2 0.6 - - - -
157B GLN* 1.3 73.4 - - - +
159B ALA* 1.3 67.8 + - - +
161B ASN* 3.3 8.2 + - - +
162B LYS* 3.2 21.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 159 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B ALA 2.9 18.3 + - - +
156B LEU 3.1 4.7 + - - +
158B ALA* 1.3 76.7 - - - +
160B ILE* 1.3 57.7 + - - +
162B LYS* 3.1 9.0 + - - +
163B THR* 2.9 31.4 + - - -
192B ALA 3.6 2.5 - - - +
193B SER* 4.0 6.5 - - - -
200B PHE* 3.6 25.1 - - + -
202B ASP* 3.9 22.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 160 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376A THR* 3.4 27.1 - - + +
377A LYS* 3.9 26.5 - - + -
416A LEU* 4.4 5.8 - - + -
428A THR* 4.0 16.2 - - + +
156B LEU* 2.8 46.8 + - + +
157B GLN* 4.1 4.7 - - - +
159B ALA* 1.3 73.2 - - - +
161B ASN* 1.3 57.9 + - - +
162B LYS 3.0 0.9 + - - -
163B THR* 4.4 0.7 - - - -
164B VAL* 2.8 47.8 + - + +
192B ALA* 3.4 26.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 161 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376A THR 4.6 4.8 + - - -
377A LYS* 3.0 40.2 + - - +
157B GLN* 2.5 42.4 + - - +
158B ALA* 3.3 6.0 + - - +
160B ILE* 1.3 76.3 - - - +
162B LYS* 1.3 57.9 + - - +
164B VAL 4.1 8.2 - - - +
165B LYS* 5.9 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 162 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B ALA 3.2 10.4 + - - +
159B ALA* 3.1 11.4 + - - +
160B ILE 3.0 0.6 - - - -
161B ASN* 1.3 78.5 - - - +
163B THR* 1.3 63.8 + - - +
164B VAL 3.8 0.4 - - - -
165B LYS* 3.5 23.1 + - - -
202B ASP* 5.6 6.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 163 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B ALA 2.9 13.2 + - - -
160B ILE 3.8 0.7 - - - -
162B LYS* 1.3 79.0 - - - +
164B VAL* 1.3 63.9 + - + +
165B LYS* 3.7 14.6 + - - +
191B LYS* 3.8 23.6 - - + +
192B ALA 3.1 21.2 + - - +
193B SER* 3.3 19.2 - - - +
194B ALA* 4.2 2.3 + - + +
202B ASP* 5.4 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 164 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A LYS* 4.0 14.5 + - + -
379A GLU* 3.1 32.8 - - - +
416A LEU* 3.9 9.4 - - + -
428A THR* 5.1 0.2 - - + -
160B ILE* 2.8 41.5 + - + +
161B ASN 4.1 9.5 - - - +
162B LYS 4.7 0.3 - - - -
163B THR* 1.3 72.9 - - + +
165B LYS* 1.3 67.6 + - - +
190B VAL* 3.9 27.4 - - + -
191B LYS 4.1 9.6 - - - +
----------------------------------------------------------
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