Contacts of the helix formed by residues 288 - 301 (chain A) in PDB entry 3PII
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 THR 288 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A GLY* 3.8 22.4 + - - +
103A GLU* 3.1 29.9 + - - +
104A THR* 4.8 6.4 - - - +
155A LYS* 4.8 2.8 + - - -
287A GLY* 1.3 75.8 - - - +
289A ARG* 1.3 78.2 + - + +
290A LYS* 3.2 22.2 - - + +
291A ASP* 2.9 24.5 + - - -
292A LEU* 2.9 22.4 + - - +
99C LEU* 4.6 10.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 289 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A PRO* 6.1 1.6 - - + -
88A LEU* 6.0 2.0 - - + -
103A GLU* 2.9 43.2 + - - +
129A ASP* 3.1 29.9 + - - +
130A TYR* 3.8 42.7 + - + +
131A VAL 5.1 2.5 - - - -
132A VAL* 4.3 20.2 - - + +
288A THR* 1.3 70.8 - - + +
290A LYS* 1.3 57.8 + - - +
292A LEU* 3.0 9.5 + - - +
293A GLN* 2.8 33.9 + - - +
93C GLY 4.3 7.1 + - - -
94C HIS* 4.8 3.6 + - - -
99C LEU* 3.9 38.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 290 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A THR* 3.1 14.0 - - + +
289A ARG* 1.3 79.0 - - - +
291A ASP* 1.3 64.3 + - - +
293A GLN* 3.8 15.7 - - - +
294A GLU* 2.8 62.2 + - - +
163B LYS* 3.9 17.2 - - - +
166B GLU* 4.6 4.8 + - - -
232B HIS* 5.8 2.6 + - - -
96C ASP* 4.2 25.6 - - - +
99C LEU* 3.9 34.4 - - + +
100C SER* 3.8 19.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 291 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A VAL* 3.8 7.0 - - + -
154A TYR* 3.4 16.1 - - + -
155A LYS* 2.6 45.4 + - + +
158A LYS* 2.8 33.5 + - - +
287A GLY* 3.9 4.9 - - - -
288A THR* 2.9 36.1 + - - +
290A LYS* 1.3 78.9 - - - +
292A LEU* 1.3 56.9 + - - +
294A GLU* 4.5 0.6 - - - +
295A ALA* 3.0 23.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 292 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A PRO* 4.0 15.7 - - + -
132A VAL* 4.0 15.3 - - + -
146A ILE* 3.6 21.8 - - + +
147A PHE* 3.6 40.8 - - + +
151A VAL* 3.3 23.3 - - + -
287A GLY 5.3 1.6 - - - +
288A THR 2.9 11.5 + - - +
289A ARG* 3.4 10.3 - - - +
291A ASP* 1.3 73.6 - - - +
293A GLN* 1.3 67.4 + - - +
294A GLU 3.2 1.1 - - - -
296A LEU* 2.9 48.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 293 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A VAL* 3.7 24.6 - - + +
133A LYS 5.4 0.9 - - - +
135A PRO* 5.6 0.7 - - - +
289A ARG* 2.8 22.4 + - - +
290A LYS* 3.8 11.4 - - + +
292A LEU* 1.3 72.5 - - - +
294A GLU* 1.3 63.1 + - + +
296A LEU* 3.2 7.2 + - - +
297A GLN* 3.1 23.1 + - - +
94C HIS 4.6 4.6 + - - +
96C ASP* 3.6 21.6 + - - -
99C LEU* 3.6 27.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 294 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A TYR* 2.3 41.4 + - + +
158A LYS* 2.9 24.3 + - - -
290A LYS* 2.8 49.6 + - + +
293A GLN* 1.3 75.8 - - + +
295A ALA* 1.3 63.0 + - - +
297A GLN* 3.3 7.8 + - - +
298A PHE* 3.2 30.8 + - + -
163B LYS* 3.5 21.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 295 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A ILE* 3.8 10.4 - - + +
151A VAL* 3.9 17.5 - - + +
154A TYR* 3.7 19.5 - - + -
183A TYR* 2.5 36.8 + - + +
291A ASP 3.0 18.7 + - - +
292A LEU 3.8 3.8 - - - +
294A GLU* 1.3 76.9 - - - +
296A LEU* 1.3 62.0 + - - +
297A GLN 3.5 0.3 + - - -
298A PHE 3.6 1.0 + - - -
299A ALA* 3.6 10.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 296 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A VAL* 4.1 11.0 - - + -
133A LYS 3.8 22.0 - - - +
134A ILE* 4.5 0.9 - - - -
135A PRO* 3.9 19.0 - - + +
138A LEU* 4.3 19.1 - - + +
143A ALA* 4.5 1.1 - - + +
146A ILE* 3.1 31.6 - - + -
147A PHE* 3.8 34.5 - - + -
292A LEU* 2.9 25.7 + - + +
293A GLN* 3.2 5.8 + - - +
295A ALA* 1.3 76.3 - - - +
297A GLN* 1.3 56.8 + - - +
299A ALA* 3.1 6.8 + - - +
300A ALA* 2.9 25.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 297 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A PRO* 4.4 12.8 - - + +
293A GLN 3.1 12.4 + - - +
294A GLU* 3.3 11.0 + - - +
296A LEU* 1.3 74.7 - - - +
298A PHE* 1.3 67.1 + - + +
300A ALA* 3.1 16.6 + - - +
301A GLU* 3.0 58.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 298 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A TYR* 3.7 29.2 - + - -
183A TYR* 3.7 32.5 - + + -
186A ALA* 3.9 32.8 - - + -
187A MET* 4.8 3.4 - - + -
294A GLU* 3.2 25.0 + - + -
295A ALA 3.8 0.9 - - - +
296A LEU 3.4 0.2 - - - -
297A GLN* 1.3 79.5 - - - +
299A ALA* 1.3 61.9 + - - +
301A GLU* 3.1 13.5 + - - +
303A LYS* 3.0 39.1 + - + +
304A VAL* 4.3 6.7 - - + -
164B PRO* 3.6 32.8 - - + -
165B GLY* 3.8 13.5 - - - -
188B GLY 5.1 2.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 299 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A LEU* 3.9 22.9 - - + +
142A GLU* 5.6 1.1 - - + +
146A ILE* 4.1 18.8 - - + -
295A ALA 3.6 4.0 + - - +
296A LEU 3.1 9.7 + - - +
297A GLN 3.1 0.8 - - - -
298A PHE* 1.3 75.8 - - - +
300A ALA* 1.3 55.1 + - - +
302A GLY* 2.6 28.6 + - - -
304A VAL* 3.4 36.5 - - + +
305A LYS* 5.8 0.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 300 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A PRO* 3.9 26.0 - - + -
137A ASN* 4.3 26.7 - - - +
138A LEU* 4.1 14.9 - - + +
296A LEU 2.9 13.5 + - - +
297A GLN* 3.4 20.4 - - - +
299A ALA* 1.3 75.5 - - - +
301A GLU* 1.3 56.4 + - - +
302A GLY 3.2 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 301 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A GLN* 3.0 41.5 + - - +
298A PHE* 3.6 15.7 - - - +
299A ALA 2.8 3.6 + - - -
300A ALA* 1.3 74.3 - - - +
302A GLY* 1.3 62.1 + - - +
303A LYS* 3.4 37.0 + - + +
165B GLY* 6.0 1.2 - - - -
167B TRP* 5.8 1.6 - - - -
190B ASN* 4.1 20.3 + - - -
----------------------------------------------------------
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