Contacts of the helix formed by residues 287 - 304 (chain A) in PDB entry 1P4D
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 287 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A GLY 3.3 5.4 + - - +
286A PHE* 1.3 78.2 - - - +
288A ILE* 1.3 66.4 + - - +
289A ARG* 4.0 7.5 + - - +
290A ALA* 3.1 30.8 + - + +
291A TYR* 2.9 21.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 288 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A MET* 3.6 22.2 - - + +
96A LEU 4.5 2.5 - - - +
97A GLY* 3.7 28.7 - - - +
281A LEU* 3.2 35.4 - - + -
286A PHE* 3.3 36.5 + - + +
287A ASP* 1.3 69.3 + - - +
289A ARG* 1.3 67.3 + - + +
291A TYR* 2.8 24.5 + - - +
292A ARG* 2.9 16.1 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
287A ASP* 3.4 7.3 + - - +
288A ILE* 1.3 87.7 - - + +
290A ALA* 1.3 58.7 + - - +
292A ARG* 3.2 7.2 + - - +
293A ASP* 2.6 38.7 + - - +
40B GLN* 5.7 7.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 290 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A ASP* 3.1 34.2 + - + +
288A ILE 3.2 0.6 - - - -
289A ARG* 1.3 79.0 - - - +
291A TYR* 1.3 63.1 + - - +
293A ASP* 3.3 8.8 + - - +
294A ALA* 3.1 23.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 291 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A MET* 3.7 21.3 - - - -
213A TYR* 3.8 27.3 - + - -
214A GLU* 4.6 4.4 + - - +
226A MET* 3.4 20.9 - - + +
227A PRO* 2.5 34.9 + - - +
228A GLY* 4.7 1.3 - - - -
229A VAL* 3.7 15.7 - - + -
286A PHE* 3.4 26.0 - + + -
287A ASP 2.9 13.0 + - - +
288A ILE* 2.8 14.3 + - - +
290A ALA* 1.3 77.4 - - - +
292A ARG* 1.3 57.6 + - - +
294A ALA* 3.5 10.2 - - + +
295A ALA* 3.3 17.5 + - - +
298A ARG* 4.9 8.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 292 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A MET* 3.6 16.8 - - + -
97A GLY 3.3 28.5 + - - -
98A GLY* 3.6 0.6 - - - -
99A ASP* 3.4 29.2 + - - +
101A ARG* 3.7 15.1 + - - +
213A TYR* 3.6 20.6 + - + +
288A ILE* 2.9 19.1 + - - +
289A ARG* 3.8 7.9 - - - +
291A TYR* 1.3 74.5 - - - +
293A ASP* 1.3 61.6 + - - +
294A ALA 3.0 1.6 - - - -
295A ALA* 2.9 10.5 + - - +
296A ASP* 2.8 38.0 + - - +
36B ARG* 6.1 2.6 - - - +
39B GLU* 2.9 41.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 293 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A ARG* 2.6 34.1 + - - +
290A ALA* 3.8 7.2 - - - +
292A ARG* 1.3 76.7 - - - +
294A ALA* 1.3 57.0 - - - +
296A ASP* 3.1 14.1 + - - +
297A GLN* 2.9 48.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 294 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A ALA 3.1 13.5 + - - +
291A TYR* 3.5 15.5 - - + +
292A ARG 3.0 0.4 - - - -
293A ASP* 1.3 79.2 - - - +
295A ALA* 1.3 56.2 + - - +
297A GLN* 3.5 11.5 + - - +
298A ARG* 3.0 48.4 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
101A ARG* 5.4 0.9 - - - +
211A LEU 3.4 3.5 - - - +
212A GLY* 3.2 14.7 - - - -
213A TYR* 3.9 47.6 - - + +
291A TYR 3.3 8.2 + - - +
292A ARG 2.9 9.5 + - - +
294A ALA* 1.3 80.1 - - - +
296A ASP* 1.3 59.5 + - - +
298A ARG* 3.6 10.9 - - - +
299A ALA* 3.1 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 296 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A ARG* 3.7 21.0 + - - -
211A LEU 4.6 0.9 - - - +
292A ARG* 2.8 22.6 + - - +
293A ASP* 3.5 16.9 - - - +
295A ALA* 1.3 74.5 - - - +
297A GLN* 1.3 61.0 + - + +
299A ALA* 3.3 3.6 + - - +
300A ASP* 3.0 36.0 + - - +
36B ARG* 3.2 54.1 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
293A ASP* 2.9 32.1 + - + +
294A ALA* 3.9 9.3 - - - +
296A ASP* 1.3 73.9 - - + +
298A ARG* 1.3 61.3 + - - +
300A ASP* 3.5 6.4 + - - +
301A LEU* 2.9 36.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 298 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A GLY 2.8 26.5 + - - +
213A TYR* 4.2 5.7 - - - +
214A GLU* 3.6 42.4 + - - +
291A TYR* 4.9 9.3 + - - -
294A ALA* 3.0 29.3 + - - +
295A ALA* 3.6 23.2 - - - +
297A GLN* 1.3 76.4 - - - +
299A ALA* 1.3 61.6 + - - +
301A LEU* 3.1 15.3 - - + +
302A ARG* 2.9 51.1 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
210A ALA 4.5 7.4 - - - +
211A LEU 3.6 17.7 - - - +
212A GLY* 3.7 9.1 - - - -
295A ALA 3.1 18.9 + - - +
296A ASP* 3.4 6.5 - - - +
298A ARG* 1.3 76.8 - - - +
300A ASP* 1.3 66.2 + - - +
302A ARG* 3.0 19.4 + - - +
303A THR* 3.2 18.6 + - + +
36B ARG* 4.7 5.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 300 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A ASP 3.0 17.3 + - - +
297A GLN* 3.9 6.0 - - - +
299A ALA* 1.3 74.6 - - - +
301A LEU* 1.3 63.4 + - - +
303A THR* 2.7 24.9 + - - +
304A LEU* 3.0 19.8 + - + +
36B ARG* 2.5 39.1 + - - -
115B ARG 4.8 3.8 - - - +
119B ALA* 3.7 24.9 + - + +
135B LEU* 6.3 0.4 - - + -
137B GLY* 3.9 12.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 301 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A GLN* 2.9 23.1 + - + +
298A ARG* 3.1 15.9 - - + +
300A ASP* 1.3 77.8 - - - +
302A ARG* 1.3 55.4 + - + +
304A LEU* 3.6 6.6 - - - +
305A THR* 2.2 34.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 302 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A GLU* 3.5 24.2 + - - +
212A GLY 3.5 24.0 + - - -
213A TYR 3.8 8.1 + - - -
214A GLU* 5.3 3.0 - - - +
298A ARG* 2.9 35.6 + - + +
299A ALA* 3.0 10.0 + - - +
301A LEU* 1.3 78.1 - - + +
303A THR* 1.3 64.8 + - + +
305A THR* 3.6 18.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 303 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A ALA 3.2 14.8 + - - +
300A ASP* 2.7 19.6 + - - +
302A ARG* 1.3 78.5 - - + +
304A LEU* 1.3 60.7 + - - +
305A THR 3.3 3.6 + - - -
115B ARG 5.4 1.3 - - - +
116B GLN* 3.1 46.9 - - - +
119B ALA* 3.4 21.9 - - + +
602B EDO 3.9 24.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 304 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A ASP* 3.0 20.4 + - + +
301A LEU* 3.6 3.4 - - - +
302A ARG 3.2 0.2 - - - -
303A THR* 1.3 90.8 + - - +
305A THR* 1.3 63.7 + - - +
306A PRO* 3.9 9.1 - - - +
116B GLN 5.7 0.4 - - - +
119B ALA* 3.8 19.5 - - + +
120B LEU* 3.8 26.7 - - + -
135B LEU* 3.6 33.0 - - + -
602B EDO 4.5 8.7 - - - +
----------------------------------------------------------
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