Contacts of the helix formed by residues 287 - 304 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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286C PHE* 1.3 78.4 - - + +
288C ILE* 1.3 66.0 + - - +
289C ARG* 3.2 9.4 + - - +
290C ALA* 2.7 44.3 + - + +
291C TYR* 3.1 21.5 + - - +
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Residues in contact with ILE 288 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93C MET* 3.4 26.2 - - + +
96C LEU* 4.1 6.7 - - + +
97C GLY* 2.8 38.8 - - - +
281C LEU* 5.1 15.3 - - + -
286C PHE* 3.5 16.7 + - + +
287C ASP* 1.3 74.2 - - - +
289C ARG* 1.3 94.0 + - + +
291C TYR* 3.7 4.3 + - - +
292C ARG* 3.4 18.3 + - + +
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Residues in contact with ARG 289 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287C ASP* 3.2 5.5 + - - +
288C ILE* 1.3 99.0 - - + +
290C ALA* 1.3 66.4 + - - +
291C TYR 2.9 2.0 - - - -
292C ARG* 2.9 18.1 + - - +
293C ASP* 3.0 22.4 + - - +
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Residues in contact with ALA 290 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287C ASP* 2.7 42.9 + - + +
289C ARG* 1.3 72.3 - - - +
291C TYR* 1.3 59.8 + - - +
293C ASP* 3.7 10.7 + - - +
294C ALA* 3.5 19.1 + - - +
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Residues in contact with TYR 291 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93C MET* 3.6 22.7 - - - -
213C TYR* 4.1 23.1 - + - -
214C GLU* 4.2 9.8 + - - +
226C MET* 3.6 19.6 - - + +
227C PRO* 3.2 31.3 + - - +
228C GLY* 5.6 0.7 - - - -
229C VAL* 3.7 18.6 - - + -
286C PHE* 3.9 24.5 - + + -
287C ASP 3.1 15.6 + - - +
288C ILE 3.7 4.5 - - - +
289C ARG 2.9 0.8 - - - -
290C ALA* 1.3 76.0 - - - +
292C ARG* 1.3 65.0 + - - +
293C ASP 3.2 0.5 + - - -
294C ALA* 3.3 15.4 + - + +
295C ALA* 3.3 10.4 + - - +
298C ARG* 4.1 18.3 + - - -
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Residues in contact with ARG 292 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93C MET* 5.3 4.7 - - + -
97C GLY 4.6 5.7 + - - -
98C GLY* 3.7 5.3 - - - -
99C ASP* 3.0 50.5 + - - +
100C LYS 5.1 0.4 - - - +
101C ARG* 3.4 32.7 - - - +
213C TYR* 3.8 17.9 - - + +
288C ILE* 3.4 12.0 + - + +
289C ARG* 2.9 11.0 + - - +
291C TYR* 1.3 79.4 - - - +
293C ASP* 1.3 62.8 + - - +
295C ALA* 2.9 22.9 - - - +
296C ASP* 3.1 20.5 + - - +
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Residues in contact with ASP 293 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289C ARG* 3.0 27.7 + - - +
290C ALA* 3.7 11.5 - - - +
292C ARG* 1.3 72.2 - - - +
294C ALA* 1.3 68.4 + - - +
295C ALA 2.9 1.3 - - - -
296C ASP* 2.7 27.6 + - - +
297C GLN* 2.8 27.5 + - + +
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Residues in contact with ALA 294 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290C ALA 3.5 9.4 + - - +
291C TYR* 3.3 14.0 + - + +
293C ASP* 1.3 78.9 - - - +
295C ALA* 1.3 52.5 + - - +
297C GLN* 3.6 20.1 + - - +
298C ARG* 2.6 59.0 + - - +
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Residues in contact with ALA 295 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101C ARG* 5.2 0.2 - - - +
211C LEU 4.3 6.1 - - - +
212C GLY* 3.5 22.9 - - - -
213C TYR* 4.1 25.4 - - + +
291C TYR 3.3 5.8 + - - +
292C ARG* 2.9 18.6 + - + +
293C ASP 2.8 1.0 + - - -
294C ALA* 1.3 77.5 - - - +
296C ASP* 1.3 50.0 + - - +
298C ARG* 3.1 14.2 + - - +
299C ALA* 2.6 37.6 + - - +
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Residues in contact with ASP 296 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101C ARG* 3.5 27.8 + - - -
211C LEU 4.9 0.6 - - - +
292C ARG* 3.1 25.2 + - - +
293C ASP* 2.7 22.4 + - - +
295C ALA* 1.3 71.7 - - - +
297C GLN* 1.3 51.4 + - + +
299C ALA* 3.0 7.4 + - - +
300C ASP* 2.7 49.4 + - - +
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Residues in contact with GLN 297 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293C ASP* 2.8 31.6 + - + +
294C ALA* 3.6 17.6 + - - +
296C ASP* 1.3 72.6 - - + +
298C ARG* 1.3 64.6 + - - +
300C ASP* 3.0 10.2 + - - +
301C LEU* 2.9 28.7 + - - +
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Residues in contact with ARG 298 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212C GLY 3.3 17.4 + - - +
213C TYR* 4.5 4.6 - - - +
214C GLU* 3.5 41.9 + - - +
291C TYR* 4.1 21.2 - - - -
294C ALA* 2.6 36.6 + - - +
295C ALA* 3.3 27.2 - - - +
297C GLN* 1.3 73.9 - - - +
299C ALA* 1.3 57.1 + - - +
301C LEU* 3.9 8.5 + - - +
302C ARG* 3.0 37.7 + - - +
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Residues in contact with ALA 299 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210C ALA 4.0 7.6 - - - +
211C LEU 4.1 4.9 - - - +
212C GLY* 3.6 22.9 - - - +
295C ALA 2.6 19.6 + - - +
296C ASP* 3.4 7.6 - - - +
298C ARG* 1.3 73.4 - - - +
300C ASP* 1.3 68.3 + - - +
302C ARG* 3.0 26.4 + - - +
303C THR* 3.6 7.3 + - - -
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Residues in contact with ASP 300 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296C ASP* 2.7 39.9 + - - +
297C GLN* 3.6 8.0 + - - +
299C ALA* 1.3 73.6 - - - +
301C LEU* 1.3 63.5 + - + +
302C ARG 3.2 0.7 + - - -
303C THR* 3.3 16.7 + - - -
304C LEU* 3.3 23.6 + - + +
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Residues in contact with LEU 301 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297C GLN 2.9 16.6 + - - +
298C ARG* 4.0 9.2 - - - +
300C ASP* 1.3 77.2 - - + +
302C ARG* 1.3 56.5 + - - +
304C LEU* 2.5 45.5 + - + +
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Residues in contact with ARG 302 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209C GLU* 3.3 34.1 + - - +
210C ALA* 5.2 6.5 + - - +
212C GLY* 3.8 14.8 + - - -
213C TYR 4.1 5.7 + - - -
214C GLU* 5.4 3.4 - - - +
298C ARG* 3.0 33.2 + - - +
299C ALA* 3.0 14.2 + - - +
301C LEU* 1.3 73.3 - - + +
303C THR* 1.3 65.2 + - - +
304C LEU 2.8 5.4 + - - -
305C THR* 3.0 20.1 + - - -
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Residues in contact with THR 303 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299C ALA 3.6 8.2 + - - -
300C ASP* 3.3 10.8 + - - -
302C ARG* 1.3 77.9 - - - +
304C LEU* 1.3 62.7 + - + +
305C THR* 3.5 4.7 + - - -
306C PRO* 5.4 1.4 - - - +
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Residues in contact with LEU 304 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300C ASP* 3.5 21.8 - - + +
301C LEU* 2.5 33.8 + - + +
302C ARG 2.8 3.5 - - - +
303C THR* 1.3 81.5 - - + +
305C THR* 1.3 60.2 + - - +
306C PRO 5.3 0.7 - - - -
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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