Contacts of the helix formed by residues 287 - 313 (chain A) in PDB entry 2PA5
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 287 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A MET* 1.3 76.1 - - - +
288A ILE* 1.3 59.6 + - - +
289A GLN* 3.6 9.1 + - - +
290A GLU* 3.0 38.5 + - - +
291A LEU* 2.8 27.4 + - - +
539A GLY 3.6 17.3 - - - +
540A THR* 4.2 10.5 - - + +
541A LEU* 5.1 0.2 - - - -
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Residues in contact with ILE 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A THR* 1.3 74.2 - - - +
289A GLN* 1.3 57.7 + - - +
291A LEU* 3.2 8.2 + - + +
292A VAL* 2.9 35.6 + - + +
535A LEU* 3.9 29.6 - - + -
539A GLY 4.3 2.8 + - - +
541A LEU* 4.1 5.8 - - + -
571A ILE* 4.1 22.7 - - + -
572A LEU* 4.8 2.0 - - + -
575A ALA* 3.8 34.1 - - + -
580A MET* 4.2 24.5 - - + +
581A VAL* 4.2 13.9 - - + -
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Residues in contact with GLN 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A THR* 3.3 9.0 + - - +
288A ILE* 1.3 79.4 - - - +
290A GLU* 1.3 66.5 + - + +
292A VAL* 3.4 7.3 + - - +
293A ASP* 3.2 34.3 + - - +
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Residues in contact with GLU 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A ALA 3.9 5.0 - - - +
286A MET* 3.4 21.2 - - + +
287A THR* 3.0 41.7 + - - +
289A GLN* 1.3 79.0 - - + +
291A LEU* 1.3 57.7 + - - +
293A ASP* 3.4 9.6 + - - +
294A TYR* 2.9 29.5 + - - +
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Residues in contact with LEU 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A MET* 4.0 24.2 - - + -
287A THR 2.8 16.8 + - - +
288A ILE* 3.6 9.4 - - + +
290A GLU* 1.3 74.7 - - - +
292A VAL* 1.3 64.6 + - - +
294A TYR* 3.2 3.8 + - + +
295A VAL* 3.0 32.0 + - + +
541A LEU* 4.1 21.3 - - + -
543A VAL* 4.9 0.9 - - + +
568A TYR* 3.8 33.9 - - + +
571A ILE* 3.6 33.0 - - + -
572A LEU* 3.9 23.1 - - + -
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Residues in contact with VAL 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A ILE* 2.9 28.7 + - + +
289A GLN* 3.6 9.6 - - - +
291A LEU* 1.3 77.6 - - - +
293A ASP* 1.3 62.5 + - - +
295A VAL* 3.9 1.4 - - - +
296A ASN* 2.9 54.2 + - - +
572A LEU* 3.5 25.9 - - + +
581A VAL* 4.8 17.3 - - + -
582A SER 5.8 3.8 - - - +
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Residues in contact with ASP 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A GLN* 3.2 26.2 + - - +
290A GLU* 3.6 11.0 - - - +
292A VAL* 1.3 84.0 - - - +
294A TYR* 1.3 57.3 + - - +
296A ASN* 3.8 6.6 + - - +
297A ALA* 2.9 32.1 + - - +
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Residues in contact with TYR 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A MET* 3.7 29.4 - - + -
290A GLU 2.9 18.4 + - - +
291A LEU* 3.4 5.4 - - - +
293A ASP* 1.3 77.1 - - - +
295A VAL* 1.3 61.9 + - - +
297A ALA* 3.5 0.8 + - - -
298A ARG* 3.2 79.2 + - - +
303A ILE* 4.0 2.9 - - + -
306A GLU* 2.6 24.3 + - - -
544A PHE* 5.1 4.2 - - + +
568A TYR* 3.3 38.5 + + - -
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Residues in contact with VAL 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A LEU* 3.0 16.3 + - + +
292A VAL 4.1 1.1 - - - +
294A TYR* 1.3 76.7 - - + +
296A ASN* 1.3 60.9 + - - +
298A ARG 4.5 0.2 - - - +
299A GLN* 2.7 34.1 + - - -
303A ILE* 4.5 10.3 - - + -
565A TYR* 4.6 22.4 - - + +
568A TYR* 3.5 37.5 - - + -
569A LYS* 4.8 8.5 - - + +
572A LEU* 3.9 26.2 - - + -
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Residues in contact with ASN 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A VAL* 2.9 42.3 + - - +
293A ASP* 3.8 8.8 + - - +
295A VAL* 1.3 78.0 - - - +
297A ALA* 1.3 66.2 + - - +
298A ARG 3.3 0.5 + - - -
299A GLN* 3.7 8.7 + - - +
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Residues in contact with ALA 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293A ASP 2.9 19.0 + - - +
294A TYR* 3.5 6.1 - - - +
295A VAL 3.3 0.2 - - - -
296A ASN* 1.3 77.7 - - - +
298A ARG* 1.3 72.2 + - + +
299A GLN* 5.1 0.5 - - - +
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Residues in contact with ARG 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A TYR* 3.2 83.0 + - - +
295A VAL 4.2 0.2 - - - +
297A ALA* 1.3 90.2 - - + +
299A GLN* 1.3 77.8 + - - +
301A GLN* 5.2 0.2 - - - +
302A GLY* 3.0 33.4 + - - -
303A ILE* 3.9 13.0 - - + -
306A GLU* 4.0 7.1 + - - -
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Residues in contact with GLN 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A VAL* 2.7 23.8 + - - -
296A ASN* 3.7 6.2 + - - +
297A ALA 3.6 1.6 - - - +
298A ARG* 1.3 80.5 - - - +
300A LYS* 1.3 67.1 + - - +
301A GLN* 4.4 4.7 - - + +
303A ILE* 3.0 20.7 + - - +
565A TYR* 4.6 2.9 - - - -
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Residues in contact with LYS 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299A GLN* 1.3 74.8 - - - +
301A GLN* 1.3 59.7 + - - +
303A ILE* 3.3 2.3 + - - +
304A TYR* 2.9 71.3 + - + -
562A GLU* 4.7 8.8 + - - -
565A TYR* 3.7 48.2 + - + +
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Residues in contact with GLN 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A ARG 5.2 0.7 - - - +
299A GLN* 3.3 3.8 - - + +
300A LYS* 1.3 80.3 - - - +
302A GLY* 1.3 58.1 + - - +
304A TYR* 3.2 22.5 + - - +
305A GLU* 2.9 56.3 + - - +
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Residues in contact with GLY 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A ARG* 3.0 37.2 + - - +
301A GLN* 1.3 77.9 - - - +
303A ILE* 1.3 57.7 + - - +
305A GLU* 3.3 15.6 + - - +
306A GLU* 2.9 27.0 + - - +
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Residues in contact with ILE 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A TYR* 4.0 6.7 - - + -
295A VAL* 4.5 11.9 - - + -
298A ARG* 3.9 27.1 - - + -
299A GLN 3.0 21.9 + - - +
300A LYS 3.8 3.8 - - - +
302A GLY* 1.3 75.4 - - - +
304A TYR* 1.3 63.1 + - - +
306A GLU* 3.2 8.1 + - - +
307A TYR 3.1 17.8 + - - -
564A TYR* 3.6 16.2 - - + -
565A TYR* 3.8 30.3 - - + -
568A TYR* 3.5 48.7 - - + -
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Residues in contact with TYR 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A LYS* 2.9 51.9 + - + +
301A GLN* 3.4 28.0 - - - +
303A ILE* 1.3 75.3 - - - +
305A GLU* 1.3 62.1 + - - +
307A TYR* 3.3 5.2 + - - +
308A GLU* 3.1 28.0 + - + +
561A PRO* 3.5 46.6 - - + +
562A GLU* 3.8 25.6 + - - +
565A TYR* 3.7 18.1 - - + -
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Residues in contact with GLU 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A GLN* 2.9 47.1 + - - +
302A GLY* 3.5 13.9 - - - +
303A ILE 3.3 0.2 - - - -
304A TYR* 1.3 76.5 - - - +
306A GLU* 1.3 63.2 + - - +
308A GLU* 3.2 10.2 + - + +
309A ASP* 3.0 28.4 + - - +
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Residues in contact with GLU 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A TYR* 2.6 30.1 + - - -
298A ARG* 4.0 9.5 + - - -
302A GLY 2.9 13.0 + - - +
303A ILE* 3.2 11.4 + - - +
305A GLU* 1.3 78.2 - - - +
307A TYR* 1.3 61.5 + - - +
309A ASP* 3.2 15.0 + - - +
310A ILE* 3.1 21.5 + - - +
544A PHE* 3.8 20.1 - - + +
564A TYR* 2.5 32.6 + - + +
568A TYR* 2.6 20.9 + - - -
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Residues in contact with TYR 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A ILE 3.1 7.1 + - - +
304A TYR 3.3 7.8 + - - +
306A GLU* 1.3 75.1 - - - +
308A GLU* 1.3 66.2 + - - +
310A ILE* 3.1 13.0 + - + +
311A ARG* 2.8 59.1 + - + +
547A VAL* 5.6 0.7 - - + -
551A ARG* 4.0 11.4 + - - -
558A ILE* 2.6 41.6 + - + -
559A GLN* 3.1 19.3 + - - -
560A THR* 3.7 2.7 - - - -
561A PRO* 3.6 34.3 - - + -
564A TYR* 3.6 44.8 - + + -
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Residues in contact with GLU 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A TYR* 3.1 19.1 + - + +
305A GLU* 3.2 11.4 + - + +
307A TYR* 1.3 91.2 - - - +
309A ASP* 1.3 56.8 + - - +
311A ARG* 3.3 21.9 + - - +
312A ARG* 2.9 41.7 + - + +
561A PRO* 4.2 13.8 - - + +
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Residues in contact with ASP 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A GLU* 3.0 21.3 + - - +
306A GLU* 3.2 16.2 + - + +
308A GLU* 1.3 74.9 - - - +
310A ILE* 1.3 67.1 + - + +
312A ARG* 3.5 12.5 + - - +
313A GLU* 3.6 18.7 + - - +
544A PHE* 5.7 4.3 - - + -
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Residues in contact with ILE 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A GLU 3.1 8.2 + - - +
307A TYR* 3.1 12.0 + - + +
309A ASP* 1.3 79.9 - - - +
311A ARG* 1.3 64.7 - - - +
313A GLU* 3.1 26.7 + - - +
544A PHE* 3.6 28.0 - - + +
547A VAL* 4.2 9.9 - - + -
548A SER* 4.0 14.4 - - - +
551A ARG* 3.5 39.4 + - - +
564A TYR* 3.4 43.3 - - + +
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Residues in contact with ARG 311 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A TYR* 2.8 49.9 + - + +
308A GLU* 3.6 24.0 - - - +
309A ASP 3.3 0.2 - - - -
310A ILE* 1.3 77.8 - - - +
312A ARG* 1.3 61.4 + - + +
313A GLU 3.5 6.4 + - - +
551A ARG* 3.9 19.7 + - - +
559A GLN 5.4 2.2 - - - -
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Residues in contact with ARG 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A GLU* 2.9 26.5 + - + +
309A ASP* 3.9 8.1 - - - +
310A ILE 3.2 0.6 - - - -
311A ARG* 1.3 77.2 - - + +
313A GLU* 1.3 65.7 + - - +
314A ASN* 3.6 6.4 + - - +
----------------------------------------------------------
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Residues in contact with GLU 313 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A ASP 3.6 16.1 + - - +
310A ILE* 3.1 16.4 + - - +
311A ARG 3.7 8.0 - - - +
312A ARG* 1.3 81.4 - - - +
314A ASN* 1.3 69.5 + - - +
315A PRO* 3.7 4.5 - - - +
551A ARG* 5.5 2.3 + - - -
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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
------------------------------------------------------------
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