Contacts of the helix formed by residues 292 - 308 (chain A) in PDB entry 3PMM
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 ALA 292 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278A LEU* 4.1 15.1 - - + +
291A GLU* 1.3 71.4 - - - +
293A SER* 1.3 66.7 + - - +
295A THR* 3.2 9.0 + - - -
296A ALA* 2.9 19.4 + - - +
326A ILE* 3.4 10.7 - - + +
329A ASN* 4.7 4.5 - - + +
336A LEU* 3.8 18.6 - - + -
337A LEU 3.2 27.8 - - - +
338A GLN* 2.9 12.7 + - + +
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Residues in contact with SER 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A ARG* 2.9 21.7 + - - -
291A GLU* 2.6 22.9 + - - -
292A ALA* 1.3 77.0 - - - +
294A ALA* 1.3 62.5 + - - +
296A ALA* 3.1 6.5 + - - +
297A GLY 3.1 16.3 + - - -
336A LEU* 3.7 9.7 - - - +
339A THR* 3.9 17.3 + - - +
362A TYR* 4.2 2.7 - - - -
363A GLY* 4.0 12.1 - - - -
366A MSE 3.2 27.0 - - - +
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Residues in contact with ALA 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A ALA* 3.4 19.7 - - + -
230A ARG* 3.3 30.0 - - - +
233A SER* 3.5 12.7 - - - -
279A TRP* 5.7 0.4 - - + -
291A GLU* 3.0 24.3 + - - +
293A SER* 1.3 75.1 + - - +
295A THR* 1.3 58.6 + - - +
297A GLY 3.0 2.6 + - - -
298A PHE* 2.9 36.2 + - + -
366A MSE 4.3 0.4 - - - +
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Residues in contact with THR 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A GLY 3.6 22.4 - - - +
278A LEU* 3.3 11.8 - - + +
279A TRP* 3.1 36.8 + - + +
291A GLU 2.8 18.7 + - - -
292A ALA* 3.2 13.0 + - - -
294A ALA* 1.3 78.9 - - - +
296A ALA* 1.3 56.1 + - - +
298A PHE* 3.4 2.6 + - - +
299A ALA* 2.9 27.5 + - - +
322A ALA* 4.0 10.5 - - + +
326A ILE* 3.8 15.7 - - + -
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Residues in contact with ALA 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A ALA 2.9 12.5 + - - +
293A SER* 3.1 11.2 + - - +
295A THR* 1.3 76.7 - - - +
297A GLY* 1.3 57.4 + - - +
299A ALA* 3.3 0.6 + - - -
300A TYR* 3.0 24.9 + - - +
326A ILE* 3.6 12.5 - - + +
336A LEU* 4.6 2.7 - - + -
366A MSE 3.7 31.1 - - + +
367A ALA* 4.0 3.8 - - - +
370A CYS* 3.1 25.5 - - - +
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Residues in contact with GLY 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A SER* 4.0 6.8 - - - +
236A THR* 4.5 0.5 - - - -
237A MSE 3.3 37.1 - - - +
293A SER 3.1 7.1 + - - -
294A ALA 3.0 7.3 + - - -
296A ALA* 1.3 75.4 - - - +
298A PHE* 1.3 64.0 + - - +
300A TYR* 3.4 2.2 + - - +
301A GLY* 3.0 18.7 + - - -
366A MSE 4.0 11.3 - - - +
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Residues in contact with PHE 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A ALA* 3.2 26.9 - - + -
232A ASN* 3.7 10.5 - - + -
233A SER* 3.3 22.2 - - - -
236A THR* 3.3 23.3 - - - -
269A LEU* 3.4 35.4 - - + -
279A TRP* 3.5 39.7 - + + -
283A LEU* 4.0 12.6 - - + -
294A ALA* 2.9 31.6 + - + -
295A THR 3.7 4.3 - - - +
297A GLY* 1.3 75.1 - - - +
299A ALA* 1.3 58.1 + - - +
301A GLY 3.3 0.3 + - - -
302A ILE* 2.9 42.2 + - + +
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Residues in contact with ALA 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A THR 2.9 19.1 + - - +
296A ALA* 3.5 7.0 - - - +
297A GLY 3.2 0.2 - - - -
298A PHE* 1.3 76.5 - - - +
300A TYR* 1.3 64.2 + - - +
302A ILE* 4.2 3.4 - - - +
303A LEU* 2.9 33.0 + - - +
319A ALA* 4.8 4.9 - - - +
322A ALA* 4.0 20.2 - - + +
323A ILE* 3.9 19.7 - - + +
326A ILE* 5.2 0.4 - - + -
370A CYS* 3.9 11.9 - - + -
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Residues in contact with TYR 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A TYR* 5.0 0.7 - + - -
76A GLN* 2.8 40.0 + - - -
237A MSE 3.8 35.2 - - + -
241A ASP* 2.9 34.6 + - - -
296A ALA 3.0 14.6 + - - +
297A GLY* 3.6 7.6 - - - +
299A ALA* 1.3 76.6 - - - +
301A GLY* 1.3 60.6 + - - +
303A LEU* 3.7 5.3 - - - +
304A LYS* 2.9 43.5 + - + +
369A LEU* 3.4 38.1 - - + -
370A CYS* 3.6 14.0 - - + +
373A GLU* 3.8 16.7 - - + +
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Residues in contact with GLY 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A THR* 3.2 33.9 - - - -
237A MSE 4.2 0.2 - - - -
240A PRO* 3.8 6.9 - - - +
266A ILE* 4.8 0.4 - - - +
297A GLY 3.0 11.9 + - - -
298A PHE 3.3 2.2 + - - -
300A TYR* 1.3 82.7 - - - +
302A ILE* 1.3 59.3 + - - +
304A LYS* 3.9 0.8 - - - +
305A ALA* 2.9 31.2 + - - +
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Residues in contact with ILE 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A THR* 4.2 4.0 - - + -
266A ILE* 3.9 37.7 - - + -
269A LEU* 4.8 7.2 - - + -
279A TRP* 4.4 15.0 - - + -
298A PHE* 2.9 25.5 + - + +
299A ALA* 4.2 1.8 - - - +
301A GLY* 1.3 73.0 - - - +
303A LEU* 1.3 67.7 + - - +
305A ALA* 3.4 1.0 + - - +
306A VAL* 2.9 24.6 + - + +
315A TYR* 3.7 38.1 - - + +
318A VAL* 3.9 25.1 - - + -
319A ALA* 4.0 13.7 - - + +
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Residues in contact with LEU 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A ALA 2.9 25.5 + - - +
302A ILE* 1.3 78.9 - - - +
304A LYS* 1.3 57.0 + - - +
306A VAL* 3.7 6.4 - - + +
307A ARG* 2.9 29.6 + - - +
316A ALA* 5.5 3.8 - - + +
319A ALA* 3.5 22.7 - - + -
320A GLU 5.3 0.7 - - - +
323A ILE* 3.9 17.3 - - + -
370A CYS 3.7 23.1 - - - +
373A GLU* 3.5 17.7 - - + +
374A TYR* 3.8 23.1 - - + +
377A LYS* 4.2 27.8 - - + +
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Residues in contact with LYS 304 (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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76A GLN* 5.1 2.0 + - - +
240A PRO* 3.8 20.6 - - + -
241A ASP* 2.7 28.2 + - - +
244A GLU* 2.8 42.0 + - - -
300A TYR* 2.9 34.2 + - + +
301A GLY* 3.9 4.3 - - - +
303A LEU* 1.3 76.9 - - - +
305A ALA* 1.3 57.8 + - - +
307A ARG* 3.2 28.9 + - - +
308A LYS* 2.9 45.6 + - + +
373A GLU* 3.6 15.7 + - + +
382A FMT 4.6 8.9 + - - -
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Residues in contact with ALA 305 (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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240A PRO* 4.2 2.6 - - + +
262A LEU* 3.8 28.5 - - + -
266A ILE* 4.2 5.6 - - + -
301A GLY 2.9 19.0 + - - +
302A ILE 3.8 2.9 - - - +
304A LYS* 1.3 76.2 - - - +
306A VAL* 1.3 61.0 + - - +
308A LYS 3.7 0.3 + - - -
309A ARG 3.1 2.1 + - - -
310A TYR* 2.9 40.9 + - + +
311A VAL* 3.5 19.7 + - + -
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Residues in contact with VAL 306 (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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302A ILE* 2.9 21.6 + - + +
303A LEU* 3.7 7.4 - - + +
305A ALA* 1.3 74.1 - - - +
307A ARG* 1.3 67.6 + - - +
309A ARG* 3.0 6.9 + - - +
311A VAL* 3.9 12.1 - - + -
312A GLY 3.8 18.2 - - - +
313A GLN* 2.9 55.8 + - - +
315A TYR* 3.9 15.0 - - + -
316A ALA* 4.0 19.3 - - + +
319A ALA* 6.1 0.2 - - + -
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Residues in contact with ARG 307 (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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76A GLN* 5.7 0.8 + - - -
244A GLU* 4.8 4.6 + - - -
303A LEU 2.9 17.3 + - - +
304A LYS* 3.2 29.5 + - - +
306A VAL* 1.3 79.2 - - - +
308A LYS* 1.3 73.6 + - + +
309A ARG* 3.4 8.8 + - - +
373A GLU* 2.8 39.1 + - - +
376A ARG* 3.7 53.2 - - - +
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Residues in contact with LYS 308 (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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244A GLU* 3.3 35.6 + - + +
255A ARG* 5.3 1.6 + - - -
304A LYS* 2.9 35.4 + - + +
307A ARG* 1.3 92.3 - - + +
309A ARG* 1.3 69.6 + - - +
310A TYR* 3.3 52.2 + - + +
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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) + - + + + + + -
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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