Contacts of the helix formed by residues 291 - 305 (chain A) in PDB entry 3PM0
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 291 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155A PHE* 3.4 14.8 - - - -
207A ALA 3.6 4.0 - - - +
208A VAL 4.2 2.5 - - - -
209A CYS 3.5 1.3 - - - +
210A PHE* 2.5 33.0 + - - +
211A GLY* 2.6 28.6 + - - -
279A HIS* 2.5 19.6 + - - -
289A PRO* 3.6 2.5 - - - +
290A ARG* 1.3 87.0 + - - +
292A MET* 1.3 63.0 + - - +
293A MET* 3.4 10.3 - - + +
294A ASP* 3.5 14.2 - - + +
295A ALA* 3.2 20.9 + - - +
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Residues in contact with MET 292 (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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151A MET* 3.8 17.0 - - + -
152A MET* 4.6 11.7 - - - +
155A PHE* 3.6 16.4 - - + -
156A PHE* 5.6 0.7 - - - -
205A MET* 5.6 0.9 - - - -
208A VAL* 3.4 27.0 + - - +
209A CYS* 3.8 15.5 + - - -
291A ASP* 1.3 74.5 - - - +
293A MET* 1.3 60.8 + - - +
294A ASP 3.4 0.2 - - - -
295A ALA* 3.6 3.0 - - - +
296A PHE* 3.0 49.3 + - + -
324A ILE* 3.4 19.5 - - + -
327A ILE* 3.1 55.4 - - + -
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Residues in contact with MET 293 (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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209A CYS 3.2 20.3 + - - +
210A PHE* 4.3 17.3 - - + -
272A ILE* 3.8 17.5 - - + +
275A LYS* 4.0 11.0 - - + -
276A PHE* 3.6 46.2 - - + +
279A HIS* 3.3 37.0 - - + +
291A ASP* 4.0 0.2 - - + -
292A MET* 1.3 78.9 - - - +
294A ASP* 1.3 63.8 + - - +
296A PHE* 3.7 3.1 - - - +
297A ILE* 3.0 27.4 + - + +
320A VAL* 4.6 9.0 - - - -
324A ILE* 4.3 15.2 - - + +
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Residues in contact with ASP 294 (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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279A HIS* 3.5 31.4 - - - +
283A LEU* 3.3 31.9 - - + +
288A ALA 4.5 0.7 - - - +
289A PRO* 3.4 22.4 - - + +
290A ARG* 3.3 31.1 + - - +
291A ASP* 3.5 7.3 + - - +
292A MET 3.4 0.2 - - - -
293A MET* 1.3 80.3 - - - +
295A ALA* 1.3 55.8 + - - +
297A ILE* 4.5 4.3 - - - -
298A LEU* 3.0 31.2 + - - +
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Residues in contact with ALA 295 (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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151A MET* 3.8 23.5 - - - +
155A PHE* 4.4 6.1 - - + -
289A PRO* 4.1 9.6 - - + +
291A ASP 3.2 18.6 + - - +
292A MET* 3.6 9.0 - - - +
293A MET 3.1 0.8 - - - -
294A ASP* 1.3 79.9 - - - +
296A PHE* 1.3 61.3 + - - +
298A LEU* 3.9 4.6 - - - +
299A SER* 3.3 22.2 + - - -
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Residues in contact with PHE 296 (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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147A ALA* 4.0 11.2 - - + -
148A ALA* 4.5 4.9 - - - -
151A MET* 3.3 38.6 - - + -
292A MET* 3.0 55.0 + - + +
293A MET* 3.7 2.2 - - - +
295A ALA* 1.3 74.3 - - - +
297A ILE* 1.3 61.0 + - - +
299A SER* 3.4 5.7 + - - -
300A ALA* 2.9 29.5 + - - +
315A LEU* 3.6 32.8 - - + +
320A VAL* 3.7 25.9 - - + +
323A THR* 4.1 13.7 - - - -
324A ILE* 4.2 11.7 - - + -
327A ILE* 4.1 10.5 - - + -
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Residues in contact with ILE 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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276A PHE* 3.9 24.7 - - + +
279A HIS* 3.7 16.6 - - + -
280A CYS* 3.1 48.2 - - - +
283A LEU* 4.1 12.3 - - + -
293A MET* 3.0 16.3 + - + +
294A ASP* 3.8 4.7 - - - +
296A PHE* 1.3 73.6 - - - +
298A LEU* 1.3 65.5 + - - +
300A ALA* 3.1 3.3 + - - +
301A GLU* 2.9 50.8 + - + +
317A LEU* 4.3 9.2 - - + -
320A VAL* 4.4 4.9 - - + -
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Residues in contact with LEU 298 (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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283A LEU* 4.0 16.4 - - + +
285A PRO 5.8 3.8 - - - +
287A ALA 4.9 4.9 - - - +
289A PRO* 3.8 34.3 - - + -
294A ASP 3.0 16.0 + - - +
295A ALA* 3.9 5.4 - - - +
297A ILE* 1.3 75.8 - - - +
299A SER* 1.3 53.2 + - - +
301A GLU* 3.0 8.6 + - + +
302A LYS* 2.7 61.7 + - + +
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Residues in contact with SER 299 (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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151A MET* 5.0 6.3 - - - -
295A ALA 3.3 17.4 + - - -
296A PHE* 3.5 9.6 - - - -
298A LEU* 1.3 78.5 - - - +
300A ALA* 1.3 58.5 + - - +
302A LYS* 3.4 7.6 + - - +
303A LYS* 2.9 27.2 + - - +
314A ARG* 3.2 33.6 + - - +
315A LEU 4.3 2.9 + - - -
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Residues in contact with ALA 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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296A PHE 2.9 17.0 + - - +
297A ILE 3.1 5.6 + - - +
299A SER* 1.3 73.6 - - - +
301A GLU* 1.3 61.3 + - - +
303A LYS* 3.3 2.8 + - - +
304A ALA* 3.0 28.2 + - - +
315A LEU 3.4 24.5 - - - +
316A ASP* 4.1 1.2 - - - -
317A LEU* 3.7 37.0 + - + +
320A VAL* 4.2 4.0 - - + -
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Residues in contact with GLU 301 (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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280A CYS* 4.9 9.5 - - - +
283A LEU* 4.6 14.3 - - - +
297A ILE* 2.9 40.0 + - + +
298A LEU* 3.6 8.5 - - + +
300A ALA* 1.3 74.7 - - - +
302A LYS* 1.3 73.9 + - + +
303A LYS 3.1 0.4 - - - -
304A ALA* 3.7 5.5 - - - +
305A ALA* 2.8 34.9 + - - +
317A LEU* 4.8 17.5 - - + +
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Residues in contact with LYS 302 (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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298A LEU* 2.7 41.4 + - + +
299A SER* 3.6 7.2 - - - +
301A GLU* 1.3 88.1 + - + +
303A LYS* 1.3 60.5 + - - +
305A ALA* 3.5 31.4 - - - +
306A GLY 3.8 3.3 - - - +
307A ASP 4.2 3.0 - - - -
314A ARG* 3.5 26.8 + - - +
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Residues in contact with LYS 303 (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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143A VAL* 4.9 6.7 - - - +
299A SER 2.9 16.0 + - - +
300A ALA* 3.5 6.7 - - - +
301A GLU 3.1 0.4 - - - -
302A LYS* 1.3 76.4 - - - +
304A ALA* 1.3 62.4 + - - +
305A ALA 3.1 0.2 - - - -
306A GLY 2.9 21.7 - - - +
314A ARG* 3.0 51.8 + - + +
315A LEU 3.4 15.7 - - - +
316A ASP* 3.0 35.3 + - - +
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Residues in contact with ALA 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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300A ALA 3.0 16.8 + - - +
301A GLU* 3.9 5.6 - - - +
303A LYS* 1.3 79.7 - - - +
305A ALA* 1.3 57.6 + - - +
306A GLY 3.0 7.1 + - - -
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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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301A GLU 2.8 19.9 + - - +
302A LYS* 3.5 25.1 - - - +
303A LYS 3.1 0.2 - - - -
304A ALA* 1.3 74.5 - - - +
306A GLY* 1.3 64.4 + - - +
307A ASP* 3.3 4.3 + - - -
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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
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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