Contacts of the helix formed by residues 297 - 310 (chain A) in PDB entry 5PAH
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 ARG 297 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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237A CYS 5.5 2.0 - - - +
238A THR* 3.7 17.8 - - + +
261A ARG* 5.4 7.0 - - - +
295A SER 3.9 1.0 + - - -
296A ASP* 1.3 74.8 + - - +
298A SER* 1.3 67.5 + - - +
300A ALA* 3.2 2.6 + - - +
301A GLN* 3.0 54.4 + - + +
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Residues in contact with SER 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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296A ASP* 3.2 11.8 + - - -
297A ARG* 1.3 83.7 + - - +
299A PHE* 1.3 64.3 + - - +
301A GLN* 3.3 8.6 + - - +
302A PHE* 3.0 22.5 + - - +
392A PHE* 4.0 17.9 - - - +
393A ASN* 3.0 34.6 + - - +
396A LYS* 5.3 0.5 - - - +
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Residues in contact with PHE 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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290A HIS* 5.3 0.7 - - - -
293A LEU* 3.4 50.3 - - + +
294A PHE* 3.7 21.5 - + - -
296A ASP* 2.9 17.2 + - + +
298A SER* 1.3 75.7 - - - +
300A ALA* 1.3 57.9 + - - +
302A PHE* 3.2 16.1 + + - +
303A SER* 2.9 54.5 + - - -
329A VAL* 4.1 26.7 - - + -
343A TYR* 3.9 28.3 - + - -
392A PHE* 4.0 32.7 - + + +
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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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238A THR* 3.9 25.1 - - + -
240A PHE* 3.8 25.5 - - + -
261A ARG* 4.3 11.2 + - - +
294A PHE* 4.4 2.2 - - - +
296A ASP 2.9 18.6 + - - +
297A ARG* 3.5 5.8 - - - +
299A PHE* 1.3 82.5 - - - +
301A GLN* 1.3 61.6 - - - +
303A SER* 3.5 2.9 + - - -
304A GLN* 3.1 24.1 + - - +
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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
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261A ARG* 3.6 23.3 - - - +
297A ARG* 3.0 49.2 + - + +
298A SER* 3.7 11.6 + - - +
300A ALA* 1.3 74.3 - - - +
302A PHE* 1.3 66.9 + - - +
304A GLN* 3.3 5.8 + - - +
305A GLU* 3.0 24.4 + - - +
393A ASN* 4.3 4.3 + - - -
396A LYS* 2.9 36.6 + - + +
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Residues in contact with PHE 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 SER 3.0 14.7 + - - +
299A PHE* 3.2 31.6 + + - +
301A GLN* 1.3 77.0 - - - +
303A SER* 1.3 64.1 + - - +
305A GLU* 3.2 12.0 + - - +
306A ILE* 3.4 24.7 + - + +
324A ILE* 5.5 0.4 - - + -
328A THR* 3.5 42.2 - - + -
329A VAL* 4.2 9.9 - - + -
343A TYR* 4.7 5.8 - + - -
367A LEU* 5.8 0.4 - - + -
392A PHE* 3.8 19.3 - + + +
395A ALA* 3.7 17.3 - - + -
396A LYS* 3.7 29.3 - - - +
399A VAL* 3.7 24.5 - - + -
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Residues in contact with SER 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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240A PHE* 4.2 7.9 - - - -
258A LEU* 3.7 18.8 - - - +
294A PHE* 3.5 17.0 - - - -
299A PHE* 2.9 48.0 + - - -
300A ALA 3.7 4.9 - - - -
302A PHE* 1.3 76.0 - - - +
304A GLN* 1.3 62.8 + - - +
306A ILE* 3.2 21.7 + - - +
307A GLY 3.2 8.8 + - - -
329A VAL* 4.6 4.8 - - - +
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Residues in contact with GLN 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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240A PHE* 5.1 0.8 - - + -
258A LEU 3.5 15.7 - - - +
259A ALA* 2.9 28.8 + - - +
261A ARG* 2.9 42.2 + - + +
300A ALA 3.1 14.5 + - - +
301A GLN* 3.7 5.4 - - - +
303A SER* 1.3 77.5 - - - +
305A GLU* 1.3 60.1 + - - +
307A GLY* 3.1 2.6 + - - -
308A LEU* 2.9 39.6 + - + +
414A TYR* 3.2 32.5 - - - +
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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
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301A GLN 3.0 11.7 + - - +
302A PHE 3.2 10.5 + - - +
304A GLN* 1.3 73.3 - - - +
306A ILE* 1.3 66.1 + - - +
308A LEU* 3.3 18.3 + - - +
309A ALA* 3.0 24.9 + - - +
396A LYS* 3.8 25.4 - - + +
399A VAL* 3.7 20.0 - - + +
400A ARG* 3.3 49.0 + - - +
403A ALA* 5.6 3.0 - - + +
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Residues in contact with ILE 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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255A LEU* 4.2 27.4 - - + -
258A LEU* 4.8 2.7 - - + -
302A PHE* 3.4 39.5 + - + +
303A SER* 3.2 10.7 + - - +
305A GLU* 1.3 77.2 - - - +
307A GLY* 1.3 64.4 + - - +
309A ALA* 3.3 4.6 + - - +
310A SER* 3.2 19.9 + - - -
321A LEU* 4.5 23.2 - - + +
324A ILE* 4.8 7.4 - - + -
325A TYR* 4.6 10.5 - - + -
328A THR* 4.2 9.4 - - - +
329A VAL* 4.2 13.0 - - + -
399A VAL* 4.0 22.7 - - + -
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Residues in contact with GLY 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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255A LEU 3.2 25.7 - - - +
258A LEU* 4.0 2.6 - - - +
259A ALA* 3.7 14.7 - - - +
303A SER 3.2 4.9 + - - -
304A GLN 3.1 7.8 + - - -
306A ILE* 1.3 82.7 - - - +
308A LEU* 1.3 59.9 + - - +
310A SER* 2.7 22.2 + - - -
311A LEU* 3.5 10.4 + - - +
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Residues in contact with LEU 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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259A ALA* 4.0 19.5 - - + -
304A GLN* 2.9 39.9 + - + +
305A GLU* 3.8 22.2 - - - +
306A ILE 3.2 0.2 - - - -
307A GLY* 1.3 76.7 - - - +
309A ALA* 1.3 60.0 + - - +
310A SER 3.3 0.5 + - - -
311A LEU* 3.4 6.9 + - + +
408A ARG* 2.9 22.1 + - - -
412A VAL* 3.5 31.4 - - + +
413A ARG* 4.6 1.8 - - - -
414A TYR* 4.3 19.7 - - + +
421A ILE* 4.1 17.0 - - + -
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Residues in contact with ALA 309 (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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305A GLU 3.0 16.4 + - - +
306A ILE 3.3 5.4 + - - +
308A LEU* 1.3 76.5 - - - +
310A SER* 1.3 62.0 + - - +
313A ALA* 3.8 4.9 - - - +
321A LEU* 3.8 22.2 - - + -
399A VAL* 4.6 4.9 - - + -
402A PHE* 5.9 0.2 - - + -
403A ALA* 3.6 25.4 - - + -
406A ILE* 3.6 16.2 - - + +
408A ARG* 3.4 23.1 + - - +
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Residues in contact with SER 310 (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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252A ARG* 4.1 4.9 + - - +
255A LEU* 3.8 14.5 - - - -
256A GLY* 3.6 22.0 + - - -
306A ILE 3.2 11.4 + - - -
307A GLY 2.7 19.4 + - - -
308A LEU 3.1 1.2 - - - -
309A ALA* 1.3 79.3 - - - +
311A LEU* 1.3 64.6 + - - +
312A GLY 3.1 3.6 + - - -
313A ALA* 3.1 9.9 + - - -
318A ILE* 3.4 25.6 - - - +
321A LEU* 3.6 17.3 - - - -
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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