Contacts of the helix formed by residues 317 - 331 (chain A) in PDB entry 5E0F
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 317 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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267A ARG* 3.1 32.6 + - - -
312A ILE 4.0 1.2 - - - +
313A LEU* 3.8 14.9 - - + -
314A THR* 2.8 30.8 + - - +
316A TRP* 1.3 81.2 - - - +
318A ALA* 1.3 63.6 + - - +
319A ARG 3.1 3.5 + - - -
320A LEU* 3.2 8.4 + - + -
321A TYR* 2.9 17.7 + - - +
346A ARG* 5.7 1.0 + - - -
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Residues in contact with ALA 318 (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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315A PHE 3.3 17.2 + - - +
316A TRP 3.4 3.2 + - - -
317A ASP* 1.3 74.6 - - - +
319A ARG* 1.3 62.4 + - - +
321A TYR* 3.5 6.1 - - - +
322A LYS* 3.0 36.8 + - - +
388A TRP* 3.8 19.3 - - + -
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Residues in contact with ARG 319 (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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317A ASP 3.1 1.2 + - - -
318A ALA* 1.3 79.1 - - - +
320A LEU* 1.3 83.5 + - + +
322A LYS* 3.5 14.7 + - - +
323A MET* 3.4 17.3 + - - +
430A ASN 5.4 0.6 + - - -
431A ASN* 5.0 4.4 + - - -
481A ASN 3.2 24.2 + - - -
482A SER* 4.2 2.8 + - - +
483A ALA 2.8 29.5 + - - +
484A GLU* 3.2 25.7 + - - +
485A ASP* 5.1 0.7 - - - +
486A PRO* 3.6 27.3 - - + +
487A PHE* 5.5 0.9 - - - -
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Residues in contact with LEU 320 (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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266A ILE* 3.8 29.5 - - + +
267A ARG* 4.4 17.7 - - + +
313A LEU* 3.9 24.0 - - + -
317A ASP* 3.2 7.4 + - + +
319A ARG* 1.3 96.4 - - + +
321A TYR* 1.3 60.4 + - - +
323A MET* 3.1 25.3 + - + +
324A ALA* 2.9 28.9 + - - +
431A ASN* 4.2 8.1 - - - +
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Residues in contact with TYR 321 (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 VAL* 3.7 15.8 - - + +
297A ASP* 2.6 34.2 + - - -
313A LEU* 3.3 30.7 - - - +
314A THR* 3.3 19.5 - - - +
315A PHE 4.1 9.0 - - - -
317A ASP 2.9 17.8 + - - +
318A ALA* 3.5 5.2 - - - +
319A ARG 3.2 0.2 - - - -
320A LEU* 1.3 77.1 - - - +
322A LYS* 1.3 62.2 + - - +
324A ALA* 3.2 2.8 + - - +
325A VAL* 2.9 46.3 + - + +
338A VAL* 5.7 0.9 - - + +
339A MET* 3.5 19.8 + - - +
385A GLU* 4.1 23.2 + - + -
388A TRP* 4.1 15.3 - + - -
391A ILE* 4.1 8.7 - - + -
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Residues in contact with LYS 322 (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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318A ALA* 3.0 35.1 + - - +
319A ARG* 3.8 10.7 - - - +
321A TYR* 1.3 75.3 - - - +
323A MET* 1.3 58.4 + - - +
325A VAL* 3.8 5.8 - - - +
326A GLY* 2.8 24.1 + - - -
388A TRP* 3.7 25.8 - - + -
390A GLN* 3.3 42.6 - - + +
391A ILE* 4.4 8.9 - - + +
484A GLU* 4.7 14.3 + - - +
485A ASP* 2.8 22.9 + - - +
487A PHE* 3.5 22.1 - - + -
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Residues in contact with MET 323 (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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266A ILE* 4.4 12.3 - - + -
274A MET* 4.6 2.9 - - - +
319A ARG* 3.4 6.9 + - - +
320A LEU* 3.1 27.4 + - + +
322A LYS* 1.3 79.0 - - - +
324A ALA* 1.3 56.8 + - - +
326A GLY 3.3 0.3 + - - -
327A PHE* 2.9 26.3 + - - +
429A PHE* 3.3 37.0 - - + -
431A ASN* 3.6 35.0 - - - +
486A PRO* 3.4 41.5 - - + +
487A PHE* 3.9 13.8 - - + -
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Residues in contact with ALA 324 (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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262A LEU* 3.5 28.1 - - + +
266A ILE* 4.1 12.9 - - + +
296A VAL* 4.0 15.5 - - + -
313A LEU* 3.9 20.9 - - + -
320A LEU 2.9 12.7 + - - +
321A TYR 3.7 7.0 - - - +
323A MET* 1.3 76.6 - - - +
325A VAL* 1.3 61.4 + - - +
327A PHE* 3.3 1.9 + - - +
328A MET* 3.0 20.4 + - - +
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Residues in contact with VAL 325 (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 VAL* 3.8 21.8 - - + -
321A TYR* 2.9 49.7 + - + +
322A LYS 3.9 2.7 - - - +
324A ALA* 1.3 75.3 - - - +
326A GLY* 1.3 57.2 + - - +
328A MET* 3.3 11.3 + - + +
329A LEU* 2.9 50.7 + - + +
338A VAL* 4.7 6.5 - - + -
391A ILE* 4.0 29.6 - - + -
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Residues in contact with GLY 326 (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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322A LYS 2.8 17.8 + - - -
323A MET 3.7 1.3 - - - -
324A ALA 3.2 0.2 - - - -
325A VAL* 1.3 77.0 - - - +
327A PHE* 1.3 62.2 + - - +
329A LEU 3.4 0.3 + - - -
330A ALA* 3.0 25.5 + - - +
390A GLN 5.5 0.4 - - - -
394A MET* 3.6 27.9 - - - +
427A ILE* 3.9 1.3 - - - +
429A PHE* 4.1 5.4 - - - -
487A PHE* 4.1 9.0 - - - -
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Residues in contact with PHE 327 (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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262A LEU* 4.0 16.8 - - + -
266A ILE* 5.5 0.4 - - + -
274A MET* 4.0 14.1 - - + -
277A LEU* 3.7 39.7 - - + -
280A TRP* 3.5 35.0 - + - -
323A MET 2.9 17.1 + - - +
324A ALA* 3.7 5.8 - - - +
326A GLY* 1.3 76.0 - - - +
328A MET* 1.3 64.1 + - - +
330A ALA* 3.3 3.5 + - - +
331A HIS* 3.0 38.2 + + + +
409A TRP* 4.7 6.5 - + - -
417A VAL* 5.2 1.3 - - + -
419A PHE* 3.6 27.8 - + - -
429A PHE* 3.6 24.0 - + + -
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Residues in contact with MET 328 (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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258A TYR* 3.2 36.8 + - + +
262A LEU* 4.5 0.7 - - + -
294A VAL* 4.1 2.2 - - + -
295A PHE* 3.6 37.0 - - - -
296A VAL* 4.0 9.4 - - + +
324A ALA 3.0 17.6 + - - +
325A VAL* 3.5 15.7 - - + +
327A PHE* 1.3 77.6 - - - +
329A LEU* 1.3 85.6 + - + +
331A HIS* 3.3 11.6 + - - +
333A TYR 5.0 0.5 - - - +
336A THR* 3.7 20.0 - - + +
337A ARG 3.8 19.3 - - - +
338A VAL* 4.6 3.6 - - + -
398A ARG* 3.2 12.6 + - - -
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Residues in contact with LEU 329 (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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12A SER* 3.6 23.8 - - - +
325A VAL* 2.9 37.2 + - + +
326A GLY 4.0 0.9 - - - +
328A MET* 1.3 83.5 - - + +
330A ALA* 1.3 56.8 + - - +
336A THR* 3.7 20.0 - - + +
338A VAL* 4.3 9.2 - - + -
391A ILE* 3.9 6.3 - - + +
394A MET* 3.6 39.3 - - + +
395A VAL* 3.7 19.5 - - + +
398A ARG* 2.8 40.6 + - - +
421A ARG* 4.8 0.7 + - - -
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Residues in contact with ALA 330 (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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326A GLY 3.0 17.2 + - - +
327A PHE* 3.9 1.6 - - - +
329A LEU* 1.3 77.3 - - - +
331A HIS* 1.3 58.8 + - - +
394A MET* 3.8 7.8 - - + +
397A PHE* 3.8 24.0 - - + -
419A PHE* 3.6 19.8 - - + -
421A ARG* 2.8 34.6 + - - +
427A ILE* 3.9 14.1 - - + -
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Residues in contact with HIS 331 (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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258A TYR* 4.7 2.7 - - - +
278A LYS 5.3 0.4 + - - -
280A TRP* 3.5 49.3 + + + +
327A PHE* 3.0 35.2 + + + +
328A MET 3.3 7.1 + - - +
330A ALA* 1.3 78.0 - - - +
332A PRO* 1.3 78.6 - - + +
333A TYR* 3.1 38.0 + - + +
398A ARG* 2.7 23.7 + - - -
406A PHE* 3.8 35.4 - + - -
419A PHE* 4.1 5.8 - + + -
421A ARG* 3.9 0.2 - - - -
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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
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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