Contacts of the helix formed by residues 323 - 340 (chain A) in PDB entry 5U3W
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 PRO 323 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322A LYS* 1.3 84.2 - - + +
324A PHE* 1.3 73.4 + - + +
325A SER 3.5 2.0 - - - -
326A ASP* 3.7 12.2 + - + +
327A ILE* 3.4 22.2 + - - +
416A MET* 5.5 2.6 - - + +
419A ARG* 5.9 4.0 - - + -
420A ILE* 3.7 32.0 - - + +
423A THR* 4.8 5.6 - - - +
424A GLU* 3.3 33.9 - - + +
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Residues in contact with PHE 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A SER* 3.8 29.6 - - - +
243A VAL* 4.0 11.9 - - + -
246A PHE* 3.7 46.4 - + + -
320A LEU* 4.6 8.5 - - + -
321A ARG* 2.9 24.5 + - + +
323A PRO* 1.3 90.2 - - + +
325A SER* 1.3 67.0 + - - +
327A ILE* 3.4 13.7 - - + +
328A ILE* 3.3 22.2 - - + +
420A ILE* 4.3 19.5 - - + -
424A GLU* 3.9 23.3 - - + -
427A THR* 3.9 19.7 - - - -
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Residues in contact with SER 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A LEU 3.6 23.0 - - - +
318A ARG* 3.6 16.0 + - - +
320A LEU* 3.2 24.4 + - - +
321A ARG 3.3 7.8 + - - -
322A LYS* 3.8 9.2 + - - +
324A PHE* 1.3 75.4 - - - +
326A ASP* 1.3 73.7 + - - +
328A ILE* 3.2 13.5 + - - +
329A GLU* 3.3 17.0 + - - +
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Residues in contact with ASP 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* 3.1 49.7 + - - +
323A PRO* 3.7 11.5 + - + +
324A PHE 3.3 0.6 - - - -
325A SER* 1.3 86.4 + - - +
327A ILE* 1.3 57.0 + - - +
329A GLU* 5.4 1.3 - - - -
330A PRO* 3.0 28.0 - - - +
416A MET* 3.5 15.9 - - - +
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Residues in contact with ILE 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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246A PHE* 5.1 4.3 - - + -
323A PRO 3.4 12.1 + - - +
324A PHE* 3.4 16.6 - - + +
326A ASP* 1.3 78.1 - - - +
328A ILE* 1.3 63.0 + - + +
330A PRO* 4.1 0.4 - - - -
331A LYS* 2.7 35.0 + - - +
413A HIS* 3.6 25.8 - - + +
416A MET* 3.7 25.6 - - + -
417A MET* 3.2 38.6 - - + -
420A ILE* 3.9 14.1 - - + -
502A 7U1 4.0 21.3 - - + -
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Residues in contact with ILE 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A VAL* 4.7 7.4 - - + -
246A PHE* 6.5 0.2 - - - -
249A CYS* 4.7 7.6 - - - -
317A LEU* 4.0 39.9 - - + -
320A LEU* 4.3 13.5 - - + -
324A PHE* 3.3 19.1 - - + +
325A SER* 3.2 7.3 + - - +
326A ASP 3.2 0.4 - - - -
327A ILE* 1.3 85.7 - - + +
329A GLU* 1.3 67.1 + - - +
330A PRO 3.4 0.9 - - - -
331A LYS* 3.0 21.1 + - - +
332A PHE* 3.7 27.7 + - + -
502A 7U1 3.6 30.0 - - + -
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Residues in contact with GLU 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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314A ARG* 2.9 46.0 + - - +
318A ARG* 2.9 37.7 + - + +
325A SER 3.3 11.7 + - - +
326A ASP* 5.0 1.3 - - - +
328A ILE* 1.3 79.1 - - - +
330A PRO* 1.3 72.4 - - + +
331A LYS 3.1 1.0 + - - -
332A PHE* 3.1 12.8 + - - +
333A GLU* 3.2 30.5 + - - +
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Residues in contact with PRO 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 ASP* 3.0 23.8 - - - +
327A ILE 4.1 2.7 - - - -
328A ILE 3.5 3.4 - - - -
329A GLU* 1.3 94.8 - - + +
331A LYS* 1.3 64.0 + - + +
332A PHE 3.3 0.2 - - - -
333A GLU* 3.5 18.6 + - - +
334A PHE* 3.2 22.2 + - - +
409A LEU* 3.8 20.3 - - + +
412A GLU* 5.2 7.0 - - - +
416A MET* 4.5 13.0 - - + -
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Residues in contact with LYS 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A PHE* 3.6 41.7 - - + +
294A LEU* 3.8 13.1 - - + +
298A VAL* 6.2 0.2 - - - -
327A ILE* 2.7 33.1 + - - +
328A ILE 3.0 10.2 + - - +
330A PRO* 1.3 84.3 - - + +
332A PHE* 1.3 59.6 + - - +
334A PHE* 3.6 6.9 + - - +
335A ALA* 3.0 28.5 + - - +
409A LEU* 4.6 11.9 + - + +
413A HIS* 2.9 39.0 + - - +
416A MET* 4.0 9.7 - - - +
502A 7U1 3.7 21.5 - - + -
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Residues in contact with PHE 332 (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 VAL* 3.6 20.9 - - + -
299A ASN 3.7 7.4 - - - -
302A GLY* 3.6 40.2 - - - -
303A LEU* 4.2 17.5 - - + -
314A ARG* 3.5 49.8 - - + +
317A LEU* 4.0 10.5 - - + -
328A ILE* 3.8 33.0 - - + -
329A GLU* 3.1 12.1 + - - +
331A LYS* 1.3 77.9 - - + +
333A GLU* 1.3 66.1 + - - +
335A ALA* 3.7 4.4 - - - +
336A VAL* 3.0 30.2 + - + +
502A 7U1 5.0 6.3 - + - -
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Residues in contact with GLU 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A ARG* 3.9 7.9 - - - +
329A GLU* 3.2 40.3 + - - +
330A PRO* 3.7 17.3 - - - +
332A PHE* 1.3 79.3 - - - +
334A PHE* 1.3 63.8 + - - +
336A VAL* 4.4 2.9 - - - +
337A LYS* 3.5 31.4 + - - +
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Residues in contact with PHE 334 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A PHE* 4.1 17.9 - - + -
292A ALA* 4.4 4.0 - - - -
295A ALA* 5.2 0.4 - - + -
330A PRO 3.2 15.2 + - - +
331A LYS 3.8 5.8 - - - +
333A GLU* 1.3 79.7 - - - +
335A ALA* 1.3 62.0 + - - +
337A LYS* 3.3 13.8 + - - +
338A PHE* 2.8 59.4 + + + +
402A LYS* 4.2 22.6 + - + -
405A ASP* 4.2 17.0 - - + -
406A LEU* 3.4 40.2 - - + -
409A LEU* 3.9 23.3 - - + -
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Residues in contact with ALA 335 (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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291A PHE 5.6 0.4 - - - +
294A LEU* 5.5 1.6 - - + -
295A ALA* 3.8 28.5 - - + +
298A VAL* 3.6 29.8 - - + -
331A LYS 3.0 19.7 + - - +
332A PHE 3.2 1.8 + - - +
334A PHE* 1.3 78.8 - - + +
336A VAL* 1.3 59.3 + - - +
338A PHE* 3.8 0.6 - - - +
339A ASN* 2.8 35.8 + - - +
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Residues in contact with VAL 336 (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 VAL* 4.8 3.6 - - + -
299A ASN* 4.3 6.3 - - - +
300A LYS* 3.9 38.6 - - + +
314A ARG* 4.3 9.4 - - - +
332A PHE* 3.0 20.2 + - + +
333A GLU* 4.4 3.6 - - - +
334A PHE 3.3 0.2 - - - -
335A ALA* 1.3 77.3 - - - +
337A LYS* 1.3 65.6 + - + +
339A ASN* 3.5 6.9 + - - +
340A ALA* 3.3 19.6 + - - +
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Residues in contact with LYS 337 (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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333A GLU* 3.5 22.9 + - - +
334A PHE* 3.3 12.2 + - - +
335A ALA 3.2 0.2 - - - -
336A VAL* 1.3 78.4 - - + +
338A PHE* 1.3 65.5 + - - +
340A ALA* 3.2 19.7 + - - +
341A LEU* 4.0 7.1 + - - +
402A LYS* 4.0 23.2 + - - +
405A ASP* 5.9 0.8 + - - -
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Residues in contact with PHE 338 (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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194A LYS* 5.5 2.9 + - - -
292A ALA* 3.9 18.2 - - + -
295A ALA* 3.8 18.2 - - + -
334A PHE* 2.8 47.0 + + + +
335A ALA* 3.8 4.0 - - - +
337A LYS* 1.3 71.2 - - - +
339A ASN* 1.3 65.0 + - - +
341A LEU* 3.1 25.1 + - + +
342A GLU 4.2 1.0 + - - -
343A LEU* 3.8 24.6 + - + +
348A LEU* 3.9 17.3 - - + -
351A PHE* 3.8 35.9 - + - -
399A LEU* 4.0 14.1 - - + -
402A LYS* 3.9 22.1 - - + +
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Residues in contact with ASN 339 (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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194A LYS* 3.9 23.5 + - - +
198A ARG* 5.4 13.8 + - - +
295A ALA* 2.9 40.3 + - - +
296A SER* 4.2 0.3 + - - -
298A VAL* 3.0 19.4 + - - +
299A ASN* 5.1 1.0 - - - +
335A ALA 2.8 27.5 + - - +
336A VAL* 3.9 6.7 - - - +
337A LYS 3.3 0.2 - - - -
338A PHE* 1.3 76.1 - - - +
340A ALA* 1.3 60.6 + - - +
341A LEU 3.0 1.3 - - - -
342A GLU* 3.1 20.0 + - - +
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Residues in contact with ALA 340 (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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336A VAL 3.3 11.3 + - - +
337A LYS* 3.2 15.6 + - - +
339A ASN* 1.3 76.2 - - - +
341A LEU* 1.3 64.2 + - + +
342A GLU* 3.2 15.1 + - - +
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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
------------------------------------------------------------
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