Contacts of the helix formed by residues 343 - 362 (chain A) in PDB entry 5F0L
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 343 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341A ASP* 3.8 7.8 - - - +
342A MET* 1.3 88.6 - - + +
344A SER* 1.3 65.3 + - - +
345A GLU* 3.4 28.7 - - - +
346A ASP* 3.2 39.8 + - - +
347A VAL* 3.2 12.6 + - - +
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Residues in contact with SER 344 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A MET 3.6 2.2 + - - -
343A PRO* 1.3 72.3 - - - +
345A GLU* 1.3 64.5 + - - +
347A VAL* 3.4 10.4 + - - +
348A VAL* 3.2 27.4 + - - +
383A LEU* 3.6 30.9 - - - +
385A LEU* 5.1 6.5 - - - +
394A VAL* 3.9 21.3 - - - -
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Residues in contact with GLU 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A PRO* 3.4 21.4 - - - +
344A SER* 1.3 81.7 + - - +
346A ASP* 1.3 64.1 + - - +
348A VAL* 3.5 3.1 + - - +
349A SER* 2.7 35.5 + - - +
393A ALA* 3.8 42.9 - - + +
394A VAL* 3.9 16.4 - - - +
397A GLU* 3.6 8.8 - - + +
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Residues in contact with ASP 346 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A ASN* 5.4 1.6 + - - +
296A LYS* 3.6 22.6 - - + +
342A MET* 3.6 24.2 - - + +
343A PRO* 3.2 34.5 + - - +
345A GLU* 1.3 85.1 - - - +
347A VAL* 1.3 66.1 + - - +
348A VAL 3.1 0.2 - - - -
349A SER* 3.1 17.7 + - - -
350A LEU* 3.1 17.7 + - - +
506A EDO 3.6 20.3 + - - -
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Residues in contact with VAL 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A ILE* 3.9 41.1 - - + -
342A MET* 4.0 14.8 - - + +
343A PRO 3.2 15.0 + - - +
344A SER* 3.6 11.2 - - - +
346A ASP* 1.3 75.3 - - - +
348A VAL* 1.3 60.6 + - + +
350A LEU* 3.5 6.6 + - - +
351A GLN* 3.3 21.2 + - - +
379A ILE* 4.0 38.8 - - + -
383A LEU* 6.3 1.3 - - + -
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Residues in contact with VAL 348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A SER* 3.2 17.6 + - - +
345A GLU* 3.8 5.6 - - - +
346A ASP 3.1 0.4 - - - -
347A VAL* 1.3 78.1 - - + +
349A SER* 1.3 63.2 + - - +
350A LEU 3.1 2.0 - - - -
351A GLN* 3.1 8.7 + - + +
352A VAL* 3.0 22.4 + - - +
376A THR* 5.1 3.6 - - + -
379A ILE* 5.3 5.6 - - + -
380A PHE* 4.0 28.3 - - + -
394A VAL* 4.5 6.7 - - + +
397A GLU* 3.6 24.9 - - + +
398A LEU* 3.9 19.1 - - + +
401A LEU* 4.3 13.2 - - + -
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Residues in contact with SER 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A LYS* 3.8 21.4 + - - +
300A ILE* 4.0 14.8 - - - +
345A GLU* 2.7 23.2 + - - +
346A ASP* 3.1 12.0 + - - -
348A VAL* 1.3 75.8 - - - +
350A LEU* 1.3 59.8 + - - +
352A VAL* 3.5 14.4 - - - +
353A SER* 3.5 5.4 + - - -
397A GLU* 3.3 28.3 + - - +
400A ARG* 5.0 5.3 + - - +
508A EDO 4.3 2.8 + - - -
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Residues in contact with LEU 350 (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 LYS* 4.0 30.3 - - + +
299A ILE* 4.1 27.4 - - + -
300A ILE* 4.0 11.7 - - + -
332A VAL* 3.8 19.5 - - + +
335A VAL* 5.9 1.1 - - + -
336A ILE* 3.7 25.1 - - + -
342A MET* 3.6 27.8 - - + -
346A ASP 3.1 12.4 + - - +
347A VAL* 3.5 7.4 - - - +
348A VAL 3.1 0.4 - - - -
349A SER* 1.3 74.1 - - - +
351A GLN* 1.3 61.5 + - - +
352A VAL 3.1 1.3 - - - -
353A SER* 2.9 20.5 + - - +
354A LEU* 2.9 18.8 + - - +
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Residues in contact with GLN 351 (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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332A VAL* 4.5 11.3 - - - +
336A ILE* 4.8 2.6 - - - +
347A VAL* 3.3 18.7 + - - +
348A VAL* 3.1 13.9 + - + +
350A LEU* 1.3 77.4 - - - +
352A VAL* 1.3 61.4 + - - +
354A LEU* 3.6 19.1 + - - +
355A ILE* 3.2 20.6 + - - +
372A VAL* 3.4 30.6 - - + +
375A THR* 4.1 13.1 - - - +
376A THR* 3.7 19.1 + - + +
379A ILE* 3.9 25.3 - - + +
401A LEU* 3.8 18.8 - - + -
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Residues in contact with VAL 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A VAL 3.0 13.1 + - - +
349A SER* 3.5 8.7 - - - +
350A LEU 3.1 0.2 - - - -
351A GLN* 1.3 77.6 - - - +
353A SER* 1.3 57.3 + - - +
355A ILE* 3.2 7.0 + - - +
356A ASN* 2.9 26.3 + - - +
397A GLU* 3.8 22.7 - - - +
400A ARG* 3.7 20.4 - - - +
401A LEU* 3.7 33.2 - - + +
404A ILE* 3.5 28.9 - - + +
508A EDO 4.1 10.8 - - - +
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Residues in contact with SER 353 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A ILE* 4.0 17.5 - - - +
303A ILE* 3.5 33.6 - - - +
304A ASP* 5.0 1.1 - - - -
349A SER 3.5 2.1 + - - -
350A LEU* 2.9 25.5 + - - +
352A VAL* 1.3 80.1 - - - +
354A LEU* 1.3 52.3 + - - +
356A ASN* 3.7 6.2 - - - -
357A LEU* 2.8 34.7 + - - +
508A EDO 3.4 20.4 - - - -
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Residues in contact with LEU 354 (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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303A ILE* 4.9 2.9 - - + -
325A PHE* 4.2 7.2 - - + -
328A PHE* 3.8 20.2 - - + +
329A SER* 3.7 44.2 - - - +
332A VAL* 4.5 16.6 - - + -
350A LEU 2.9 16.2 + - - +
351A GLN* 3.7 36.8 - - - +
353A SER* 1.3 75.7 + - - +
355A ILE* 1.3 64.1 + - - +
357A LEU* 3.6 10.1 - - + +
358A ALA* 3.1 23.0 + - - +
372A VAL* 4.0 16.5 - - + +
375A THR* 6.4 0.2 - - + -
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Residues in contact with ILE 355 (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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351A GLN 3.2 10.1 + - - +
352A VAL* 3.4 7.0 - - - +
354A LEU* 1.3 76.8 - - - +
356A ASN* 1.3 59.4 + - - +
358A ALA* 2.9 8.4 + - - +
359A MET* 2.8 46.2 + - + +
369A VAL* 4.4 15.0 - - + +
372A VAL* 3.5 25.1 - - + -
373A LEU* 4.2 12.1 - - + -
401A LEU* 3.3 45.5 - - + +
404A ILE* 4.2 16.2 - - + -
405A PRO* 4.4 12.6 - - + -
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Residues in contact with ASN 356 (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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303A ILE* 5.3 1.6 - - - +
304A ASP* 4.1 11.3 + - - -
307A ALA* 4.6 8.5 - - - +
352A VAL 2.9 15.9 + - - +
353A SER* 3.4 9.5 + - - +
355A ILE* 1.3 77.4 - - - +
357A LEU* 1.3 60.0 + - - +
359A MET* 3.8 7.8 - - - +
360A LYS* 3.1 59.8 + - - +
404A ILE* 4.7 16.1 - - + +
508A EDO 3.6 28.2 + - - -
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Residues in contact with LEU 357 (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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303A ILE* 3.9 32.7 - - + +
306A LEU* 4.6 8.1 - - + -
307A ALA* 5.0 3.4 - - - +
324A LEU* 4.3 22.0 - - + +
325A PHE* 4.6 7.0 - - + -
328A PHE* 3.6 39.9 - - + -
353A SER 2.8 21.2 + - - +
354A LEU* 3.6 11.0 - - + +
355A ILE 3.1 0.2 - - - -
356A ASN* 1.3 70.4 - - - +
358A ALA* 1.3 60.8 + - - +
359A MET 3.3 0.2 + - - -
360A LYS* 3.3 1.9 + - - -
361A CYS* 2.8 60.6 + - + +
362A TYR* 6.0 0.7 - - + -
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Residues in contact with ALA 358 (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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325A PHE* 4.2 12.6 - - + -
354A LEU 3.1 11.2 + - - +
355A ILE* 2.9 10.8 + - - +
357A LEU* 1.3 79.8 - - - +
359A MET* 1.3 56.5 + - - +
362A TYR* 3.0 45.2 + - - +
365A ARG 4.9 0.7 - - - +
368A TYR* 4.0 26.9 - - + -
369A VAL* 4.4 14.4 - - + +
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Residues in contact with MET 359 (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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311A HIS* 5.1 0.3 + - - -
355A ILE* 2.8 36.9 + - + +
356A ASN* 3.8 10.1 - - - +
358A ALA* 1.3 72.6 - - - +
360A LYS* 1.3 61.7 + - + +
363A PRO* 3.3 33.6 - - - +
369A VAL* 3.7 22.9 - - + -
404A ILE* 4.2 4.7 - - + +
405A PRO* 4.2 19.3 - - + -
408A THR* 3.5 40.6 - - + +
409A TYR* 4.0 33.7 - - + +
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Residues in contact with LYS 360 (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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307A ALA* 4.1 29.4 - - + +
308A LEU* 5.4 9.1 - - + +
310A ALA* 3.4 9.1 - - - +
311A HIS* 3.4 50.1 + - + +
356A ASN* 3.1 48.7 + - - +
357A LEU 4.3 0.7 - - - +
359A MET* 1.3 79.3 - - + +
361A CYS* 1.3 60.0 + - - +
363A PRO* 4.3 5.6 - - - +
408A THR* 6.2 4.0 - - + -
508A EDO 5.8 0.2 + - - -
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Residues in contact with CYS 361 (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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306A LEU 4.0 11.9 - - - -
307A ALA* 4.7 2.5 - - - -
310A ALA* 4.1 8.1 - - - -
318A ILE* 3.5 32.0 - - + +
324A LEU* 3.6 4.5 - - + -
357A LEU* 2.8 48.1 + - + +
360A LYS* 1.3 73.9 - - - +
362A TYR* 1.3 89.0 + - + +
363A PRO* 3.7 4.4 - - - +
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Residues in contact with TYR 362 (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 ILE* 4.4 8.2 - - + +
319A PRO 5.2 0.5 + - - -
322A ILE 3.5 9.9 + - - -
323A LYS* 4.1 3.5 - - - -
324A LEU* 3.3 28.2 + - + +
325A PHE* 4.1 20.0 - - + -
357A LEU* 6.0 0.9 - - + -
358A ALA* 3.0 25.4 + - - +
361A CYS* 1.3 104.1 - - + +
363A PRO* 1.4 67.6 - - - +
364A ASP* 3.2 15.0 - - - +
365A ARG* 3.1 23.4 + - + +
368A TYR* 3.8 37.0 - + + -
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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