Contacts of the helix formed by residues 338 - 356 (chain A) in PDB entry 1VOM
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 GLN 338 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328A ARG* 5.0 9.7 + - - -
332A ASP* 4.0 19.0 + - - -
337A SER* 1.3 75.7 - - - +
339A GLU* 1.3 70.6 + - - +
341A GLN* 3.5 15.1 + - - +
342A MET* 3.0 28.9 + - - +
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Residues in contact with GLU 339 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A SER* 2.8 26.6 + - - +
338A GLN* 1.3 86.2 + - + +
340A GLU* 1.3 62.6 + - + +
342A MET* 3.3 7.3 + - - +
343A SER* 2.8 34.0 + - - -
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Residues in contact with GLU 340 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335A GLY 4.3 1.4 - - - +
336A PHE* 3.4 13.7 - - + +
337A SER* 2.6 44.9 + - - +
339A GLU* 1.3 73.0 - - + +
341A GLN* 1.3 64.1 + - - +
343A SER* 3.0 4.5 + - - -
344A ILE* 2.9 26.4 + - - +
432A TRP* 4.0 15.0 - - + -
436A LYS* 2.5 40.6 + - - -
607A VAL* 4.5 14.2 - - + +
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Residues in contact with GLN 341 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A ARG* 4.1 19.5 + - - +
331A MET* 3.8 30.4 - - - +
332A ASP* 3.0 26.0 + - - +
336A PHE* 2.7 35.6 + - + -
337A SER 2.7 20.4 + - - +
338A GLN* 3.5 20.6 + - - +
340A GLU* 1.3 72.3 - - - +
342A MET* 1.3 56.8 + - - +
344A ILE* 3.0 12.1 + - - +
345A PHE* 2.9 46.7 + - + -
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Residues in contact with MET 342 (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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292A GLU* 5.8 9.4 - - + +
295A ALA* 6.3 2.5 - - - -
296A LEU* 4.2 21.8 - - + -
338A GLN 3.0 18.3 + - - +
339A GLU* 3.4 8.3 - - - +
340A GLU 3.2 0.2 - - - -
341A GLN* 1.3 75.9 - - - +
343A SER* 1.3 64.1 + - - +
345A PHE* 3.6 26.9 - - + -
346A LYS* 2.9 39.9 + - - +
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Residues in contact with SER 343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A GLU 2.8 16.2 + - - -
340A GLU 3.0 3.1 + - - -
342A MET* 1.3 75.7 - - - +
344A ILE* 1.4 53.5 + - - +
346A LYS* 3.1 15.1 + - - +
347A ILE* 2.8 40.8 + - - +
605A ASP* 2.8 34.2 + - - +
606A ASN* 5.1 2.3 + - - +
607A VAL* 3.5 24.7 + - - +
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Residues in contact with ILE 344 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A PHE* 3.4 35.2 - - + -
331A MET* 4.4 8.5 - - + -
336A PHE* 3.9 15.7 - - + -
340A GLU 2.9 17.5 + - - +
341A GLN* 3.3 16.2 - - - +
343A SER* 1.4 75.9 - - - +
345A PHE* 1.3 66.1 + - + +
347A ILE* 3.3 10.7 + - - +
348A ILE* 3.1 24.6 + - - +
429A LEU* 4.3 10.2 - - + +
432A TRP* 3.6 32.5 - - + -
433A LEU* 3.6 16.4 - - + -
607A VAL* 5.3 1.6 - - + -
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Residues in contact with PHE 345 (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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225A PHE* 4.4 0.7 - + - -
280A ILE* 3.9 19.3 - - + -
284A LEU* 3.8 28.7 - - + +
292A GLU* 5.5 3.4 - - - -
296A LEU* 4.1 4.5 - - + -
324A PHE* 3.8 26.7 - + - -
327A THR* 5.5 0.2 - - + -
328A ARG* 4.0 23.8 - - + -
331A MET* 4.0 22.9 - - + -
341A GLN* 2.9 36.6 + - + -
342A MET* 3.6 19.5 - - + -
343A SER 3.2 0.2 - - - -
344A ILE* 1.3 86.8 - - + +
346A LYS* 1.3 57.2 + - - +
348A ILE* 3.2 11.5 + - + +
349A ALA* 2.7 35.7 + - - +
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Residues in contact with LYS 346 (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 LEU* 3.5 26.0 - - + -
342A MET* 2.9 42.2 + - - +
343A SER* 3.1 12.9 + - - +
345A PHE* 1.3 74.2 - - - +
347A ILE* 1.3 58.1 + - + +
349A ALA* 4.2 0.9 - - - -
350A GLY* 2.5 35.7 + - - -
380A THR 5.9 0.2 - - - -
381A VAL* 3.5 35.9 - - + +
382A PHE* 4.2 2.3 - - - -
605A ASP* 4.2 13.2 + - - +
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Residues in contact with ILE 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A SER 2.8 19.8 + - - +
344A ILE 3.6 4.0 - - - +
346A LYS* 1.3 77.9 - - + +
348A ILE* 1.4 63.0 + - - +
350A GLY* 3.2 1.6 + - - -
351A ILE* 2.9 36.8 + - + +
382A PHE* 3.8 14.7 - - + -
425A LEU* 4.7 11.0 - - + +
429A LEU* 3.9 30.5 - - + -
607A VAL* 3.8 28.9 - - + -
608A VAL* 3.7 27.8 - - + -
611A LEU* 3.9 17.9 - - + -
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Residues in contact with ILE 348 (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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225A PHE* 3.7 29.4 - - + -
280A ILE* 4.0 12.6 - - + -
281A PHE* 3.5 32.2 - - + -
284A LEU* 3.9 17.9 - - + -
344A ILE 3.1 16.9 + - - +
345A PHE* 3.2 11.6 + - + +
347A ILE* 1.4 75.9 - - - +
349A ALA* 1.3 64.1 + - - +
351A ILE* 3.3 8.4 + - + +
352A LEU* 3.1 27.5 + - + +
426A TYR* 3.8 27.6 - - + -
429A LEU* 3.8 9.6 - - + -
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Residues in contact with ALA 349 (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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284A LEU* 4.4 1.5 - - + +
296A LEU* 3.9 23.1 - - + +
298A LEU* 3.7 27.6 - - + -
345A PHE 2.7 21.7 + - - +
346A LYS* 3.6 6.7 - - - +
348A ILE* 1.3 75.5 - - - +
350A GLY* 1.3 63.1 + - - +
352A LEU* 3.2 8.7 + - - +
353A HIS* 3.1 26.5 + - - -
381A VAL* 4.5 3.6 - - + -
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Residues in contact with GLY 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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346A LYS 2.5 16.9 + - - -
349A ALA* 1.3 72.5 - - - +
351A ILE* 1.4 52.6 + - - +
353A HIS* 3.1 3.3 + - - +
354A LEU* 2.8 37.6 + - - +
378A ALA* 3.8 4.1 - - - +
381A VAL* 3.3 22.6 - - - +
382A PHE* 3.3 22.9 - - - -
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Residues in contact with ILE 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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268A VAL* 3.6 27.1 - - + -
281A PHE* 3.9 12.1 - - + -
306A TYR* 3.4 11.2 - - + -
347A ILE* 2.9 27.4 + - + +
348A ILE* 3.5 10.1 - - + +
349A ALA 3.2 0.2 - - - -
350A GLY* 1.4 73.0 - - - +
352A LEU* 1.4 64.2 + - - +
354A LEU* 3.3 7.9 + - - +
355A GLY 2.9 18.4 + - - -
382A PHE* 3.6 1.7 - - - -
422A VAL* 3.7 13.5 - - + -
425A LEU* 4.0 22.9 - - + -
426A TYR* 3.8 45.1 - - + +
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Residues in contact with LEU 352 (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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281A PHE* 3.6 31.9 - - + +
284A LEU* 5.0 1.1 - - + -
285A LEU* 4.0 28.3 - - + -
298A LEU* 4.7 2.0 - - + -
304A PHE* 3.7 36.1 - - + +
305A ASN 5.5 0.2 + - - -
306A TYR* 4.3 16.2 - - + +
307A LEU* 3.7 29.6 - - + -
348A ILE* 3.1 22.4 + - + +
349A ALA* 3.2 13.9 + - - +
351A ILE* 1.4 77.2 - - - +
353A HIS* 1.3 61.8 + - - +
355A GLY* 3.2 10.6 + - - -
356A ASN* 3.3 8.0 + - - -
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Residues in contact with HIS 353 (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 LEU 2.9 25.2 + - - -
297A HIS* 3.2 31.4 + - + +
298A LEU* 4.6 3.2 - - - +
304A PHE* 4.0 16.6 - + - -
349A ALA 3.1 22.7 + - - -
350A GLY* 3.1 8.8 + - - +
352A LEU* 1.3 70.8 - - - +
354A LEU* 1.4 58.2 + - - +
356A ASN* 2.6 36.1 + - - +
357A ILE 3.3 3.8 + - - -
374A ALA* 3.3 27.4 + - - +
377A ALA* 3.6 29.2 - - + +
378A ALA* 3.7 6.5 - - + -
381A VAL* 4.5 3.4 - - + -
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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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350A GLY 2.8 19.2 + - - +
351A ILE* 3.5 8.7 - - - +
353A HIS* 1.4 70.3 - - - +
355A GLY* 1.3 55.0 + - - +
357A ILE* 2.9 31.9 + - + +
378A ALA* 3.9 12.7 - - + +
382A PHE* 3.7 13.7 - - + -
389A LEU* 4.3 13.5 - - + -
393A LEU* 5.0 2.0 - - + -
418A ARG* 2.6 38.6 + - + -
421A LEU* 3.6 31.9 - - + -
422A VAL* 3.5 27.1 - - + -
425A LEU* 3.6 19.1 - - + -
600A PHE* 5.4 0.2 - - + -
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Residues in contact with GLY 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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305A ASN* 3.0 23.6 + - - +
306A TYR* 3.3 38.6 - - - -
351A ILE 2.9 11.1 + - - -
352A LEU 3.2 4.0 + - - -
353A HIS 3.0 0.4 - - - -
354A LEU* 1.3 79.1 - - - +
356A ASN* 1.3 63.2 + - - +
357A ILE 3.3 0.7 - - - +
418A ARG* 3.6 11.1 + - - -
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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 SER 3.1 13.5 + - - +
304A PHE* 3.0 32.7 - - - -
305A ASN* 3.1 40.7 + - - +
352A LEU 3.3 5.5 + - - -
353A HIS* 2.6 22.9 + - - +
355A GLY* 1.3 73.6 - - - +
357A ILE* 1.3 63.5 + - - -
358A LYS* 3.3 6.6 + - - +
374A ALA* 3.6 15.4 - - + +
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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
------------------------------------------------------------
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