Contacts of the helix formed by residues 342 - 360 (chain D) in PDB entry 2GPV
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 LEU 342 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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265D LEU* 4.4 7.0 - - + -
268D LEU* 3.8 28.3 - - + -
332D MET* 4.3 10.3 - - + -
337D SER* 2.9 8.0 + - - +
340D ALA* 3.8 27.8 - - + +
341D GLY* 1.3 76.2 - - - +
343D LEU* 1.3 57.2 + - - +
344D ASP 3.3 2.2 - - - -
345D LEU* 3.0 14.2 + - + +
346D ASN* 2.8 52.0 + - - +
434D HIS* 3.6 24.2 - - + +
503D OHT 3.6 31.0 - - + -
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Residues in contact with LEU 343 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334D GLU* 4.1 32.1 - - + +
337D SER* 3.2 19.4 + - - +
338D LYS* 4.5 23.6 - - + -
341D GLY* 3.5 3.3 - - - -
342D LEU* 1.3 75.5 - - - +
344D ASP* 1.3 67.2 + - - +
346D ASN* 4.2 0.2 - - - +
347D ASN* 2.8 62.5 + - - +
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Residues in contact with ASP 344 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341D GLY 5.3 3.3 - - - +
342D LEU 3.3 0.4 - - - -
343D LEU* 1.3 86.8 + - - +
345D LEU* 1.3 58.2 + - - +
347D ASN* 3.8 6.1 - - - +
348D ALA* 3.1 26.9 + - - +
430D LYS* 5.1 6.8 + - + +
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Residues in contact with LEU 345 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342D LEU* 3.0 16.4 + - + +
344D ASP* 1.3 78.8 - - - +
346D ASN* 1.3 60.7 + - - +
348D ALA* 3.3 5.5 - - + +
349D ILE* 3.0 27.3 + - + +
427D THR* 4.3 14.1 - - + +
430D LYS* 4.3 11.2 - - + -
431D ALA* 3.8 41.1 - - + +
434D HIS* 3.6 31.4 - - + -
503D OHT 3.7 32.1 - - + -
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Residues in contact with ASN 346 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324D LEU* 3.6 20.4 - - + +
326D TYR* 2.6 28.9 + - - -
332D MET* 3.9 20.0 - - - +
337D SER* 2.7 31.7 + - - +
342D LEU* 2.8 27.1 + - - +
343D LEU 4.2 1.3 - - - +
345D LEU* 1.3 71.0 - - - +
347D ASN* 1.3 54.8 + - - +
348D ALA 3.1 0.2 - - - -
349D ILE* 2.9 9.3 + - - +
350D LEU* 2.7 41.1 + - + +
503D OHT 4.1 6.4 - - - +
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Residues in contact with ASN 347 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334D GLU* 5.3 2.9 - - - +
343D LEU* 2.8 46.5 + - - +
344D ASP* 3.8 6.6 - - - +
346D ASN* 1.3 76.0 - - - +
348D ALA* 1.3 60.5 + - - +
350D LEU* 3.3 17.4 + - - +
351D GLN* 3.1 20.8 + - - +
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Residues in contact with ALA 348 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344D ASP 3.1 14.3 + - - +
345D LEU* 3.3 12.3 - - + +
347D ASN* 1.3 74.4 - - - +
349D ILE* 1.3 66.1 + - - +
351D GLN* 2.9 29.3 + - - +
352D LEU* 3.4 5.0 + - - +
423D LEU* 5.1 1.8 - - + +
427D THR* 3.8 26.6 + - + +
430D LYS* 4.4 21.3 - - + +
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Residues in contact with ILE 349 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310D ILE* 4.2 17.3 - - + -
313D VAL* 4.0 22.0 - - + -
314D VAL* 4.1 11.1 - - + +
324D LEU* 3.6 25.1 - - + -
326D TYR* 3.4 24.9 - - + +
345D LEU* 3.0 21.7 + - + +
346D ASN* 2.9 14.0 + - - +
348D ALA* 1.3 74.7 - - - +
350D LEU* 1.3 57.2 + - - +
352D LEU* 3.3 9.4 + - - +
353D VAL* 3.2 21.7 + - - +
427D THR* 4.0 17.7 - - + -
503D OHT 4.0 15.3 - - + -
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Residues in contact with LEU 350 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322D ASP* 4.6 25.8 - - + +
323D GLU* 4.0 14.6 - - - +
324D LEU* 3.4 35.2 - - + -
346D ASN* 2.7 24.3 + - + +
347D ASN* 3.6 20.9 - - - +
348D ALA 3.1 0.2 - - - -
349D ILE* 1.3 70.8 - - - +
351D GLN* 1.3 60.6 + - - +
352D LEU 3.1 1.8 - - - -
353D VAL* 3.6 15.2 - - + +
354D LYS* 2.8 31.4 + - - +
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Residues in contact with GLN 351 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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378A ASP* 2.9 42.8 + - - +
379A SER 3.5 10.5 + - - -
380A MET* 3.9 24.2 - - - +
347D ASN 3.1 10.6 + - - +
348D ALA* 2.9 18.4 + - - +
350D LEU* 1.3 75.6 - - - +
352D LEU* 1.3 61.1 + - - +
354D LYS* 3.5 14.8 + - + +
355D LYS* 3.2 25.4 + - - +
423D LEU* 4.2 22.1 - - + +
426D GLN* 5.4 1.0 + - - -
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Residues in contact with LEU 352 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310D ILE* 4.6 2.2 - - + -
311D LEU* 5.7 0.4 - - + -
314D VAL* 3.9 19.7 - - + -
348D ALA 3.4 1.9 + - - +
349D ILE* 3.3 11.1 + - - +
350D LEU 3.1 0.6 - - - -
351D GLN* 1.3 77.1 - - - +
353D VAL* 1.3 64.4 + - - +
355D LYS* 3.3 7.1 + - + +
356D TYR* 3.1 55.0 + - + +
420D THR* 3.8 24.0 - - - +
423D LEU* 3.8 22.4 - - + -
424D LEU* 3.5 39.0 - - + +
427D THR* 4.1 15.0 - - + +
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Residues in contact with VAL 353 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314D VAL* 3.6 36.3 - - + +
317D SER* 3.8 32.8 - - - +
318D LEU* 4.0 4.8 - - + +
320D PHE 5.1 0.9 - - - +
323D GLU 5.7 0.4 - - - +
324D LEU* 4.0 10.3 - - + -
349D ILE 3.2 12.4 + - - +
350D LEU* 3.3 15.7 + - + +
352D LEU* 1.3 76.7 - - - +
354D LYS* 1.3 65.5 + - - +
355D LYS 3.0 0.5 + - - -
356D TYR* 3.2 2.9 + - - +
357D LYS* 2.9 43.0 + - + +
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Residues in contact with LYS 354 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385A VAL* 4.3 30.5 - - - +
350D LEU 2.8 21.9 + - - +
351D GLN* 3.6 15.9 - - + +
353D VAL* 1.3 74.6 - - - +
355D LYS* 1.3 59.7 + - - +
357D LYS* 3.6 10.6 - - - +
358D SER* 3.0 24.3 + - - +
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Residues in contact with LYS 355 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376A ASN* 5.1 2.2 + - - -
378A ASP* 2.9 32.9 + - - -
389A GLN* 5.6 5.8 - - - +
351D GLN* 3.2 11.7 + - - +
352D LEU* 3.6 10.2 - - + +
353D VAL 3.1 0.8 - - - -
354D LYS* 1.3 75.2 - - - +
356D TYR* 1.3 68.5 + - + +
358D SER* 2.8 26.1 + - - +
359D MET* 3.3 13.8 + - + +
419D MET 4.6 2.8 + - - -
420D THR* 3.8 37.1 + - + +
423D LEU* 3.5 28.5 - - - +
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Residues in contact with TYR 356 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311D LEU* 3.7 28.5 - - + +
314D VAL* 3.5 15.9 - - + -
318D LEU* 3.7 19.0 - - + +
352D LEU* 3.1 36.3 + - + +
355D LYS* 1.3 79.8 - - + +
357D LYS* 1.3 62.9 + - - +
359D MET* 3.1 16.6 + - - -
360D LYS 3.1 17.2 + - - -
361D LEU* 3.2 43.5 + - + -
369D LEU* 3.6 23.1 - - + +
417D MET* 4.8 1.3 - - - -
420D THR* 2.7 44.5 + - + -
421D LEU* 5.0 1.0 - - - +
424D LEU* 4.9 3.6 - - - +
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Residues in contact with LYS 357 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318D LEU* 3.3 32.9 + - + +
319D SER 5.2 1.0 - - - -
320D PHE 2.9 30.3 + - - +
321D GLU* 3.1 28.3 + - - +
322D ASP 5.3 0.6 - - - +
353D VAL* 2.9 30.0 + - + +
354D LYS* 3.6 11.0 - - - +
356D TYR* 1.3 75.9 - - - +
358D SER* 1.3 62.9 + - - +
360D LYS* 3.1 18.2 + - - +
361D LEU 5.3 0.2 - - - +
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Residues in contact with SER 358 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385A VAL* 6.2 0.2 - - - +
354D LYS* 3.0 17.3 + - - +
355D LYS* 2.8 15.0 + - - +
357D LYS* 1.3 75.1 - - - +
359D MET* 1.3 64.3 + - - +
360D LYS* 3.4 10.4 + - - +
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Residues in contact with MET 359 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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389A GLN* 6.0 2.7 - - - +
355D LYS* 3.5 19.7 - - + +
356D TYR* 3.1 20.7 + - - +
358D SER* 1.3 80.7 - - - +
360D LYS* 1.3 65.2 + - - +
361D LEU* 4.4 1.1 - - - +
413D ARG* 2.8 36.2 + - - +
416D LYS* 3.4 49.6 - - + +
417D MET* 4.1 27.1 - - + +
420D THR* 4.1 19.3 - - + -
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Residues in contact with LYS 360 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356D TYR 3.1 3.4 + - - -
357D LYS* 3.1 12.4 + - - +
358D SER 4.2 7.9 - - - +
359D MET* 1.3 82.1 - - - +
361D LEU* 1.3 67.7 + - - +
362D GLU* 3.2 19.4 - - - +
407D HIS* 6.5 0.4 - - + -
413D ARG* 3.3 3.8 + - - +
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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