Contacts of the helix formed by residues 342 - 360 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265E LEU* 4.0 9.2 - - + -
268E LEU* 3.9 27.6 - - + -
332E MET* 4.8 1.8 - - - -
337E SER 3.1 11.3 + - - +
340E ALA* 3.5 31.0 - - + +
341E GLY* 1.3 75.8 - - - +
343E LEU* 1.3 59.5 + - - +
344E ASP 3.4 2.5 - - - -
345E LEU* 3.3 13.1 + - + -
346E ASN* 2.9 46.6 + - - +
434E HIS* 3.5 29.2 - - + +
504E OHT 3.6 26.9 - - + -
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Residues in contact with LEU 343 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334E GLU* 4.4 28.9 - - + +
337E SER* 3.5 17.6 + - - +
338E LYS* 4.5 30.1 - - + -
341E GLY 3.7 2.8 - - - -
342E LEU* 1.3 74.8 - - - +
344E ASP* 1.3 68.3 + - - +
346E ASN* 4.2 0.2 - - - +
347E ASN* 2.8 65.0 + - - +
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Residues in contact with ASP 344 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341E GLY 5.5 0.4 + - - -
342E LEU 3.4 0.4 - - - -
343E LEU* 1.3 84.8 - - - +
345E LEU* 1.3 63.3 + - - +
347E ASN* 3.5 10.2 + - - +
348E ALA* 3.1 21.7 + - - +
430E LYS* 5.9 1.1 - - - +
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Residues in contact with LEU 345 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342E LEU* 3.3 17.8 + - + +
343E LEU 3.2 0.8 - - - -
344E ASP* 1.3 76.1 - - - +
346E ASN* 1.3 61.1 + - - +
348E ALA* 3.0 8.8 + - + +
349E ILE* 3.0 38.0 + - + +
427E THR* 4.2 12.1 - - + +
430E LYS* 3.9 16.4 - - + -
431E ALA* 3.6 47.1 - - + +
434E HIS* 4.1 29.4 - - + +
504E OHT 4.4 19.1 - - + -
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Residues in contact with ASN 346 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324E LEU* 3.0 21.1 - - + +
326E TYR* 2.5 27.1 + - - -
332E MET* 4.0 23.2 - - - +
337E SER* 2.8 34.7 + - - +
342E LEU* 2.9 28.3 + - - +
343E LEU 4.2 1.1 - - - +
345E LEU* 1.3 70.0 - - - +
347E ASN* 1.3 59.9 + - - +
349E ILE* 3.1 8.1 + - - +
350E LEU* 2.8 34.4 + - + +
504E OHT 4.4 2.3 - - - +
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Residues in contact with ASN 347 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334E GLU* 5.2 2.6 - - - +
343E LEU* 2.8 54.0 + - - +
344E ASP* 3.5 10.9 + - - +
345E LEU 3.2 0.2 - - - -
346E ASN* 1.3 74.6 - - - +
348E ALA* 1.3 59.1 + - - +
350E LEU* 3.0 18.2 + - - +
351E GLN* 2.9 25.3 + - - +
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Residues in contact with ALA 348 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380B MET* 6.4 1.8 - - - -
344E ASP 3.1 9.7 + - - +
345E LEU* 3.0 11.9 + - - +
347E ASN* 1.3 78.7 - - - +
349E ILE* 1.3 63.2 + - - +
351E GLN* 3.1 25.9 + - - +
352E LEU* 3.3 7.1 + - - +
423E LEU* 5.1 2.3 - - + +
427E THR* 3.9 27.0 + - + +
430E LYS* 4.8 18.8 - - + +
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Residues in contact with ILE 349 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310E ILE* 4.0 13.0 - - + -
313E VAL* 4.2 10.1 - - + -
314E VAL* 3.8 18.8 - - + -
324E LEU* 3.3 24.9 - - + -
326E TYR* 3.6 24.2 - - + +
345E LEU* 3.0 22.1 + - + +
346E ASN* 3.4 14.6 - - - +
348E ALA* 1.3 76.4 - - - +
350E LEU* 1.3 62.0 + - - +
352E LEU* 3.2 10.5 + - - +
353E VAL* 3.1 18.5 + - - +
427E THR* 4.0 17.9 - - + -
504E OHT 3.6 19.5 - - + -
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Residues in contact with LEU 350 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322E ASP* 4.0 28.9 - - + +
323E GLU* 4.0 17.5 - - - +
324E LEU* 3.3 32.1 - - + -
346E ASN* 2.8 19.6 + - + +
347E ASN* 3.0 19.9 + - - +
349E ILE* 1.3 75.0 - - - +
351E GLN* 1.3 53.8 + - - +
353E VAL* 3.1 12.7 + - + +
354E LYS* 2.7 37.0 + - - +
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Residues in contact with GLN 351 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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378B ASP* 3.1 32.5 + - - +
379B SER 4.4 2.6 + - - -
380B MET* 3.0 38.6 - - - +
347E ASN 2.9 10.4 + - - +
348E ALA* 3.1 15.6 + - - +
350E LEU* 1.3 78.1 - - - +
352E LEU* 1.3 61.6 + - - +
354E LYS* 3.5 12.4 + - + +
355E LYS* 3.2 21.1 + - - +
423E LEU* 3.7 28.5 - - + +
426E GLN* 4.9 0.6 - - - +
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Residues in contact with LEU 352 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310E ILE* 4.1 9.6 - - + -
311E LEU* 6.1 0.2 - - + -
314E VAL* 3.7 26.9 - - + -
348E ALA 3.3 3.9 + - - +
349E ILE* 3.2 9.1 + - - +
351E GLN* 1.3 75.0 - - - +
353E VAL* 1.3 67.4 + - - +
355E LYS* 3.0 14.8 + - + +
356E TYR* 3.1 32.3 + - + -
420E THR* 4.0 10.5 - - - +
423E LEU* 3.6 36.3 - - + +
424E LEU* 3.8 38.8 - - + +
427E THR* 4.5 11.0 - - + +
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Residues in contact with VAL 353 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314E VAL* 3.9 32.3 - - - +
317E SER* 3.9 33.0 - - - +
318E LEU* 4.4 4.7 - - + -
320E PHE 5.0 1.1 - - - +
323E GLU 5.6 0.4 - - - +
324E LEU* 4.1 8.1 - - + -
349E ILE 3.1 14.1 + - - +
350E LEU* 3.1 19.2 + - + +
352E LEU* 1.3 77.2 - - - +
354E LYS* 1.3 64.2 + - - +
356E TYR* 3.2 2.3 + - - +
357E LYS* 2.9 43.5 + - + +
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Residues in contact with LYS 354 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385B VAL* 4.3 27.0 - - - +
350E LEU 2.7 19.9 + - - +
351E GLN* 3.5 13.0 - - + +
353E VAL* 1.3 74.1 - - - +
355E LYS* 1.3 62.1 + - - +
357E LYS* 3.6 9.4 - - - +
358E SER* 3.1 25.6 + - - +
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Residues in contact with LYS 355 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376B ASN* 4.1 6.8 + - - -
378B ASP* 3.0 32.1 + - - -
389B GLN* 5.6 7.2 - - - +
392B GLN* 5.9 4.7 - - - +
351E GLN 3.2 8.2 + - - +
352E LEU* 3.0 11.6 + - + +
354E LYS* 1.3 81.5 - - - +
356E TYR* 1.3 64.1 + - + +
358E SER* 3.2 23.1 + - - -
359E MET* 3.4 15.1 + - + +
419E MET 3.6 9.5 + - - -
420E THR* 3.5 43.4 - - + +
423E LEU* 4.1 14.6 - - - +
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Residues in contact with TYR 356 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311E LEU* 3.9 20.4 - - + +
314E VAL* 3.4 30.5 - - + -
318E LEU* 3.7 19.1 - - + +
352E LEU* 3.1 29.3 + - + +
353E VAL 3.9 0.2 - - - +
355E LYS* 1.3 75.9 - - + +
357E LYS* 1.3 65.5 + - - +
359E MET* 3.3 10.8 + - - +
360E LYS 3.1 16.8 + - - -
361E LEU* 3.2 41.5 + - + -
369E LEU* 3.4 23.8 - - + +
417E MET* 4.7 0.9 - - - -
420E THR* 2.4 52.2 + - + -
421E LEU* 4.9 3.5 - - - +
424E LEU* 5.2 2.8 - - - +
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Residues in contact with LYS 357 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318E LEU* 3.2 30.9 - - + +
319E SER 5.2 0.6 - - - -
320E PHE 2.8 30.2 + - - -
321E GLU* 2.8 32.7 + - - +
322E ASP* 4.7 3.0 + - - +
353E VAL* 2.9 32.9 + - + +
354E LYS* 3.6 10.3 - - - +
355E LYS 3.2 0.2 - - - -
356E TYR* 1.3 77.0 - - - +
358E SER* 1.3 60.9 + - - +
360E LYS* 3.1 19.3 + - - +
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Residues in contact with SER 358 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354E LYS* 3.1 16.3 + - - +
355E LYS* 3.2 12.0 + - - -
357E LYS* 1.3 79.1 - - - +
359E MET* 1.3 60.9 + - - +
360E LYS* 3.7 8.9 + - - +
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Residues in contact with MET 359 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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389B GLN* 6.0 2.2 - - - +
355E LYS* 3.4 18.4 + - + +
356E TYR* 3.3 14.6 + - - +
357E LYS 3.2 0.6 - - - -
358E SER* 1.3 76.7 - - - +
360E LYS* 1.3 66.6 + - - +
361E LEU 4.5 0.7 - - - +
413E ARG* 2.9 33.7 + - + +
416E LYS* 3.3 57.9 - - + +
417E MET* 3.8 33.0 - - + +
420E THR* 4.2 16.8 - - + -
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Residues in contact with LYS 360 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356E TYR 3.1 4.2 + - - -
357E LYS* 3.1 15.3 + - - +
358E SER 4.3 7.4 - - - +
359E MET* 1.3 80.1 - - - +
361E LEU* 1.3 68.8 + - - +
362E GLU* 3.4 12.7 - - - +
413E ARG* 3.2 11.5 + - - +
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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