Contacts of the helix formed by residues 420 - 441 (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 THR 420 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352E LEU* 4.0 7.2 - - - +
355E LYS* 3.5 31.2 - - + +
356E TYR* 2.4 47.6 + - + -
359E MET* 4.2 11.4 - - + -
369E LEU* 3.9 2.1 - - - +
416E LYS 3.5 11.4 - - - +
417E MET 2.9 19.6 + - - +
419E MET* 1.3 79.1 - - - +
421E LEU* 1.3 63.5 + - - +
422E PRO* 3.4 0.9 - - - -
423E LEU* 3.5 8.7 + - - +
424E LEU* 3.4 14.7 + - - +
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Residues in contact with LEU 421 (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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419B MET* 5.3 2.9 - - + -
422B PRO* 3.9 12.1 - - + +
307E GLU* 5.2 2.2 - - - +
356E TYR* 4.9 0.4 - - - +
369E LEU* 3.9 30.7 - - + +
372E ILE* 4.2 23.6 - - + -
373E ALA* 4.7 8.3 - - + +
376E ASN* 4.7 13.9 - - + +
417E MET 4.4 0.4 - - - +
418E LEU* 3.5 32.1 - - + +
420E THR* 1.3 80.1 + - - +
422E PRO* 1.3 71.2 - - + +
424E LEU* 3.0 26.8 + - + +
425E ARG* 2.9 23.0 + - - +
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Residues in contact with PRO 422 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376B ASN* 4.3 7.0 - - - +
378B ASP* 4.6 0.4 - - - +
421B LEU* 3.8 28.3 - - + -
422B PRO* 3.9 22.2 - - + -
425B ARG* 3.4 35.0 - - + +
418E LEU 3.9 4.9 - - - +
419E MET* 3.2 20.4 - - - +
420E THR 3.5 0.7 - - - -
421E LEU* 1.3 94.3 - - + +
423E LEU* 1.3 55.6 + - - +
425E ARG* 3.2 2.3 + - - +
426E GLN* 2.8 30.8 + - - +
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Residues in contact with LEU 423 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378B ASP* 3.7 27.4 + - + +
425B ARG* 3.7 5.4 - - - +
348E ALA* 5.3 2.0 - - + +
351E GLN* 3.7 28.5 - - + +
352E LEU* 3.6 37.9 - - + +
355E LYS* 4.1 12.8 - - - +
420E THR 3.5 10.0 + - - +
421E LEU 3.3 0.6 - - - -
422E PRO* 1.3 79.5 - - - +
424E LEU* 1.3 57.6 + - - +
426E GLN* 3.0 28.9 - - - +
427E THR* 2.9 42.2 + - - +
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Residues in contact with LEU 424 (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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307E GLU* 3.7 46.4 - - + +
310E ILE* 4.2 7.0 - - + -
311E LEU* 4.1 37.2 - - + +
352E LEU* 3.8 27.9 - - + +
356E TYR* 5.2 2.2 - - - +
373E ALA* 4.4 7.2 - - + -
420E THR 3.4 7.3 + - - +
421E LEU* 3.0 30.4 + - + +
423E LEU* 1.3 78.9 - - - +
425E ARG* 1.3 53.3 + - - +
427E THR* 3.2 1.2 + - - -
428E SER* 2.6 37.6 + - - -
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Residues in contact with ARG 425 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422B PRO* 3.5 45.9 - - + +
423B LEU 3.6 1.0 - - - +
425B ARG* 5.6 0.2 - - + -
426B GLN* 2.8 49.0 - - + +
303E SER 6.1 0.2 - - - -
307E GLU* 2.8 39.3 + - - +
373E ALA* 6.3 0.2 - - - +
376E ASN* 2.6 34.1 + - - +
377E SER* 3.7 13.5 + - - +
378E ASP* 3.0 22.8 + - - +
421E LEU 2.9 14.4 + - - +
422E PRO 3.7 3.8 - - - +
424E LEU* 1.3 72.9 - - - +
426E GLN* 1.3 60.6 + - - +
428E SER* 3.7 0.7 - - - -
429E THR* 3.0 38.6 + - - +
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Residues in contact with GLN 426 (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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377B SER 5.0 2.1 - - - +
378B ASP 4.1 11.5 + - - -
425B ARG* 3.1 43.5 + - + +
426B GLN* 6.1 1.1 - - - +
429B THR* 5.1 7.5 + - - +
351E GLN* 4.9 0.6 - - - +
422E PRO 2.8 18.0 + - - +
423E LEU* 3.0 31.6 - - + +
425E ARG* 1.3 79.0 - - - +
427E THR* 1.3 56.8 + - - +
429E THR* 3.5 5.8 + - - -
430E LYS* 3.2 49.7 + - - +
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Residues in contact with THR 427 (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* 3.8 13.6 - - + +
345E LEU* 4.2 5.3 - - + +
348E ALA* 3.9 28.6 + - + +
349E ILE* 4.0 30.1 - - + +
352E LEU* 4.5 6.2 - - + +
423E LEU* 2.9 34.6 + - - +
424E LEU 3.8 2.9 - - - -
426E GLN* 1.3 76.1 + - - +
428E SER* 1.3 66.3 + - - +
430E LYS* 3.3 9.8 + - - +
431E ALA* 3.1 21.5 + - - +
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Residues in contact with SER 428 (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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303E SER 5.4 2.1 + - - -
306E MET* 3.0 26.3 - - - +
307E GLU* 3.2 33.3 + - - +
310E ILE* 3.7 12.6 - - - -
424E LEU 2.6 20.9 + - - -
425E ARG 3.7 4.3 - - - -
427E THR* 1.3 73.1 - - - +
429E THR* 1.3 61.4 + - - +
431E ALA 3.4 1.2 + - - -
432E VAL* 3.1 26.6 + - - +
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Residues in contact with THR 429 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426B GLN* 4.9 12.1 - - + +
429B THR* 5.1 15.9 - - + -
430B LYS* 6.3 1.8 - - - +
433B GLN* 5.6 4.9 - - - +
425E ARG* 3.0 24.8 + - - +
426E GLN* 3.7 6.2 - - - -
428E SER* 1.3 74.7 - - - +
430E LYS* 1.3 65.6 + - - +
432E VAL* 3.3 5.9 + - + +
433E GLN* 3.0 29.0 + - + +
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Residues in contact with LYS 430 (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* 5.9 4.9 - - - -
344E ASP 5.9 2.0 - - - +
345E LEU* 3.9 12.3 - - + -
348E ALA* 4.8 18.5 - - + +
426E GLN* 3.2 44.1 + - - +
427E THR* 3.3 14.9 + - - +
429E THR* 1.3 75.5 - - - +
431E ALA* 1.3 52.7 + - - +
433E GLN* 3.4 5.0 + - - +
434E HIS* 2.7 36.6 + - - +
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Residues in contact with ALA 431 (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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306E MET* 4.0 14.4 - - - -
310E ILE* 4.0 17.3 - - + -
345E LEU* 3.6 26.9 - - + -
427E THR 3.1 9.4 + - - +
428E SER 3.7 7.6 - - - +
429E THR 3.2 0.2 - - - -
430E LYS* 1.3 77.9 - - - +
432E VAL* 1.3 52.8 + - - +
434E HIS* 3.5 1.6 - - - +
435E PHE* 2.8 36.4 + - - +
504E OHT 3.7 11.7 - - + -
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Residues in contact with VAL 432 (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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443A LYS* 6.0 0.9 - - - -
305E TRP* 4.7 11.0 - - + +
306E MET* 3.4 35.4 - - + -
428E SER* 3.1 19.4 + - - +
429E THR* 3.9 5.6 - - + +
431E ALA* 1.3 74.3 - - - +
433E GLN* 1.3 63.6 + - - +
435E PHE* 3.2 5.0 + - + +
436E TYR* 3.1 55.0 + - + +
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Residues in contact with GLN 433 (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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433B GLN* 4.8 16.1 - - - +
429E THR* 3.0 22.8 + - + +
430E LYS* 3.7 4.7 - - - +
432E VAL* 1.3 79.1 - - - +
434E HIS* 1.3 56.0 + - - +
436E TYR* 3.6 10.2 + - - +
437E ASN* 2.8 68.1 + - - +
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Residues in contact with HIS 434 (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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265E LEU* 5.7 0.6 - - - +
340E ALA 5.5 0.2 + - - -
341E GLY 3.8 19.1 + - - -
342E LEU* 3.5 21.5 - - + +
345E LEU* 4.1 17.3 - - + +
430E LYS 2.7 21.2 + - - +
431E ALA 3.1 5.1 + - - +
433E GLN* 1.3 73.3 - - - +
435E PHE* 1.3 61.9 + - - +
437E ASN* 3.4 12.3 + - + +
438E ILE* 3.1 41.0 + - + +
504E OHT 3.9 20.4 - + - -
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Residues in contact with PHE 435 (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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446A MET* 5.9 0.4 - - + -
269E CYS* 4.3 14.1 - - - -
305E TRP* 5.2 6.3 - + - -
306E MET* 5.2 2.5 - - + -
431E ALA 2.8 20.5 + - - +
432E VAL* 3.2 7.6 + - - +
434E HIS* 1.3 70.6 - - - +
436E TYR* 1.3 104.1 + + - +
438E ILE* 3.3 14.9 + - + +
439E LYS* 3.1 36.8 + - + +
504E OHT 3.4 80.5 - + + -
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Residues in contact with TYR 436 (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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440A LEU 4.3 15.3 - - - +
441A GLU* 4.1 28.9 - - + -
442A GLY 4.5 14.8 - - - -
443A LYS* 3.9 24.3 - - + +
446A MET* 3.5 26.4 - - + +
305E TRP* 4.1 6.5 + + - -
432E VAL* 3.1 38.2 + - + +
433E GLN* 4.3 12.3 - - - +
435E PHE* 1.3 104.2 - + - +
437E ASN* 1.3 64.2 + - - +
439E LYS* 3.4 17.2 + - + +
440E LEU* 3.6 14.3 - - - +
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Residues in contact with ASN 437 (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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433E GLN* 2.8 50.2 + - - +
434E HIS* 3.4 12.6 + - + +
436E TYR* 1.3 78.2 - - - +
438E ILE* 1.3 63.2 + - + +
439E LYS 3.3 3.3 + - - -
440E LEU* 3.5 16.9 + - - +
441E GLU* 3.4 18.2 + - - +
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Residues in contact with ILE 438 (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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265E LEU* 3.9 36.1 - - + -
434E HIS* 3.4 39.3 - - + +
435E PHE* 3.3 20.8 + - + +
437E ASN* 1.3 79.3 - - + +
439E LYS* 1.3 63.8 + - - +
441E GLU* 3.2 43.8 - - + +
504E OHT 5.1 2.9 - - + -
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Residues in contact with LYS 439 (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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440A LEU* 3.9 28.5 - - + +
435E PHE* 3.1 39.8 + - + +
436E TYR* 3.5 14.8 - - + +
437E ASN 3.2 0.6 - - - -
438E ILE* 1.3 78.1 - - + +
440E LEU* 1.3 69.7 + - - +
441E GLU 3.4 3.8 + - - -
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Residues in contact with LEU 440 (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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440A LEU* 4.1 35.9 - - + +
436E TYR 3.6 16.2 - - - +
437E ASN* 3.6 14.4 - - - +
439E LYS* 1.3 79.1 - - - +
441E GLU* 1.3 59.7 + - - +
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Residues in contact with GLU 441 (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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437E ASN 3.4 11.0 + - - +
438E ILE* 3.2 44.2 - - + +
439E LYS 3.3 3.8 - - - -
440E LEU* 1.3 84.5 - - - +
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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
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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