Contacts of the helix formed by residues 415 - 434 (chain E) in PDB entry 6BAA
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 GLY 415 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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414E ALA* 1.3 77.2 - - - +
416E GLN* 1.3 52.0 + - - +
418E CYS* 3.3 11.8 + - - +
419E ASN* 2.7 42.2 + - - -
1209E GLU* 5.3 0.2 + - - -
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Residues in contact with GLN 416 (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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414E ALA* 3.1 6.3 - - - +
415E GLY* 1.3 76.3 - - - +
417E ILE* 1.3 62.0 + - + +
419E ASN* 3.3 20.5 + - - +
420E LEU* 2.8 27.2 + - - +
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Residues in contact with ILE 417 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395E ILE* 5.1 2.7 - - + -
399E ILE* 4.2 13.5 - - + -
414E ALA* 2.9 25.7 + - - +
416E GLN* 1.3 76.8 - - + +
418E CYS* 1.3 66.4 + - - +
420E LEU* 3.2 11.9 + - + +
421E VAL* 3.0 24.5 + - + +
613E PHE* 4.6 27.8 - - + -
1204E PHE* 3.6 26.0 - - + -
1208E VAL* 4.1 17.9 - - + -
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Residues in contact with CYS 418 (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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414E ALA* 3.0 19.5 + - - -
415E GLY* 3.5 11.9 - - - +
417E ILE* 1.3 78.0 - - - +
419E ASN* 1.3 58.1 + - - +
421E VAL* 4.0 0.9 - - - +
422E ALA* 2.8 35.1 + - + +
1201E VAL* 4.8 7.8 - - + +
1204E PHE* 3.9 18.4 - - + -
1205E ALA* 3.5 38.8 - - - -
1208E VAL* 5.4 1.3 - - - -
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Residues in contact with ASN 419 (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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415E GLY 2.7 30.4 + - - +
416E GLN* 3.5 26.0 + - - +
418E CYS* 1.3 75.7 - - - +
420E LEU* 1.3 59.2 + - - +
422E ALA* 4.5 2.2 - - - +
423E ILE* 2.9 47.3 + - + +
424E ASP* 5.1 0.2 - - - +
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Residues in contact with LEU 420 (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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395E ILE* 4.8 14.1 - - + -
416E GLN 2.8 13.6 + - - +
417E ILE* 3.3 16.4 - - + +
419E ASN* 1.3 74.8 - - - +
421E VAL* 1.3 62.4 + - + +
424E ASP* 2.9 59.2 + - + +
425E THR* 3.7 2.3 + - - -
606E SER 5.4 0.4 - - - +
609E LYS* 3.9 25.4 - - + +
610E LEU* 4.6 7.2 - - + +
613E PHE* 3.9 41.7 - - + -
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Residues in contact with VAL 421 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392E GLN* 4.3 30.3 + - + +
395E ILE* 3.8 28.5 - - + -
417E ILE* 3.0 8.9 + - + +
418E CYS 4.1 2.5 - - - +
420E LEU* 1.3 78.2 - - + +
422E ALA* 1.3 64.4 + - - +
423E ILE 3.2 0.9 + - - -
425E THR* 3.3 27.3 + - - +
426E ASN 4.2 1.0 + - - -
1200E LEU* 4.8 11.4 - - + -
1201E VAL* 5.3 4.7 - - + -
1204E PHE* 3.5 40.6 - - + -
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Residues in contact with ALA 422 (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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418E CYS* 2.8 21.3 + - + +
419E ASN* 4.3 3.4 - - - +
421E VAL* 1.3 78.3 - - - +
423E ILE* 1.3 69.1 + - + +
426E ASN* 4.0 14.7 + - - +
1201E VAL* 4.5 20.4 - - + -
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Residues in contact with ILE 423 (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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419E ASN* 2.9 28.9 + - + +
422E ALA* 1.3 89.0 - - + +
424E ASP* 1.3 73.8 + - - +
425E THR 3.3 2.0 - - - -
426E ASN* 3.1 7.1 + - - +
427E GLN* 2.9 44.2 + - + +
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Residues in contact with ASP 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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420E LEU* 2.9 45.4 + - + +
423E ILE* 1.3 85.9 - - - +
425E THR* 1.3 61.5 - - - +
427E GLN* 3.2 5.9 + - - +
428E LEU* 2.9 29.7 + - + +
602E LYS 5.3 0.2 - - - +
605E VAL* 5.0 6.4 - - - +
606E SER* 3.0 38.7 + - - +
609E LYS* 3.8 14.9 - - - +
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Residues in contact with THR 425 (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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388E ARG* 3.4 44.4 - - + +
391E ILE* 4.3 13.0 - - + +
392E GLN* 4.3 10.3 - - + +
395E ILE* 4.3 14.0 - - - +
420E LEU 4.1 0.7 + - - -
421E VAL* 3.3 28.2 + - - +
423E ILE 3.3 0.2 - - - -
424E ASP* 1.3 74.3 - - - +
426E ASN* 1.3 59.9 + - - +
428E LEU* 3.1 14.8 + - + +
429E MET* 2.9 27.2 + - - +
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Residues in contact with ASN 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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388E ARG* 5.7 2.0 - - - +
421E VAL 4.2 1.4 + - - -
422E ALA 4.0 14.6 + - - +
423E ILE* 3.1 10.9 + - - +
425E THR* 1.3 79.1 - - - +
427E GLN* 1.3 60.8 + - + +
429E MET* 3.2 17.0 + - - +
430E TRP* 2.9 52.7 + - - +
2001E GBM 5.4 2.6 - - - +
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Residues in contact with GLN 427 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423E ILE* 2.9 35.2 + - + +
424E ASP* 3.3 12.6 - - - +
426E ASN* 1.3 81.4 - - - +
428E LEU* 1.3 50.9 + - - +
430E TRP* 3.7 8.1 - - - +
431E PHE* 2.6 37.7 + - - +
599E SER* 5.3 3.3 - - - +
602E LYS* 3.3 47.7 - - + +
603E ALA* 6.0 2.0 - - - -
606E SER* 3.8 11.2 - - - +
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Residues in contact with LEU 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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291E LEU* 6.2 4.5 - - + -
384E GLY* 5.8 0.2 - - - -
387E LEU* 6.0 5.2 - - + -
388E ARG* 6.6 0.2 - - - -
391E ILE* 3.7 36.3 - - + -
424E ASP* 2.9 21.2 + - + +
425E THR* 3.3 16.4 - - + +
427E GLN* 1.3 74.7 - - - +
429E MET* 1.3 58.0 - - - +
431E PHE* 3.7 11.0 - - + +
432E PHE* 2.8 46.9 + - + +
603E ALA* 5.4 7.2 - - + +
606E SER* 4.3 20.4 - - - +
607E VAL* 5.5 4.5 - - + +
610E LEU* 5.6 7.4 - - + -
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Residues in contact with MET 429 (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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384E GLY* 3.9 18.4 - - - +
385E ILE* 3.4 42.6 - - + -
387E LEU* 6.3 0.2 - - - -
388E ARG* 3.4 51.4 - - + +
425E THR 2.9 12.6 + - - +
426E ASN* 3.4 19.1 - - - +
428E LEU* 1.3 75.8 - - - +
430E TRP* 1.3 64.0 + - - +
432E PHE* 3.4 1.9 + - - +
433E PHE* 3.2 43.9 + - + -
1238E SER* 4.7 0.9 - - - -
2001E GBM 3.9 22.4 - - + -
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Residues in contact with TRP 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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426E ASN* 2.9 52.0 + - - +
427E GLN* 3.8 9.4 - - - +
429E MET* 1.3 75.7 - - + +
431E PHE* 1.3 65.8 + - - +
433E PHE* 3.0 31.5 + + - +
434E LEU* 3.2 31.9 + - + +
599E SER* 5.9 2.0 - - - +
2001E GBM 3.8 64.4 - + + +
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Residues in contact with PHE 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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427E GLN 2.6 23.8 + - - +
428E LEU* 3.8 9.6 - - + +
430E TRP* 1.3 72.8 - - - +
432E PHE* 1.3 88.4 + + - +
434E LEU* 3.1 9.3 + - + +
435E CYS* 2.9 45.4 + - + -
438E LEU* 5.8 7.2 - - + -
596E VAL* 6.4 0.2 - - + -
599E SER* 4.0 25.2 - - - +
600E THR* 3.4 32.1 - - + -
603E ALA* 3.7 28.3 - - + -
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Residues in contact with PHE 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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291E LEU* 5.5 14.6 - - + -
292E CYS* 5.9 7.6 - - - -
295E PHE* 5.0 5.4 - - + -
299E LEU* 3.9 26.8 - - + +
380E ALA* 4.1 7.4 - - - +
383E THR* 3.4 32.8 - - + -
384E GLY* 4.4 13.9 - - - +
387E LEU* 3.8 20.4 - - + -
428E LEU* 2.8 30.0 + - + +
429E MET 3.9 3.8 - - - +
430E TRP 3.2 0.2 - - - -
431E PHE* 1.3 99.4 - + - +
433E PHE* 1.3 65.3 + - - +
435E CYS* 3.2 14.1 + - + +
436E PRO* 3.3 10.4 - - - +
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Residues in contact with PHE 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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306E ARG* 4.4 4.0 + - - -
380E ALA* 3.6 22.3 - - - +
381E ILE* 3.4 48.2 - - + -
384E GLY* 4.0 5.4 - - - -
429E MET* 3.2 42.0 - - + -
430E TRP* 3.0 33.1 + + - +
432E PHE* 1.3 75.2 - - - +
434E LEU* 1.3 60.9 + - + +
436E PRO* 3.2 19.2 - - - +
2001E GBM 3.4 63.3 + + + +
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Residues in contact with LEU 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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430E TRP* 3.2 30.3 - - + +
431E PHE* 3.1 13.7 + - + +
433E PHE* 1.3 76.4 - - + +
435E CYS* 1.3 59.3 + - - +
436E PRO* 3.5 1.8 - - - -
437E ASN* 3.9 20.3 + - - +
438E LEU* 4.3 1.7 + - - +
592E LEU* 5.7 5.4 - - + -
595E SER* 4.2 13.5 - - - +
596E VAL* 3.7 39.7 - - + +
599E SER* 4.1 20.6 - - - +
2001E GBM 3.3 34.8 - - + +
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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