Contacts of the helix formed by residues 415 - 434 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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414H ALA* 1.3 76.3 - - - +
416H GLN* 1.3 52.8 + - - +
418H CYS* 3.3 11.7 + - - +
419H ASN* 2.7 42.1 + - - +
1209H GLU* 5.3 0.2 + - - -
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Residues in contact with GLN 416 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414H ALA* 3.1 5.7 - - - +
415H GLY* 1.3 76.4 - - - +
417H ILE* 1.3 60.8 + - + +
419H ASN* 3.3 20.3 + - - +
420H LEU* 2.8 27.4 + - - +
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Residues in contact with ILE 417 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395H ILE* 5.1 2.5 - - + -
399H ILE* 4.2 13.7 - - + -
414H ALA* 2.9 25.2 + - - +
416H GLN* 1.3 76.8 - - + +
418H CYS* 1.3 66.4 + - - +
420H LEU* 3.2 12.2 + - + +
421H VAL* 3.0 23.6 + - + +
613H PHE* 4.6 28.0 - - + -
1204H PHE* 3.6 25.6 - - + -
1208H VAL* 4.1 18.2 - - + -
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Residues in contact with CYS 418 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414H ALA* 3.0 20.1 + - - -
415H GLY* 3.3 11.9 + - - +
417H ILE* 1.3 76.5 - - - +
419H ASN* 1.3 57.3 + - - +
421H VAL* 3.5 0.9 + - - +
422H ALA* 2.8 35.1 + - + +
1201H VAL* 4.8 8.0 - - + +
1204H PHE* 3.9 18.6 - - + -
1205H ALA* 3.5 38.6 - - - -
1208H VAL* 5.4 1.6 - - - -
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Residues in contact with ASN 419 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415H GLY* 2.7 29.9 + - - +
416H GLN* 3.5 26.4 + - - +
417H ILE 3.2 0.2 - - - -
418H CYS* 1.3 75.3 - - - +
420H LEU* 1.3 60.0 + - - +
422H ALA* 4.6 2.4 - - - +
423H ILE* 2.9 45.8 + - + +
424H ASP* 5.1 0.2 - - - -
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Residues in contact with LEU 420 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395H ILE* 4.8 13.2 - - + -
416H GLN 2.8 14.9 + - - +
417H ILE* 3.2 16.1 + - + +
419H ASN* 1.3 74.3 - - - +
421H VAL* 1.3 60.9 + - + +
424H ASP* 2.9 60.1 + - + +
425H THR* 3.7 2.6 + - - -
606H SER 5.4 0.4 - - - +
609H LYS* 3.9 23.6 - - + +
610H LEU* 4.6 7.6 - - + +
613H PHE* 3.9 41.7 - - + -
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Residues in contact with VAL 421 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392H GLN* 4.3 31.4 + - + +
395H ILE* 3.8 29.2 - - + -
417H ILE 3.0 9.6 + - - +
418H CYS 4.1 2.0 - - - +
420H LEU* 1.3 77.2 - - + +
422H ALA* 1.3 65.4 + - - +
423H ILE 3.2 0.9 + - - -
425H THR* 3.3 27.2 + - - +
426H ASN 4.2 1.0 + - - -
1200H LEU* 4.8 10.5 - - + -
1201H VAL* 5.3 5.2 - - + -
1204H PHE* 3.5 40.8 - - + -
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Residues in contact with ALA 422 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418H CYS* 2.8 20.9 + - + +
419H ASN* 4.3 3.6 - - - +
421H VAL* 1.3 78.8 - - - +
423H ILE* 1.3 68.4 + - + +
426H ASN* 4.0 14.3 + - - +
1201H VAL* 4.5 20.2 - - + -
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Residues in contact with ILE 423 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419H ASN* 2.9 29.5 + - + +
422H ALA* 1.3 88.2 - - + +
424H ASP* 1.3 74.0 + - - +
425H THR 3.3 1.3 - - - -
426H ASN* 3.1 8.9 + - - +
427H GLN* 2.9 44.4 + - + +
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Residues in contact with ASP 424 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420H LEU* 2.9 44.8 + - + +
423H ILE* 1.3 86.1 - - - +
425H THR* 1.3 60.8 + - - +
427H GLN* 3.2 6.1 + - - +
428H LEU* 2.9 30.7 + - + +
602H LYS 5.3 0.3 - - - +
605H VAL* 5.0 5.9 - - - +
606H SER* 3.0 39.6 + - - +
609H LYS* 3.8 16.1 - - - +
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Residues in contact with THR 425 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388H ARG* 3.4 44.3 - - + +
391H ILE* 4.3 13.1 - - + +
392H GLN* 4.3 9.9 - - + +
395H ILE* 4.3 14.4 - - - +
420H LEU 4.1 1.0 + - - -
421H VAL* 3.3 28.3 + - - +
423H ILE 3.3 0.4 - - - -
424H ASP* 1.3 73.8 - - - +
426H ASN* 1.3 61.8 + - - +
428H LEU* 3.1 15.0 + - + +
429H MET* 2.9 26.9 + - - +
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Residues in contact with ASN 426 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388H ARG* 5.7 2.2 - - - +
421H VAL 4.2 2.0 + - - -
422H ALA 4.0 14.6 + - - +
423H ILE* 3.1 11.0 + - - +
425H THR* 1.3 78.3 - - - +
427H GLN* 1.3 60.3 + - - +
429H MET* 3.2 16.1 + - - +
430H TRP* 2.9 53.2 + - - +
2001H GBM 5.4 2.3 - - - +
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Residues in contact with GLN 427 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423H ILE* 2.9 35.3 + - + +
424H ASP* 3.3 13.9 - - - +
426H ASN* 1.3 80.9 - - - +
428H LEU* 1.3 50.3 + - - +
430H TRP* 3.4 9.4 + - - +
431H PHE* 2.6 37.8 + - - +
599H SER* 5.3 2.8 - - - +
602H LYS* 3.3 48.6 - - + +
603H ALA* 6.0 1.1 - - - -
606H SER* 3.8 11.2 - - - +
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Residues in contact with LEU 428 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291H LEU* 6.2 3.8 - - + -
387H LEU* 6.0 5.8 - - + -
388H ARG* 6.6 0.2 - - - -
391H ILE* 3.7 36.3 - - + -
424H ASP* 2.9 21.8 + - + +
425H THR* 3.1 17.7 + - + +
427H GLN* 1.3 73.3 - - - +
429H MET* 1.3 58.3 + - - +
431H PHE* 3.8 11.6 - - + +
432H PHE* 2.8 46.2 + - + +
603H ALA* 5.4 7.2 - - + +
606H SER* 4.3 19.5 - - - +
607H VAL* 5.5 4.5 - - + +
610H LEU* 5.6 7.0 - - + -
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Residues in contact with MET 429 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384H GLY* 3.9 18.8 - - - +
385H ILE* 3.4 42.6 - - + -
387H LEU* 6.3 0.7 - - - -
388H ARG* 3.4 50.5 - - + +
425H THR 2.9 12.7 + - - +
426H ASN* 3.2 18.8 + - - +
428H LEU* 1.3 77.3 - - - +
430H TRP* 1.3 64.9 + - + +
432H PHE* 3.4 2.1 + - - +
433H PHE* 3.2 44.5 + - + -
1238H SER* 4.7 0.9 - - - -
2001H GBM 3.9 21.3 - - + -
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Residues in contact with TRP 430 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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426H ASN* 2.9 52.7 + - - +
427H GLN* 3.8 9.9 - - - +
429H MET* 1.3 74.3 - - + +
431H PHE* 1.3 65.7 + - - +
433H PHE* 3.0 31.2 + + - +
434H LEU* 3.2 31.5 + - + +
599H SER* 5.9 2.7 - - - +
2001H GBM 3.8 64.1 - + + +
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Residues in contact with PHE 431 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427H GLN 2.6 23.5 + - - +
428H LEU* 3.8 10.1 - - + +
430H TRP* 1.3 72.0 - - - +
432H PHE* 1.3 89.6 + + - +
434H LEU* 3.1 9.6 + - - -
435H CYS* 2.9 44.5 + - + -
438H LEU* 5.8 7.4 - - + -
596H VAL* 6.4 0.4 - - + -
599H SER* 4.0 24.9 - - - +
600H THR* 3.4 31.9 - - + -
603H ALA* 3.7 28.5 - - + -
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Residues in contact with PHE 432 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291H LEU* 5.5 14.1 - - + -
292H CYS* 5.9 7.6 - - - -
295H PHE* 5.0 6.1 - - + -
299H LEU* 3.9 27.2 - - + +
380H ALA* 4.1 7.2 - - - +
383H THR* 3.4 33.0 - - + -
384H GLY* 4.4 13.5 - - - +
387H LEU* 3.8 20.6 - - + -
428H LEU* 2.8 31.0 + - + +
429H MET 3.9 4.3 - - - +
431H PHE* 1.3 100.9 - + - +
433H PHE* 1.3 65.8 + - - +
435H CYS* 3.2 14.6 + - + +
436H PRO* 3.3 10.2 - - - +
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Residues in contact with PHE 433 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306H ARG* 4.4 4.0 + - - -
380H ALA* 3.6 21.6 - - - +
381H ILE* 3.4 48.7 - - + -
384H GLY* 4.0 5.8 - - - -
429H MET* 3.2 42.6 - - + -
430H TRP* 3.0 32.7 + + - +
432H PHE* 1.3 76.0 - - - +
434H LEU* 1.3 60.4 + - + +
436H PRO* 3.2 19.1 - - - +
2001H GBM 3.4 63.5 + + + +
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Residues in contact with LEU 434 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430H TRP* 3.2 29.2 - - + +
431H PHE* 3.1 14.2 + - + +
433H PHE* 1.3 78.0 - - + +
435H CYS* 1.3 59.1 + - - +
436H PRO 3.5 2.0 - - - -
437H ASN* 3.9 19.4 + - + +
438H LEU* 4.3 1.7 + - - +
592H LEU* 5.7 5.8 - - + -
595H SER* 4.2 13.9 - - - +
596H VAL* 3.7 39.7 - - + +
599H SER* 4.1 20.0 - - - +
2001H GBM 3.3 34.5 - - + +
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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
------------------------------------------------------------
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