Contacts of the helix formed by residues 422 - 440 (chain B) in PDB entry 6HBU
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 422 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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416B LEU* 6.2 0.2 - - - -
417B LYS 3.4 21.8 - - - -
419B ASP 3.6 12.0 + - - -
421B THR* 1.3 76.5 - - - +
423B ILE* 1.3 62.6 + - - +
424B GLN 3.7 0.7 - - - -
425B ASN* 4.0 10.7 - - - +
426B ARG* 2.7 40.5 + - - +
591B PHE* 4.5 0.2 - - - -
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Residues in contact with ILE 423 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419B ASP 4.9 3.8 - - - +
420B SER 4.9 4.9 + - - +
421B THR* 4.4 0.4 - - - +
422B GLY* 1.3 78.4 - - - +
424B GLN* 1.3 56.7 + - - +
425B ASN 3.2 1.1 - - - -
426B ARG 4.3 0.2 - - - +
427B ALA* 2.6 34.3 + - - +
586B PHE* 3.9 17.0 - - + -
591B PHE* 3.6 41.3 - - + -
607B THR* 3.3 40.6 - - - +
609B THR 5.3 0.7 - - - +
613B TYR* 3.7 40.2 - - + -
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Residues in contact with GLN 424 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
554A LEU 5.5 0.4 + - - -
555A LEU* 4.0 34.6 + - - +
413B TYR* 4.8 1.4 + - - -
421B THR* 5.0 15.2 - - + +
422B GLY 4.3 1.0 - - - +
423B ILE* 1.3 78.1 - - - +
425B ASN* 1.3 59.7 + - - +
427B ALA* 4.6 4.1 - - - +
428B GLY* 3.1 26.7 + - - +
554B LEU* 5.1 12.5 - - - +
613B TYR* 5.6 1.9 + - - -
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Residues in contact with ASN 425 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
556A VAL* 5.1 7.7 - - - +
413B TYR* 3.5 32.4 - - + -
416B LEU* 3.8 15.7 - - + -
421B THR* 3.0 30.5 + - - +
422B GLY* 4.0 7.1 - - - +
423B ILE 3.2 0.4 - - - -
424B GLN* 1.3 80.1 - - - +
426B ARG* 1.3 58.0 + - - +
429B VAL* 2.9 32.8 + - - +
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Residues in contact with ARG 426 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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416B LEU* 3.1 48.5 + - + +
417B LYS 2.5 27.9 + - - +
418B ASN* 3.4 21.4 + - - +
422B GLY 2.7 34.0 + - - +
423B ILE 3.2 1.6 + - - -
425B ASN* 1.3 79.5 - - - +
427B ALA* 1.3 61.0 + - - +
428B GLY 3.1 0.4 - - - -
429B VAL* 3.2 22.7 - - - +
430B LEU* 3.3 17.0 - - - +
498B GLY 4.8 6.7 + - - -
499B LEU* 5.9 0.2 - - - +
585B GLU* 3.2 25.9 + - - +
586B PHE* 3.5 21.3 - - + -
589B GLN* 4.7 10.8 - - - +
591B PHE* 3.3 22.5 - - - -
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Residues in contact with ALA 427 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423B ILE 2.6 22.4 + - - +
424B GLN* 4.0 5.6 - - - +
426B ARG* 1.3 72.7 - - - +
428B GLY* 1.3 56.2 + - - +
430B LEU* 4.3 1.1 - - - -
431B PHE* 4.1 0.9 - - - +
554B LEU* 3.7 11.7 - - + +
578B PHE* 3.2 31.1 - - + -
582B GLN* 3.9 12.8 - - - +
586B PHE* 3.8 7.8 - - + -
613B TYR* 3.3 31.9 - - + +
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Residues in contact with GLY 428 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555A LEU* 3.7 21.4 - - - +
413B TYR* 4.0 9.9 - - - -
424B GLN* 3.1 21.2 + - - -
425B ASN 3.7 1.1 - - - -
426B ARG 3.1 0.2 - - - -
427B ALA* 1.3 77.8 - - - +
429B VAL* 1.3 63.3 + - - +
430B LEU 3.4 0.4 - - - -
431B PHE 3.6 5.5 + - - -
432B PHE* 3.2 27.0 - - - -
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Residues in contact with VAL 429 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409B ILE* 3.6 26.6 - - + +
413B TYR* 3.7 22.9 - - + -
416B LEU* 4.5 14.6 - - + -
425B ASN 2.9 15.9 + - - +
426B ARG* 3.2 22.2 - - - +
428B GLY* 1.3 77.9 - - - +
430B LEU* 1.3 65.9 + - + +
431B PHE 3.2 1.0 + - - -
432B PHE* 3.3 6.2 + - - +
433B LEU* 3.3 24.6 + - + +
497B LEU* 3.7 23.3 - - + -
499B LEU* 4.7 6.1 - - + -
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Residues in contact with LEU 430 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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426B ARG 3.3 17.1 + - - +
427B ALA* 4.8 0.4 - - - -
428B GLY 3.4 0.2 - - - -
429B VAL* 1.3 77.6 - - + +
431B PHE* 1.3 62.0 + - - +
432B PHE 3.4 0.2 - - - -
433B LEU* 3.7 25.0 - - + +
434B THR* 3.4 27.4 + - - +
499B LEU* 5.1 8.3 - - + -
509B MET* 5.2 2.9 - - + -
578B PHE* 3.5 15.5 - - + -
581B LEU* 3.4 45.9 - - + +
582B GLN* 3.9 15.5 - - + +
585B GLU* 3.3 25.8 - - - +
586B PHE* 4.4 4.9 - - + -
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Residues in contact with PHE 431 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431A PHE* 5.4 4.0 - + - -
549A MET* 4.4 15.3 - - + -
555A LEU* 3.7 32.8 - - + -
427B ALA 4.1 3.6 - - - +
428B GLY 3.6 9.8 + - - +
429B VAL 3.2 0.6 - - - -
430B LEU* 1.3 79.1 - - - +
432B PHE* 1.3 66.3 + + - +
434B THR* 3.0 20.0 + - - -
435B THR* 3.0 32.7 + - + +
549B MET* 3.6 26.9 - - + -
552B SER* 3.4 27.8 - - - -
554B LEU* 4.0 21.1 - - + -
555B LEU* 4.9 8.7 - - + -
574B PRO* 5.7 0.4 - - + -
578B PHE* 3.5 24.8 - + + -
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Residues in contact with PHE 432 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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546A VAL* 4.4 7.2 - - + +
549A MET* 3.7 46.2 - - + -
550A ILE* 3.7 42.2 - - + -
555A LEU* 3.7 31.4 - - + -
556A VAL* 5.5 0.4 - - + -
405B LEU* 5.6 0.3 - - - +
409B ILE* 4.2 25.1 - - + +
413B TYR* 4.1 19.5 - + - -
428B GLY 3.2 24.5 - - - -
429B VAL* 3.3 6.5 + - - +
431B PHE* 1.3 81.7 - + - +
433B LEU* 1.3 62.5 + - - +
434B THR 3.4 0.2 - - - -
435B THR* 3.5 5.3 + - - -
436B ASN* 3.2 25.3 + - - +
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Residues in contact with LEU 433 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409B ILE* 4.6 9.9 - - + -
429B VAL* 3.3 18.8 + - + +
430B LEU* 3.7 30.3 - - + +
431B PHE 3.3 0.4 - - - -
432B PHE* 1.3 78.8 - - - +
434B THR* 1.3 60.8 + - - +
436B ASN* 3.8 1.9 + - - +
437B GLN* 3.3 26.5 + - - +
489B PHE* 3.5 32.2 - - + -
493B VAL* 4.0 23.8 - - + -
497B LEU* 5.6 0.4 - - + -
499B LEU* 5.3 2.7 - - + -
509B MET* 3.7 26.9 - - + -
513B LEU* 4.3 8.5 - - + +
581B LEU* 4.4 9.4 - - + -
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Residues in contact with THR 434 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430B LEU 3.4 15.6 + - - +
431B PHE* 3.0 15.6 + - - -
433B LEU* 1.3 74.6 - - - +
435B THR* 1.3 67.1 + - - +
436B ASN 3.2 1.6 - - - -
437B GLN* 3.1 5.6 + - - +
438B CYS* 2.9 35.0 + - - -
512B THR* 6.1 0.2 - - + -
513B LEU* 5.6 1.3 - - + -
516B VAL* 4.8 8.9 - - + +
574B PRO* 4.7 12.5 + - - +
577B GLY* 3.8 6.1 - - - -
578B PHE* 3.7 31.0 - - - +
581B LEU* 3.7 20.9 - - + -
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Residues in contact with THR 435 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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546A VAL* 3.7 6.6 - - - +
549A MET* 3.6 18.1 - - - +
431B PHE* 3.0 45.2 + - + +
432B PHE* 3.5 10.2 - - - -
434B THR* 1.3 79.1 + - - +
436B ASN* 1.3 63.5 + - - +
438B CYS* 4.1 4.3 - - - -
439B PHE* 3.1 41.1 + - + +
549B MET* 4.3 14.1 - - + -
574B PRO* 5.0 10.3 - - + -
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Residues in contact with ASN 436 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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543A ILE* 4.1 18.2 - - - +
546A VAL* 4.4 7.5 - - + +
402B THR* 4.9 7.9 + - - +
405B LEU* 3.4 29.1 - - + +
432B PHE 3.2 20.9 + - - +
433B LEU 3.8 6.7 - - - +
434B THR 3.2 0.6 - - - -
435B THR* 1.3 78.6 + - - +
437B GLN* 1.3 66.2 + - - +
439B PHE* 4.4 0.2 - - - +
440B SER* 2.9 33.0 + - - -
489B PHE* 3.2 36.0 - - + -
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Residues in contact with GLN 437 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402B THR* 5.5 0.7 - - - +
433B LEU 3.3 15.5 - - - +
434B THR 3.1 3.6 + - - +
436B ASN* 1.3 85.6 + - - +
438B CYS* 1.3 58.4 - - - +
440B SER* 4.6 5.1 - - - -
441B SER* 3.0 24.8 + - - -
485B PRO* 4.2 8.2 + - - +
486B SER* 2.5 33.1 + - - +
489B PHE* 3.8 16.3 - - - -
513B LEU* 3.2 30.8 + - + +
516B VAL* 3.7 23.1 - - + -
517B ALA* 3.6 16.9 - - - +
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Residues in contact with CYS 438 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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434B THR* 2.9 21.5 + - - +
435B THR* 4.4 6.1 - - - -
437B GLN* 1.3 77.0 - - - +
439B PHE* 1.3 62.8 + - + +
441B SER* 3.0 19.9 + - - -
516B VAL* 4.4 8.7 - - - -
520B ALA* 3.9 7.9 - - - -
545B PHE* 3.1 32.8 - - + -
573B ILE* 4.0 24.0 - - - -
574B PRO* 3.7 33.9 - - + -
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Residues in contact with PHE 439 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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439A PHE* 3.5 39.5 - + - -
542A THR* 3.1 30.8 + - - +
546A VAL* 4.2 14.4 - - + -
549A MET* 5.2 0.4 - - + -
435B THR* 3.1 38.9 + - + +
436B ASN* 4.4 0.4 - - - +
438B CYS* 1.3 82.0 - - + +
440B SER* 1.3 59.7 + - - +
441B SER 3.2 0.4 - - - -
442B VAL* 3.4 13.0 + - - +
542B THR* 4.2 13.7 - - + -
545B PHE* 3.5 40.8 - + + -
546B VAL* 4.0 9.9 - - + -
549B MET* 3.8 31.6 - - + -
574B PRO* 6.3 1.6 - - + -
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Residues in contact with SER 440 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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539A LEU* 3.5 13.2 - - - +
542A THR* 4.1 8.5 - - - -
543A ILE* 3.7 14.3 - - - +
398B GLN* 3.4 25.4 + - - -
436B ASN* 2.9 24.4 + - - -
437B GLN* 4.6 7.2 - - - -
438B CYS 3.2 0.4 - - - -
439B PHE* 1.3 76.7 - - - +
441B SER* 1.3 57.3 + - - +
442B VAL 3.2 3.0 + - - -
443B SER* 3.3 9.7 + - - -
481B MET 5.7 0.2 + - - -
482B ARG* 3.3 14.4 + - - -
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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