Contacts of the helix formed by residues 605 - 621 (chain B) in PDB entry 3BYH
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 ASN 605 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397B CYS* 3.7 17.3 - - - -
491B TRP* 5.6 1.0 - - - -
494B MET* 5.3 0.9 - - - +
600B ASP* 2.9 30.1 + - - +
603B GLU* 3.7 2.6 - - + -
604B VAL* 1.3 68.7 - - - +
606B GLN* 1.3 62.0 + - - +
607B LYS* 3.4 19.6 - - - +
608B MET* 2.9 31.1 + - + +
609B ILE* 2.8 27.4 + - - +
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Residues in contact with GLN 606 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A ASP 4.3 2.6 - - - +
3A ASP* 2.1 54.9 + - - +
4A ASP* 4.7 2.1 + - - +
28A ARG* 4.3 13.9 - - - +
491B TRP* 5.9 0.2 - - + -
539B PHE* 3.2 33.9 - - + +
540B LYS* 4.1 20.9 + - + +
604B VAL 3.2 6.6 + - - +
605B ASN* 1.3 73.5 - - - +
607B LYS* 1.3 69.6 + - + +
609B ILE* 3.5 2.1 - - - +
610B LEU* 2.9 29.8 + - - +
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Residues in contact with LYS 607 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A ASP* 4.8 10.9 + - - -
21A PHE* 6.2 0.4 - - - -
28A ARG* 5.3 1.8 - - - +
491B TRP* 0.9 211.9 - - + -
494B MET* 3.8 26.7 - - + +
495B ARG* 3.4 27.1 - - - +
498B MET* 3.9 7.7 - - + +
605B ASN* 3.1 9.6 + - - +
606B GLN* 1.3 88.0 - - + +
608B MET* 1.3 64.9 + - - +
610B LEU* 3.5 7.2 + - + +
611B ILE* 3.3 27.0 + - - +
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Residues in contact with MET 608 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397B CYS* 4.3 7.4 - - - +
401B TRP* 4.0 19.1 - - + +
494B MET* 2.2 55.9 - - + -
596B LEU* 3.9 38.6 - - + +
600B ASP* 3.9 15.0 - - + +
605B ASN* 2.9 32.8 + - + +
607B LYS* 1.3 76.7 - - - +
609B ILE* 1.3 65.5 + - - +
611B ILE* 3.5 9.5 + - + +
612B LEU* 3.1 23.9 + - - +
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Residues in contact with ILE 609 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536B ILE* 5.9 0.2 - - + -
539B PHE* 3.5 41.5 - - + +
544B LEU* 3.9 17.9 - - + -
550B PHE* 3.7 36.5 - - + -
596B LEU* 5.2 1.6 - - + -
600B ASP 4.1 16.4 - - - +
601B ILE* 4.3 15.0 - - + +
604B VAL* 4.4 3.8 - - - -
605B ASN 2.8 24.4 + - - +
606B GLN 3.5 7.2 - - - +
607B LYS 3.3 0.2 - - - -
608B MET* 1.3 77.8 - - - +
610B LEU* 1.3 61.6 + - - +
612B LEU* 3.3 3.7 + - - +
613B THR* 2.9 27.8 + - - +
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Residues in contact with LEU 610 (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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498B MET* 1.8 90.0 - - + -
502B LEU* 4.1 1.3 - - + -
516B ASP* 3.4 26.2 - - + +
519B ILE* 3.6 18.7 - - + +
539B PHE* 4.0 30.3 - - + -
606B GLN 2.9 17.5 + - - +
607B LYS* 3.5 3.6 - - - +
609B ILE* 1.3 77.0 - - - +
611B ILE* 1.3 54.5 + - - +
613B THR* 3.4 2.4 + - - -
614B ALA* 2.9 24.6 + - - +
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Residues in contact with ILE 611 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401B TRP* 5.0 14.4 - - + +
405B LEU* 6.5 0.4 - - + -
494B MET* 5.2 4.0 - - + +
497B HIS* 5.0 7.9 - - + +
498B MET* 2.7 48.9 - - + +
501B LEU* 3.6 21.8 - - + -
594B VAL* 4.9 11.2 - - + -
607B LYS 3.3 11.8 + - - +
608B MET* 4.0 18.2 - - + +
609B ILE 3.3 0.4 - - - -
610B LEU* 1.3 72.1 - - - +
612B LEU* 1.3 66.6 + - - +
614B ALA* 3.5 2.6 + - - +
615B SER* 2.9 23.2 + - - -
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Residues in contact with LEU 612 (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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550B PHE* 3.9 24.9 - - + -
583B ILE* 4.1 21.1 - - + -
584B VAL* 5.6 2.0 - - + -
587B ALA* 4.1 15.0 - - + -
592B CYS* 5.1 0.4 - - - -
594B VAL* 4.0 17.9 - - + +
596B LEU* 3.9 34.1 - - + -
601B ILE* 4.2 4.9 - - + -
608B MET 3.1 18.0 + - - +
609B ILE 3.7 4.0 - - - +
611B ILE* 1.3 75.8 - - - +
613B THR* 1.3 58.8 + - - +
615B SER* 3.0 3.5 + - - -
616B ILE* 2.9 54.8 + - + +
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Residues in contact with THR 613 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519B ILE* 3.8 15.0 - - + +
522B TRP* 4.2 3.5 - - + -
523B ALA* 3.7 30.3 - - + -
539B PHE* 3.5 19.2 - - + -
549B PHE* 5.8 1.8 - - + -
550B PHE* 3.5 18.1 - - - -
553B LEU* 4.2 10.1 - - + -
609B ILE 2.9 16.3 + - - -
610B LEU 3.6 3.6 - - - -
612B LEU* 1.3 78.5 - - - +
614B ALA* 1.3 57.1 + - - +
616B ILE* 3.0 10.9 + - - +
617B MET* 2.9 28.1 + - - +
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Residues in contact with ALA 614 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498B MET* 4.2 9.4 - - + -
501B LEU* 5.0 10.1 - - + -
519B ILE* 3.6 32.0 - - + +
610B LEU 2.9 17.7 + - - +
611B ILE* 3.8 4.9 - - + +
612B LEU 3.3 0.2 - - - -
613B THR* 1.3 75.8 - - - +
615B SER* 1.3 56.8 + - - +
617B MET* 3.4 6.9 - - - +
618B TYR* 2.9 27.4 + - - +
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Residues in contact with SER 615 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
592B CYS* 3.3 26.8 - - - +
593B SER 4.0 3.8 + - - -
594B VAL* 3.9 16.3 - - - +
611B ILE* 2.9 20.2 + - - -
612B LEU 3.0 5.1 + - - -
614B ALA* 1.3 76.0 - - - +
616B ILE* 1.3 65.2 + - - +
618B TYR* 3.3 7.4 + - - +
619B TRP* 3.2 29.8 + - - -
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Residues in contact with ILE 616 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522B TRP* 4.2 7.2 - - + -
550B PHE* 5.4 4.0 - - + -
553B LEU* 4.4 14.8 - - + -
554B LEU* 3.5 32.8 - - + -
557B VAL* 3.8 28.5 - - + +
587B ALA* 3.9 3.8 - - + -
590B LEU* 5.0 3.0 - - + +
592B CYS* 3.4 25.4 - - - -
612B LEU* 2.9 40.2 + - + +
613B THR* 3.4 10.1 - - - +
615B SER* 1.3 75.6 - - - +
617B MET* 1.3 64.8 + - - +
619B TRP* 3.3 4.9 + - - +
620B SER* 2.9 20.6 + - - -
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Residues in contact with MET 617 (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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505B LEU* 3.9 22.4 - - - -
514B MET* 4.7 0.7 - - - -
518B ASP 5.0 0.2 - - - +
519B ILE* 3.2 39.0 - - + +
522B TRP* 3.1 67.7 - - + -
613B THR 2.9 10.5 + - - +
614B ALA* 3.4 9.9 - - - +
616B ILE* 1.3 77.6 - - - +
618B TYR* 1.3 64.9 + - - +
620B SER* 2.9 11.4 + - - -
621B LEU* 3.0 32.3 + - + +
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Residues in contact with TYR 618 (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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614B ALA 2.9 15.5 + - - +
615B SER* 3.4 12.8 - - - +
616B ILE 3.3 0.2 - - - -
617B MET* 1.3 78.8 - - - +
619B TRP* 1.3 95.7 + + - +
621B LEU* 3.7 9.3 + - - +
622B GLN* 3.0 49.0 + - - +
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Residues in contact with TRP 619 (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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557B VAL* 5.4 0.4 - - + -
590B LEU* 4.5 7.0 - - + -
591B GLY* 2.9 42.9 + - - -
592B CYS* 3.6 15.1 - - - +
593B SER* 4.7 1.0 - - - +
615B SER* 3.2 24.0 + - - -
616B ILE 3.3 6.2 + - - +
617B MET 3.2 0.4 - - - -
618B TYR* 1.3 99.1 - + - +
620B SER* 1.3 65.0 + - - +
621B LEU 3.3 0.2 - - - -
622B GLN* 3.4 35.0 + - + +
623B ARG* 3.1 41.5 + - - +
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Residues in contact with SER 620 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522B TRP* 3.5 27.8 + - - -
526B LYS* 3.8 14.2 + - - -
557B VAL* 3.7 23.9 - - - +
616B ILE 2.9 15.8 + - - -
617B MET 2.9 5.5 + - - -
619B TRP* 1.3 72.4 - - - +
621B LEU* 1.3 59.3 + - - +
622B GLN 3.0 10.4 + - - -
623B ARG* 3.3 24.1 + - - +
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Residues in contact with LEU 621 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505B LEU* 6.5 0.7 - - + -
522B TRP* 4.1 20.2 - - + +
617B MET* 3.0 41.3 + - + +
618B TYR* 3.7 6.9 + - - +
619B TRP 3.3 0.2 - - - -
620B SER* 1.3 74.5 - - - +
622B GLN* 1.3 63.1 + - + +
623B ARG 3.6 0.4 - - - -
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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
------------------------------------------------------------
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