Contacts of the helix formed by residues 547 - 558 (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 GLY 547 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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544B LEU 2.9 14.6 + - - -
545B SER 3.2 1.3 - - - -
546B SER* 1.3 78.4 + - - +
548B LEU* 1.3 63.2 + - - +
549B PHE 3.4 2.7 - - - -
550B PHE* 3.6 4.2 + - - -
551B LEU* 3.2 32.4 + - - +
576B LYS 6.0 0.2 - - - -
579B ASN* 4.5 4.0 - - - -
580B ALA 5.6 0.4 - - - -
583B ILE* 3.4 21.3 - - - +
601B ILE* 4.7 5.2 - - - -
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Residues in contact with LEU 548 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534B LEU* 4.2 6.7 - - + -
546B SER* 3.1 24.1 + - - +
547B GLY* 1.3 76.1 - - - +
549B PHE* 1.3 66.0 + - - +
551B LEU* 3.4 4.3 + - - +
552B ASN* 2.8 36.5 + - - +
564B TRP* 5.1 7.6 - - + -
567B VAL* 4.4 11.9 - - + -
568B THR 3.6 23.8 - - - +
569B LYS* 4.8 3.8 - - + -
570B GLY 4.3 10.1 - - - +
579B ASN* 4.5 1.8 - - - +
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Residues in contact with PHE 549 (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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523B ALA* 4.1 23.3 - - + -
524B ASN* 3.9 20.2 - - - -
527B VAL* 3.8 22.9 - - + -
534B LEU* 3.8 43.2 - - + +
535B GLN* 4.1 2.5 - - - -
536B ILE* 3.6 32.1 - - + -
543B SER 5.8 1.5 + - - +
544B LEU* 4.0 30.3 + - + +
546B SER* 4.6 1.0 + - - -
547B GLY 3.4 0.6 - - - +
548B LEU* 1.3 78.4 - - - +
550B PHE* 1.3 67.4 + + - +
552B ASN* 3.0 4.5 + - - +
553B LEU* 2.8 37.7 + - + +
613B THR* 5.8 2.0 - - + -
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Residues in contact with PHE 550 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544B LEU* 4.3 22.2 - - + -
547B GLY* 3.6 1.9 + - - -
548B LEU 3.4 0.4 - - - -
549B PHE* 1.3 82.2 - + - +
551B LEU* 1.3 53.9 + - - +
553B LEU* 3.1 18.0 + - + +
554B LEU* 2.7 41.8 + - + +
583B ILE* 3.5 28.3 - - + -
601B ILE* 4.1 24.5 - - + -
609B ILE* 3.7 45.8 - - + -
612B LEU* 3.9 30.5 - - + -
613B THR* 3.5 22.2 - - - -
616B ILE* 5.4 3.4 - - + -
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Residues in contact with LEU 551 (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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547B GLY 3.2 20.6 + - - +
548B LEU* 3.8 3.1 - - - +
550B PHE* 1.3 76.7 - - - +
552B ASN* 1.3 57.4 + - - +
554B LEU* 3.9 10.3 - - + +
555B TRP* 2.9 29.3 + - - +
562B VAL* 4.0 10.4 - - + +
564B TRP* 3.4 19.0 - - + -
567B VAL* 3.2 37.7 - - + -
579B ASN* 4.1 18.6 - - + +
582B TYR* 3.7 29.4 - - + -
583B ILE* 3.8 20.2 - - + -
586B VAL* 5.3 0.7 - - + -
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Residues in contact with ASN 552 (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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527B VAL* 4.4 14.9 - - + +
532B ARG* 2.6 41.9 + - + +
534B LEU* 3.5 24.3 - - + +
548B LEU* 2.8 28.9 + - - +
549B PHE 3.4 8.3 - - - +
551B LEU* 1.3 74.5 - - - +
553B LEU* 1.3 56.5 + - - +
555B TRP* 3.2 10.5 + - - +
556B ALA* 2.7 35.2 + - - +
564B TRP* 3.8 22.7 - - - -
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Residues in contact with LEU 553 (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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522B TRP* 3.9 16.2 - - + -
523B ALA* 3.6 40.2 - - + +
526B LYS* 3.8 26.0 - - + -
527B VAL* 3.9 12.3 - - + +
549B PHE* 2.8 21.3 + - + +
550B PHE* 3.5 20.6 - - + +
552B ASN* 1.3 78.0 - - - +
554B LEU* 1.3 57.7 + - + +
556B ALA* 3.1 5.7 + - - +
557B VAL* 2.9 31.4 + - - +
613B THR* 4.2 14.1 - - + -
616B ILE* 4.4 16.6 - - + -
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Residues in contact with LEU 554 (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* 2.7 25.3 + - + +
551B LEU* 3.9 8.5 - - + +
553B LEU* 1.3 73.8 - - + +
555B TRP* 1.3 58.4 + - - +
557B VAL* 3.3 4.8 + - - +
558B GLU 2.9 30.5 + - - +
561B VAL* 4.2 3.5 - - + +
562B VAL* 3.9 13.2 - - + -
583B ILE* 4.1 28.5 - - + +
586B VAL* 4.0 27.1 - - + -
587B ALA* 4.4 7.0 - - + +
590B LEU* 3.6 23.5 - - + +
616B ILE* 3.5 35.4 - - + -
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Residues in contact with TRP 555 (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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530B MET* 3.5 56.2 - - + +
532B ARG* 4.4 14.6 - - + -
551B LEU 2.9 20.5 + - - +
552B ASN* 3.2 21.5 + - - +
554B LEU* 1.3 76.4 - - - +
556B ALA* 1.3 61.9 + - - +
559B PRO* 2.9 65.7 + - + +
562B VAL* 3.8 10.3 - - + +
564B TRP* 3.2 36.9 - + + +
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Residues in contact with ALA 556 (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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526B LYS* 3.8 36.9 + - + +
527B VAL* 4.5 2.5 - - - -
530B MET* 3.4 38.1 - - + +
552B ASN 2.7 17.3 + - - +
553B LEU* 3.1 13.0 + - - +
555B TRP* 1.3 76.3 - - - +
557B VAL* 1.3 63.3 + - - +
559B PRO* 4.4 3.8 - - - +
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Residues in contact with VAL 557 (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 6.1 - - + -
526B LYS* 3.9 15.9 + - + +
553B LEU 2.9 19.0 + - - +
554B LEU* 3.3 8.3 + - - +
556B ALA* 1.3 78.8 - - - +
558B GLU* 1.3 65.2 + - + +
559B PRO* 4.3 1.6 - - - +
590B LEU* 4.1 20.9 - - + -
616B ILE* 3.8 24.0 - - + +
619B TRP* 5.4 0.4 - - + -
620B SER* 3.7 36.6 - - - +
623B ARG* 4.6 17.7 - - + +
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Residues in contact with GLU 558 (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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554B LEU 2.9 8.1 + - - +
555B TRP* 3.4 2.4 - - - -
557B VAL* 1.3 83.2 - - + +
559B PRO* 1.3 77.0 - - - +
560B ARG* 2.9 31.2 + - + +
561B VAL* 2.9 39.9 - - + +
562B VAL 4.1 0.7 + - - -
590B LEU* 4.0 22.7 - - + -
623B ARG* 5.0 14.6 + - - +
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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