Contacts of the helix formed by residues 544 - 554 (chain A) in PDB entry 4BL8
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 CYS 544 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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513A ARG* 3.6 33.4 - - + +
514A ILE* 3.9 12.3 - - - -
516A HIS* 4.1 1.6 - - - -
543A VAL* 1.3 77.0 - - - +
545A THR* 1.3 66.9 + - - +
546A GLU* 3.2 16.2 - - - +
547A GLU* 3.0 14.4 + - - +
548A LEU* 3.0 20.3 + - - +
580A ARG* 3.5 23.6 - - - -
582A GLU 4.4 2.9 - - - -
583A THR* 4.1 21.5 - - + -
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Residues in contact with THR 545 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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504A HIS* 6.0 0.2 - - - +
513A ARG* 4.5 1.3 + - + +
515A GLN* 3.5 25.1 - - - +
516A HIS* 3.3 33.6 - - + +
544A CYS* 1.3 73.1 - - - +
546A GLU* 1.3 78.3 + - - +
548A LEU* 3.1 3.1 + - - +
549A HIS* 2.9 42.9 + - - -
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Residues in contact with GLU 546 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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513A ARG* 3.0 30.1 + - - +
544A CYS* 3.8 7.1 - - - +
545A THR* 1.3 93.4 + - - +
547A GLU* 1.3 59.3 + - - +
549A HIS* 3.5 11.0 + - + +
550A SER* 2.9 24.2 + - - -
583A THR* 3.4 27.9 - - + +
585A PHE* 4.3 9.7 - - + -
586A GLU* 4.7 1.9 - - - +
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Residues in contact with GLU 547 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518A LEU* 5.6 0.4 - - - -
543A VAL* 3.4 20.2 - - + +
544A CYS* 3.0 24.3 + - + +
546A GLU* 1.3 74.9 - - - +
548A LEU* 1.3 64.6 + - - +
549A HIS 3.1 1.6 - - - -
550A SER* 3.1 11.3 + - - -
551A ALA* 3.1 21.3 + - - +
559A ILE* 4.3 12.1 - - + +
563A LEU* 4.0 5.8 - - + +
580A ARG* 2.6 33.7 + - - -
583A THR* 3.5 4.5 - - - -
584A ILE* 2.9 49.7 + - + +
585A PHE* 4.2 6.3 - - + -
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Residues in contact with LEU 548 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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500A HIS* 3.8 38.4 - - + -
501A VAL 4.6 7.9 - - - +
502A SER* 3.4 17.3 - - - +
504A HIS* 5.2 1.8 - - + -
516A HIS* 3.0 52.0 - - + +
517A MET 4.8 0.4 - - - +
518A LEU* 4.6 3.8 - - + -
543A VAL* 4.3 6.3 - - + +
544A CYS 3.0 11.4 + - - +
545A THR* 3.5 8.1 - - - +
547A GLU* 1.3 75.6 - - - +
549A HIS* 1.3 69.3 + - + +
551A ALA* 3.3 5.9 + - - +
552A GLN* 3.2 28.9 + - - +
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Residues in contact with HIS 549 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504A HIS* 6.1 5.2 - + - -
516A HIS* 6.2 0.2 - - - -
545A THR* 2.9 35.1 + - - -
546A GLU* 3.6 12.1 - - + +
548A LEU* 1.3 83.0 - - + +
550A SER* 1.3 58.7 + - - +
552A GLN* 3.1 21.8 + - - +
553A GLN* 2.9 50.0 + - - +
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Residues in contact with SER 550 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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546A GLU 2.9 14.7 + - - -
547A GLU* 3.1 6.3 + - - -
549A HIS* 1.3 77.0 - - - +
551A ALA* 1.3 59.2 + - - +
553A GLN* 3.8 9.7 - - - +
554A TRP* 2.9 34.7 + - - +
559A ILE* 3.3 25.4 - - - +
585A PHE* 3.3 25.1 - - - -
592A GLN* 5.5 0.2 + - - -
595A VAL* 4.7 9.1 - - - +
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Residues in contact with ALA 551 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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500A HIS* 4.6 10.1 + - + +
518A LEU* 3.7 28.5 - - + -
547A GLU 3.1 10.8 + - - +
548A LEU 3.5 9.2 - - - +
549A HIS 3.2 0.4 - - - -
550A SER* 1.3 77.5 - - - +
552A GLN* 1.3 62.3 + - - +
554A TRP 3.9 0.2 - - - -
555A ASN* 3.3 39.2 + - - +
556A GLY* 3.9 6.7 + - - -
559A ILE* 3.6 8.9 - - + +
605A ASN* 4.7 3.5 + - - +
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Residues in contact with GLN 552 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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500A HIS* 3.4 42.7 + - + +
502A SER* 3.9 15.2 + - - -
548A LEU* 3.2 19.7 + - - +
549A HIS* 3.1 33.1 + - - +
551A ALA* 1.3 77.9 - - - +
553A GLN* 1.3 61.3 + - + +
605A ASN* 3.6 8.6 - - - +
606A LEU* 3.2 41.6 + - + +
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Residues in contact with GLN 553 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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549A HIS* 2.9 36.7 + - - +
550A SER* 3.9 8.4 - - - +
552A GLN* 1.3 79.3 - - + +
554A TRP* 1.3 57.2 + - - +
592A GLN* 6.0 0.2 + - - -
595A VAL* 5.7 2.3 - - - +
599A ILE* 3.8 13.6 - - + +
604A SER* 2.7 35.4 + - - -
605A ASN 4.0 0.4 - - - -
606A LEU* 4.4 8.9 - - + +
720A LEU* 4.5 15.1 - - - +
723A LEU* 3.7 33.4 - - + +
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Residues in contact with TRP 554 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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550A SER 2.9 13.1 + - - +
551A ALA 3.9 2.0 - - - -
553A GLN* 1.3 78.3 - - - +
555A ASN* 1.3 80.7 + - - +
558A GLY* 3.6 34.3 - - - -
559A ILE* 4.0 17.7 - - + -
561A GLU* 4.7 0.9 - - - -
562A LEU* 4.6 6.3 - - + -
594A ARG* 3.7 31.6 - - - -
595A VAL* 4.0 31.9 - - + -
598A GLY* 3.0 40.7 + - - -
599A ILE* 3.8 15.3 - - + -
602A ASP* 3.1 18.1 + - + -
603A GLY 3.7 10.5 - - - +
605A ASN* 3.2 24.8 + - - +
92B PRO* 6.3 2.2 - - + -
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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