Contacts of the helix formed by residues 544 - 552 (chain D) in PDB entry 6X34
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 LEU 544 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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540D PHE* 5.0 7.9 - - + +
541D SER* 5.4 4.9 - - - +
542D ASN 4.1 1.2 + - - -
543D ASN* 1.3 78.6 - - - +
545D ASP* 1.3 67.1 + - - +
546D TRP 3.3 2.2 - - - -
547D LEU* 3.2 41.9 + - + +
548D VAL* 3.4 13.0 + - + +
564D LEU* 5.2 5.8 - - + -
567D VAL* 5.5 1.8 - - + -
568D LEU* 6.0 0.4 - - + -
574D VAL* 3.8 34.1 - - + +
577D ILE* 4.1 21.3 - - + -
578D ILE* 4.6 2.9 - - + -
582D HIS* 3.5 35.9 - - + +
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Residues in contact with ASP 545 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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543D ASN* 4.8 0.2 - - - +
544D LEU* 1.3 75.2 - - - +
546D TRP* 1.3 60.5 + - - +
548D VAL* 3.2 12.9 - - + +
549D SER* 2.9 29.4 + - - -
581D ASN* 5.5 5.2 - - - +
582D HIS* 4.6 8.4 - - + -
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Residues in contact with TRP 546 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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488D LEU* 5.1 7.4 - - + -
491D ILE* 3.5 40.6 - - + -
492D ASP* 4.7 20.2 - - + +
495D ASN* 5.8 5.4 + - + +
523D TYR* 5.9 4.7 - + - -
526D LEU* 5.4 2.0 - - + -
540D PHE* 3.9 28.0 - + - -
543D ASN* 5.3 15.2 - - + +
544D LEU* 3.3 1.6 - - - +
545D ASP* 1.3 78.1 - - - +
547D LEU* 1.3 75.3 + - + +
549D SER* 3.5 9.2 - - - -
550D LYS* 2.9 42.3 + - + +
560D ILE* 6.3 2.0 - - + -
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Residues in contact with LEU 547 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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540D PHE* 4.0 22.4 - - + -
543D ASN 5.2 0.2 - - - +
544D LEU* 3.2 32.5 + - + +
545D ASP 3.2 0.6 - - - -
546D TRP* 1.3 98.5 - - + +
548D VAL* 1.3 60.8 + - + +
550D LYS* 3.3 3.1 + - + +
551D LEU* 2.9 27.5 + - + +
560D ILE* 3.9 21.6 - - + +
563D VAL* 4.3 18.6 - - + -
564D LEU* 3.8 34.5 - - + -
567D VAL* 4.4 9.0 - - + -
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Residues in contact with VAL 548 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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544D LEU* 3.5 13.5 - - + +
545D ASP* 3.2 20.4 - - + +
547D LEU* 1.3 78.2 - - + +
549D SER* 1.3 59.2 + - - +
551D LEU* 3.4 17.7 - - + +
552D ASP* 2.9 28.4 + - - +
564D LEU* 5.0 11.7 - - + -
581D ASN* 5.7 2.0 - - - +
582D HIS* 4.1 33.7 - - + +
585D SER* 3.8 28.1 + - - +
586D ILE* 5.5 1.3 - - + -
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Residues in contact with SER 549 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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545D ASP 2.9 19.3 + - - -
546D TRP* 3.5 11.7 - - - -
547D LEU 3.2 0.2 - - - -
548D VAL* 1.3 78.0 - - - +
550D LYS* 1.3 61.3 + - - +
552D ASP* 3.3 18.6 + - - +
553D ARG* 3.8 4.5 + - - +
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Residues in contact with LYS 550 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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495D ASN* 4.7 21.2 + - - +
523D TYR* 5.0 4.6 + - + +
546D TRP* 2.9 38.2 + - + +
547D LEU* 3.9 4.3 - - + +
549D SER* 1.3 73.6 - - - +
551D LEU* 1.3 65.3 + - - +
553D ARG* 3.3 23.3 + - - +
555D GLU 5.2 1.6 - - - +
556D ALA 5.5 0.2 - - - +
557D SER* 6.1 0.2 - - - -
560D ILE* 4.3 21.8 - - + +
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Residues in contact with LEU 551 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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547D LEU* 2.9 18.3 + - + +
548D VAL* 3.4 11.9 - - + +
549D SER 3.2 0.2 - - - -
550D LYS* 1.3 77.4 - - - +
552D ASP* 1.3 62.4 + - - +
553D ARG 3.1 10.4 + - - +
557D SER* 4.3 12.2 - - - +
560D ILE* 3.6 28.2 - - + +
561D LEU* 4.4 7.9 - - + +
564D LEU* 4.1 15.5 - - + -
585D SER* 4.4 12.6 - - - +
586D ILE* 3.9 28.0 - - + -
589D LEU* 3.6 42.3 - - + +
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Residues in contact with ASP 552 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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548D VAL 2.9 12.9 + - - +
549D SER* 3.5 13.5 - - - +
550D LYS 3.3 0.6 - - - -
551D LEU* 1.3 77.1 - - - +
553D ARG* 1.3 62.2 + - - +
554D LEU* 3.6 1.4 + - - +
585D SER* 5.2 6.5 - - - +
588D SER* 6.2 0.2 - - - +
589D LEU* 5.4 3.6 - - - -
593D HIS* 4.5 9.2 - - - -
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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