Contacts of the helix formed by residues 550 - 562 (chain A) in PDB entry 6DEE
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 550 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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498A HIS* 6.5 1.1 - - + -
501A LEU* 5.3 8.1 - - + -
502A CYS* 4.1 19.1 - - - +
505A ALA* 5.8 0.9 - - - +
537A ILE* 4.1 12.8 - - + +
542A LEU* 5.1 14.4 - - + -
548A GLU* 3.4 1.0 - - - +
549A GLN* 1.3 81.3 - - + +
551A PRO* 1.3 59.4 - - - +
552A ASP 3.6 0.7 - - - -
553A LEU* 3.9 7.0 - - - +
554A CYS* 3.0 28.1 + - - +
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Residues in contact with PRO 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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537A ILE* 4.3 20.3 - - + +
538A VAL* 3.5 14.1 - - + +
541A GLY* 5.9 2.2 - - - -
548A GLU* 4.6 12.4 - - + +
549A GLN* 4.5 0.4 - - - -
550A LEU* 1.3 77.2 - - - +
552A ASP* 1.3 61.1 + - - +
554A CYS* 3.1 8.2 + - + +
555A VAL* 2.9 31.1 + - - +
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Residues in contact with ASP 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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548A GLU 5.1 5.0 + - - +
549A GLN* 4.9 2.0 - - - -
550A LEU 4.6 0.8 - - - +
551A PRO* 1.3 79.3 - - - +
553A LEU* 1.3 64.0 + - + +
555A VAL* 3.2 12.9 + - + +
556A ASN* 2.9 38.4 + - - +
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Residues in contact with LEU 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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502A CYS* 3.8 35.0 - - + +
505A ALA* 4.5 15.5 - - + +
506A LEU* 4.9 16.6 - - + +
509A ALA* 5.3 1.2 - - - +
549A GLN* 3.3 31.9 - - + +
550A LEU* 3.7 5.8 + - - +
551A PRO 3.2 0.4 - - - -
552A ASP* 1.3 82.4 - - + +
554A CYS* 1.3 60.1 + - - +
556A ASN* 3.5 15.5 + - - +
557A LEU* 2.9 27.4 + - - +
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Residues in contact with CYS 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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491A MET* 6.4 0.2 - - + -
505A ALA* 5.2 2.4 - - + +
534A LEU* 4.0 23.4 - - + +
537A ILE* 4.3 11.4 - - + -
538A VAL* 3.7 15.3 - - + -
550A LEU 3.0 20.1 + - - +
551A PRO 3.1 6.3 + - - +
553A LEU* 1.3 75.4 - - - +
555A VAL* 1.3 59.0 + - - +
557A LEU* 3.3 9.7 + - - +
558A LEU* 2.9 31.7 + - - +
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Residues in contact with VAL 555 (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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538A VAL* 3.6 28.0 - - + -
551A PRO 2.9 19.9 + - - +
552A ASP* 3.2 14.6 + - - +
554A CYS* 1.3 76.6 - - - +
556A ASN* 1.3 64.6 + - - +
558A LEU* 3.0 10.6 + - - +
559A LEU* 2.9 39.6 + - + +
586A PHE* 4.2 16.8 - - + -
589A LYS* 4.5 19.1 - - + +
590A LEU* 4.7 10.3 - - + -
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Residues in contact with ASN 556 (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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509A ALA* 4.5 10.1 - - + +
552A ASP* 2.9 27.7 + - - +
553A LEU* 3.8 16.3 - - + +
554A CYS 3.4 0.2 - - - -
555A VAL* 1.3 79.7 - - - +
557A LEU* 1.3 56.4 + - - +
559A LEU* 3.3 15.7 + - - +
560A ALA* 2.9 27.9 + - - +
600A PRO* 3.3 39.0 + - + +
601A VAL* 5.0 3.8 - - - +
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Residues in contact with LEU 557 (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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491A MET* 4.3 2.0 - - - -
505A ALA* 4.0 26.2 - - + +
508A LEU* 3.5 41.1 - - + +
509A ALA* 3.8 14.8 - - - +
530A PHE* 4.3 2.9 - - + -
534A LEU* 3.7 35.4 - - + -
553A LEU 2.9 18.7 + - - +
554A CYS* 3.4 6.7 - - - +
555A VAL 3.1 0.2 - - - -
556A ASN* 1.3 74.9 - - - +
558A LEU* 1.3 59.0 + - - +
560A ALA* 3.2 3.4 + - + -
561A LEU* 2.9 48.3 + - + +
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Residues in contact with LEU 558 (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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531A ALA* 4.1 15.5 - - + +
534A LEU* 3.7 28.0 - - + -
535A LEU* 4.2 22.4 - - + +
538A VAL* 4.3 6.5 - - + -
554A CYS 2.9 18.3 + - - +
555A VAL* 3.3 7.2 - - - +
557A LEU* 1.3 76.0 - - - +
559A LEU* 1.3 58.2 + - + +
561A LEU* 4.5 1.6 - - + -
562A ASN* 3.1 31.7 + - - +
573A ILE* 3.5 27.2 - - + +
586A PHE* 3.6 31.4 - - + -
617A PHE* 3.8 13.4 - - + -
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Residues in contact with LEU 559 (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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555A VAL* 2.9 22.6 + - + +
556A ASN* 3.4 29.6 - - - +
558A LEU* 1.3 77.6 - - + +
560A ALA* 1.3 61.0 + - - +
562A ASN* 3.5 2.3 + - - +
563A LEU* 3.2 21.5 + - - +
586A PHE* 5.8 0.9 - - + -
590A LEU* 4.2 18.2 - - + -
593A LEU* 5.7 3.6 - - + -
600A PRO* 4.5 8.5 - - + -
601A VAL* 4.8 2.7 - - + +
613A SER* 3.9 37.4 - - - +
614A VAL* 4.3 15.9 - - + -
617A PHE* 3.9 35.2 - - + -
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Residues in contact with ALA 560 (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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508A LEU 4.6 0.2 - - - +
509A ALA* 3.7 33.9 - - + +
512A PHE* 2.9 35.2 - - + +
513A SER* 5.0 0.4 - - - +
556A ASN 2.9 16.7 + - - +
557A LEU* 3.2 6.0 + - + +
559A LEU* 1.3 76.5 - - - +
561A LEU* 1.3 62.4 + - - +
563A LEU* 3.3 12.9 - - - +
564A HIS* 4.0 2.3 + - - -
601A VAL* 4.8 11.4 - - + +
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Residues in contact with LEU 561 (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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508A LEU* 6.4 0.4 - - + -
512A PHE* 3.5 44.0 - - + -
526A LEU* 5.6 7.2 - - + -
530A PHE* 3.8 33.7 - - + -
531A ALA* 5.9 1.6 - - + -
534A LEU* 3.9 13.2 - - + -
557A LEU* 2.9 26.1 + - + +
558A LEU* 4.8 0.7 - - + -
560A ALA* 1.3 75.0 - - - +
562A ASN* 1.3 56.9 + - - +
563A LEU 3.1 8.7 + - - -
564A HIS* 3.8 14.7 + - + -
565A LEU* 3.2 22.3 - - + +
573A ILE* 3.9 19.3 - - + -
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Residues in contact with ASN 562 (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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558A LEU 3.1 19.1 + - - +
559A LEU 3.8 2.5 - - - +
561A LEU* 1.3 72.9 - - - +
563A LEU* 1.3 54.2 + - - +
564A HIS 3.3 1.6 - - - -
565A LEU* 3.8 6.4 - - - +
571A ASN* 2.8 28.9 + - - +
573A ILE* 3.7 16.5 - - + +
574A MET* 3.3 23.8 - - - +
616A LYS* 2.4 38.1 + - - +
617A PHE* 3.2 33.6 - - + -
620A ASP* 3.1 10.9 - - - +
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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