Contacts of the helix formed by residues 534 - 540 (chain G) in PDB entry 5LS6
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 534 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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523G CYS* 3.5 7.0 - - - -
525G HIS* 3.5 10.5 - - - +
529G PRO 4.7 0.4 + - - +
530G CYS* 3.6 20.0 - - - -
531G ASP* 2.6 23.4 + - - +
533G SER* 1.3 69.6 - - - +
535G PRO* 1.4 70.7 - - - +
536G CYS* 2.9 24.3 + - - -
537G VAL* 3.1 6.4 + - + +
538G ILE* 3.0 20.4 + - - +
804G ZN 2.3 37.0 - - - -
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Residues in contact with PRO 535 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521G GLN 5.6 3.8 - - - +
522G PRO 6.0 0.4 - - - +
523G CYS* 4.6 12.1 - - + -
525G HIS* 4.5 12.1 - - + -
533G SER 3.3 9.4 - - - +
534G CYS* 1.4 84.9 - - + +
536G CYS* 1.3 57.0 + - - +
538G ILE* 3.6 10.4 - - + +
539G ALA* 3.0 30.5 + - - +
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Residues in contact with CYS 536 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520G TYR* 4.0 10.3 - - - -
521G GLN 3.9 18.2 - - - -
523G CYS* 3.6 3.8 - - - -
534G CYS* 2.9 12.4 + - - -
535G PRO* 1.3 75.6 - - - +
537G VAL* 1.3 63.7 + - - +
539G ALA* 3.3 4.9 + - - +
540G GLN 3.1 3.8 + - - -
541G ASN* 2.9 40.7 + - - +
542G PHE 4.1 4.0 - - - -
543G CYS* 3.9 0.9 - - - -
547G CYS* 3.8 6.5 - - - -
555G ASN* 3.7 7.9 - - - +
805G ZN 2.2 37.7 - - - -
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Residues in contact with VAL 537 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530G CYS 4.0 19.1 - - - +
531G ASP 3.0 32.8 - - - +
532G SER* 3.8 10.3 - - - +
534G CYS* 3.1 11.6 + - + +
536G CYS* 1.3 72.3 - - - +
538G ILE* 1.3 70.9 + - - +
540G GLN* 3.0 18.8 + - - +
541G ASN 4.4 1.8 - - - -
555G ASN* 3.3 31.9 - - + +
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Residues in contact with ILE 538 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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518G TYR* 6.1 0.2 - - - -
532G SER 3.1 24.9 - - - +
533G SER* 4.1 8.1 - - - +
534G CYS 3.0 24.7 + - - +
535G PRO* 3.6 10.1 - - + +
537G VAL* 1.3 78.7 - - - +
539G ALA* 1.3 62.2 + - + +
540G GLN* 3.2 7.8 + - - +
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Residues in contact with ALA 539 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516G HIS 5.0 1.4 - - - +
517G VAL* 5.6 0.3 - - - -
518G TYR* 3.9 45.6 + - + +
519G ASN 5.5 2.5 - - - +
535G PRO 3.0 20.1 + - - +
536G CYS* 3.6 5.8 - - - +
538G ILE* 1.3 76.8 - - + +
540G GLN* 1.3 68.6 + - - +
541G ASN* 3.6 15.0 + - + +
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Residues in contact with GLN 540 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516G HIS 5.0 8.9 - - - +
518G TYR* 6.2 1.1 - - + -
536G CYS 3.1 0.8 + - - -
537G VAL* 3.0 16.4 + - - +
538G ILE 3.9 9.0 - - - +
539G ALA* 1.3 81.6 - - - +
541G ASN* 1.3 62.8 + - - +
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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