Contacts of the helix formed by residues 571 - 576 (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 571 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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560G CYS* 3.7 4.0 - - - -
562G CYS* 3.5 8.8 - - - -
566G CYS* 3.4 19.7 - - + -
568G THR* 3.3 11.8 + - - +
569G LYS 3.2 13.3 - - - +
570G GLN* 1.3 76.8 - - - +
572G PRO* 1.4 66.3 - - - +
573G CYS* 3.1 32.5 + - - -
574G TYR* 3.4 8.3 - - + +
575G LEU* 3.5 12.0 + - - +
580G CYS* 4.7 0.4 - - - -
603G ASN* 4.7 0.4 - - - -
807G ZN 3.8 0.2 - - - -
808G ZN 2.7 33.2 - - - -
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Residues in contact with PRO 572 (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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557G PHE* 3.5 16.6 - - + -
558G PRO* 6.3 2.5 - - + -
559G GLY 4.4 13.5 - - - +
560G CYS* 3.7 19.7 - - + -
561G ARG 5.2 1.1 - - - +
562G CYS* 4.4 3.1 - - - -
569G LYS 5.2 0.4 - - - +
570G GLN 3.5 5.8 - - - +
571G CYS* 1.4 83.1 - - - +
573G CYS* 1.3 57.2 + - - +
575G LEU* 3.9 7.1 - - + +
576G ALA* 3.1 28.4 + - - +
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Residues in contact with CYS 573 (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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557G PHE* 3.5 28.9 - - - -
559G GLY 4.4 0.7 - - - -
560G CYS* 3.9 7.6 - - - -
571G CYS* 3.1 5.8 - - - -
572G PRO* 1.3 72.3 - - - +
574G TYR* 1.3 67.2 + - - +
575G LEU 3.1 0.9 - - - -
576G ALA 2.8 13.0 + - - -
578G ARG* 3.1 32.5 + - + +
579G GLU 4.1 7.0 - - - +
580G CYS* 4.4 3.1 - - - -
581G ASP* 5.2 0.4 - - - -
585G CYS* 3.5 11.4 - - - -
603G ASN* 3.9 4.5 - - - +
807G ZN 2.6 35.4 - - - -
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Residues in contact with TYR 574 (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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566G CYS 3.7 16.8 - - - +
567G ASN* 3.5 34.1 + - + -
568G THR* 3.3 35.9 - - - +
569G LYS* 4.0 6.5 - - + -
571G CYS* 3.4 6.7 - - + -
573G CYS* 1.3 78.1 - - - +
575G LEU* 1.3 57.9 + - - +
577G VAL* 3.2 21.5 + - - +
578G ARG 3.7 7.6 + - - -
602G LYS 5.7 0.9 - - - -
603G ASN* 3.7 14.7 - - + +
635G ASN* 5.6 6.8 - - - +
696G TYR* 5.7 0.7 + - - -
698G LYS* 3.4 28.9 + - - -
700G MET* 5.0 2.9 - - + +
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Residues in contact with LEU 575 (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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569G LYS* 3.6 52.3 - - + +
571G CYS 3.5 15.4 + - - +
572G PRO* 4.1 6.5 - - + +
573G CYS 3.1 0.8 - - - -
574G TYR* 1.3 76.4 - - - +
576G ALA* 1.3 56.3 + - - +
577G VAL* 3.2 13.2 + - - +
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Residues in contact with ALA 576 (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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542G PHE* 4.7 8.1 - - + -
557G PHE* 3.9 10.8 - - + -
572G PRO 3.1 17.2 + - - +
573G CYS 2.8 3.5 + - - +
575G LEU* 1.3 74.1 - - - +
577G VAL* 1.3 70.0 + - - +
578G ARG* 3.1 31.6 + - - +
701G MET* 5.5 0.2 - - - +
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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