Contacts of the helix formed by residues 643 - 651 (chain I) 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 TYR 643 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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616I LEU* 3.4 43.3 - - + -
619I LEU* 3.8 23.2 + - + +
620I HIS* 3.6 31.5 + + + -
623I LYS* 4.5 16.5 - - + +
639I PHE* 3.0 39.8 + + + +
642I ASN* 1.3 90.4 - - + +
644I GLY* 1.3 53.1 + - - +
645I GLN 3.2 0.2 - - - -
646I LYS* 2.7 50.6 + - - +
647I ILE* 3.1 9.4 + - + -
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Residues in contact with GLY 644 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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639I PHE 3.1 4.4 + - - -
640I VAL* 2.7 35.8 + - - -
643I TYR* 1.3 69.8 - - - +
645I GLN* 1.3 62.3 - - - +
647I ILE* 3.4 16.9 + - - +
648I ILE* 3.4 25.6 + - - +
681I LEU* 3.9 4.7 - - - +
684I MET* 4.1 9.6 - - - -
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Residues in contact with GLN 645 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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640I VAL 4.1 1.6 + - - -
642I ASN 4.0 8.3 + - - +
643I TYR 3.2 0.8 - - - +
644I GLY* 1.3 72.3 - - - +
646I LYS* 1.3 67.0 + - + +
648I ILE* 3.1 21.9 + - - +
649I LYS* 3.2 46.8 + - - +
684I MET* 4.1 26.7 + - - +
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Residues in contact with LYS 646 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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616I LEU* 4.5 17.9 - - + +
642I ASN 5.7 0.4 - - - +
643I TYR* 2.7 42.4 + - + +
645I GLN* 1.3 76.3 - - + +
647I ILE* 1.3 59.0 + - - -
649I LYS* 3.9 9.4 - - - +
650I LYS* 3.2 35.8 + - + +
652I LEU* 5.4 0.3 - - - +
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Residues in contact with ILE 647 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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613I VAL* 5.7 2.0 - - + -
616I LEU* 3.8 20.9 - - + -
639I PHE* 3.3 37.9 - - + -
640I VAL* 5.3 0.2 - - + -
643I TYR 3.1 3.9 + - - +
644I GLY* 3.6 25.1 - - - +
645I GLN 3.1 0.6 + - - -
646I LYS* 1.3 75.3 - - - +
648I ILE* 1.3 67.3 + - - +
650I LYS* 3.4 2.4 + - - +
651I ASN 3.1 17.5 + - - -
652I LEU* 3.2 47.3 + - + +
653I CYS* 4.1 4.7 - - - +
656I PHE* 4.4 16.6 - - + -
681I LEU* 4.3 15.0 - - + -
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Residues in contact with ILE 648 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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644I GLY 3.4 16.1 + - - +
645I GLN* 3.1 15.9 + - - +
647I ILE* 1.3 75.5 - - - +
649I LYS* 1.3 61.2 + - + +
651I ASN* 3.1 21.3 + - - +
653I CYS* 4.1 17.1 - - - -
681I LEU* 3.8 23.6 - - + +
684I MET* 3.6 20.4 - - + +
685I GLN* 3.5 44.9 - - + +
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Residues in contact with LYS 649 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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645I GLN* 3.2 51.6 + - - +
646I LYS* 3.9 10.5 - - - +
647I ILE 3.3 0.2 - - - -
648I ILE* 1.3 80.0 - - + +
650I LYS* 1.3 61.3 - - + +
651I ASN* 3.4 0.7 - - - +
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Residues in contact with LYS 650 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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612I GLU* 4.2 30.6 + - + -
616I LEU* 6.6 0.4 - - + -
646I LYS* 3.2 22.9 - - + +
647I ILE 3.4 2.6 + - - +
648I ILE 3.3 0.2 - - - -
649I LYS* 1.3 80.9 - - + +
651I ASN* 1.3 71.3 - - - +
652I LEU* 3.9 20.5 - - + +
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Residues in contact with ASN 651 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263G ASN* 5.0 0.3 + - - +
265G ASP* 3.1 55.9 + - - +
647I ILE 3.1 3.0 + - - -
648I ILE* 3.1 16.8 + - - +
649I LYS 3.4 1.3 - - - +
650I LYS* 1.3 83.0 - - - +
652I LEU* 1.3 63.0 + - - +
653I CYS* 3.8 8.9 - - - +
654I ARG* 4.9 6.4 + - - +
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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