Contacts of the helix formed by residues 683 - 687 (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 LYS 683 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113G TRP* 4.7 6.6 - - + -
611G LYS* 5.9 7.4 - - - -
613G HIS* 5.6 4.6 + - - -
614G LEU* 2.9 44.0 + - + +
615G LEU* 4.1 0.6 - - - +
616G LEU* 4.0 16.9 - - + +
626G ILE* 2.9 25.7 - - + +
682G ASN* 1.3 77.0 - - - +
684G ILE* 1.3 62.2 + - - +
685G ARG 3.1 1.0 + - - -
686G PHE* 3.4 18.2 + - + -
566I PHE 5.3 1.2 + - - -
568I SER* 3.2 38.0 + - - +
586I GLU* 5.3 15.0 - - - +
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Residues in contact with ILE 684 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
614G LEU* 3.7 26.7 - - + +
626G ILE* 4.1 10.1 - - + -
638G ILE* 4.8 5.2 - - + -
639G SER* 4.1 7.2 - - - +
640G GLU 3.6 10.3 - - - +
641G TYR* 3.8 21.7 - - + +
682G ASN* 3.1 27.3 + - - +
683G LYS* 1.3 78.0 - - - +
685G ARG* 1.3 54.2 + - - +
686G PHE 2.8 1.0 + - - -
687G ALA* 2.7 47.6 + - + +
695G CYS* 6.2 0.7 - - - -
710G ILE* 4.1 27.6 - - + -
722G LEU* 4.3 14.6 - - + -
724G PHE* 5.1 0.4 - - + -
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Residues in contact with ARG 685 (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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110G MET* 4.8 1.8 - - - +
111G TYR 4.3 5.1 + - - -
113G TRP* 2.9 62.4 - - - +
641G TYR* 3.7 25.7 + - + +
665G PHE* 4.5 1.9 - - - -
677G ALA* 2.5 54.3 + - + -
678G THR 3.6 12.5 + - - -
681G GLY* 4.2 1.6 - - - -
682G ASN* 2.9 29.2 + - - +
684G ILE* 1.3 78.1 - - - +
686G PHE* 1.4 76.4 + - + +
687G ALA 3.3 5.6 + - - +
726G TYR* 4.2 3.8 + - - -
809G 74D 3.2 51.9 + - - +
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Residues in contact with PHE 686 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110G MET* 3.6 34.5 - - + -
113G TRP* 3.6 26.0 - + - -
616G LEU* 4.0 16.6 - - + -
624G TRP* 3.7 17.7 - - + -
625G GLY* 3.3 30.6 - - - +
626G ILE* 4.0 7.6 - - + -
683G LYS* 3.5 20.6 - - - +
684G ILE 2.8 1.0 + - - -
685G ARG* 1.4 99.9 - - + +
687G ALA* 1.3 62.3 + - - -
688G ASN 3.1 3.8 + - - -
809G 74D 3.2 49.1 - + - +
568I SER* 5.3 2.0 - - - -
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Residues in contact with ALA 687 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
626G ILE* 3.9 6.7 - - + +
684G ILE* 2.7 35.3 + - + +
685G ARG 3.3 1.4 - - - +
686G PHE* 1.3 69.2 - - - +
688G ASN* 1.3 63.4 + - - +
722G LEU* 3.5 22.7 - - + +
723G PHE 4.8 0.2 - - - -
724G PHE* 3.8 25.3 - - + -
726G TYR* 2.7 24.4 + - - -
809G 74D 4.0 0.7 - - - +
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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