Contacts of the strand formed by residues 614 - 618 (chain J) 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 LEU 614 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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611J LYS* 6.5 0.2 - - + -
612J LYS 3.7 10.5 + - - +
613J HIS* 1.3 84.2 + - - +
615J LEU* 1.3 65.3 + - - +
626J ILE* 4.0 12.1 - - + -
627J PHE 3.6 3.4 - - - +
628J ILE* 4.2 11.7 - - + -
638J ILE* 4.0 11.7 - - + -
639J SER* 4.4 13.5 - - - -
683J LYS* 3.4 38.9 + - + +
684J ILE* 3.8 44.9 - - + +
722J LEU* 3.4 31.2 - - + -
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Residues in contact with LEU 615 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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613J HIS* 4.1 13.0 - - + +
614J LEU* 1.3 73.4 - - - +
616J LEU* 1.3 60.1 + - - +
626J ILE* 2.9 7.7 - - - +
627J PHE* 2.6 47.7 + - - +
628J ILE 5.2 0.7 - - - -
629J LYS* 4.4 26.2 - - + -
719J GLY* 5.7 1.3 - - - -
565L TYR* 3.4 50.9 - - + +
574L LEU* 4.9 6.1 - - + -
579L MET* 4.4 11.2 - - - -
581L VAL* 3.7 29.4 - - + -
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Residues in contact with LEU 616 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110J MET* 4.4 8.3 - - + -
614J LEU 4.1 1.2 + - - +
615J LEU* 1.3 73.6 - - - +
617J ALA* 1.3 60.1 + - - +
624J TRP* 3.4 37.2 - - + -
625J GLY 3.0 26.9 - - - +
626J ILE* 4.1 6.3 - - + -
683J LYS* 5.5 4.0 - - + -
686J PHE* 4.0 34.8 - - + -
565L TYR* 3.2 4.6 - - - +
566L PHE 2.8 43.5 + - - +
567L HIS 3.9 21.8 - - - +
568L SER* 4.0 15.3 - - - +
571L CYS* 5.1 1.3 - - - -
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Residues in contact with ALA 617 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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616J LEU* 1.3 77.2 - - - +
618J PRO* 1.3 74.4 - - + +
624J TRP* 3.7 7.8 - - - -
625J GLY 2.9 25.9 + - - +
627J PHE* 3.5 17.1 - - + -
563L ARG* 3.9 8.3 - - + -
564L LEU 3.2 26.7 - - - +
565L TYR* 3.8 9.4 - - + -
566L PHE* 3.8 4.7 - - - -
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Residues in contact with PRO 618 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107J VAL* 5.0 0.9 - - + -
108J PRO* 3.8 32.8 - - + -
617J ALA* 1.3 89.5 - - + +
619J SER* 1.3 68.2 + - - +
620J ASP* 3.6 1.9 + - - +
623J GLY 3.6 6.3 - - - +
624J TRP* 4.2 7.4 - - + -
627J PHE* 3.6 11.1 - - - -
563L ARG* 4.6 3.6 + - - -
564L LEU 4.4 1.1 - - - +
566L PHE* 3.2 29.2 - - + -
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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