Contacts of the strand formed by residues 614 - 618 (chain B) in PDB entry 5IJ7
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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612B LYS 3.5 12.2 + - - +
613B HIS* 1.3 87.9 + - - +
615B LEU* 1.3 61.4 + - - +
626B ILE* 3.7 17.0 - - + -
627B PHE 3.5 3.8 - - - +
628B ILE* 3.9 13.5 - - + -
638B ILE* 3.7 12.3 - - + -
639B SER* 4.5 11.0 - - - +
683B LYS* 2.8 40.9 + - + +
684B ILE* 3.8 41.7 - - + +
722B LEU* 3.6 26.2 - - + -
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Residues in contact with LEU 615 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613B HIS* 4.3 5.8 - - - +
614B LEU* 1.3 80.7 - - - +
616B LEU* 1.3 61.1 + - - +
626B ILE* 3.4 9.0 - - - +
627B PHE* 2.8 42.7 + - - +
628B ILE 4.9 1.1 - - - +
629B LYS* 3.7 37.2 - - + -
683B LYS* 4.7 1.8 - - - +
719B GLY* 6.3 0.2 - - - -
561T HIS 5.7 0.2 - - - +
565T TYR* 3.6 35.9 - - + +
566T PHE 5.8 0.4 - - - +
574T LEU* 4.4 13.7 - - + -
580T GLU* 3.4 37.2 - - + +
582T ASP* 4.4 12.6 - - + -
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Residues in contact with LEU 616 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B MET* 4.0 21.3 - - + -
615B LEU* 1.3 72.5 - - - +
617B ALA* 1.3 60.5 + - - +
624B TRP* 3.6 27.8 - - + -
625B GLY 3.5 16.2 - - - +
626B ILE* 4.1 4.9 - - + +
683B LYS* 5.2 0.8 - - + +
686B PHE* 3.8 34.8 - - + -
565T TYR* 3.4 3.0 - - - -
566T PHE* 2.7 47.9 + - + +
567T HIS 4.1 5.4 - - - +
568T SER* 3.6 36.3 - - - +
571T CYS* 4.6 0.7 - - - -
582T ASP* 4.6 2.9 + - - +
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Residues in contact with ALA 617 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
615B LEU 4.0 0.6 + - - -
616B LEU* 1.3 77.0 - - - +
618B PRO* 1.4 73.3 - - + +
624B TRP* 3.6 9.9 - - - -
625B GLY 2.9 25.8 + - - +
627B PHE* 3.4 18.3 - - + -
563T ARG* 4.0 8.7 - - - -
564T LEU 3.3 23.6 - - - +
565T TYR* 3.8 10.3 - - + -
566T PHE* 4.1 1.6 - - - -
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Residues in contact with PRO 618 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B VAL* 5.6 1.6 - - + -
108B PRO* 3.8 29.6 - - + -
617B ALA* 1.4 86.9 - - + +
619B SER* 1.3 66.9 + - - +
620B ASP* 4.6 0.2 - - - +
623B GLY 3.5 8.7 - - - +
624B TRP* 3.7 8.7 - - + -
627B PHE* 3.7 10.4 - - - -
563T ARG* 4.0 8.7 + - - -
564T LEU 4.5 1.8 - - - +
566T PHE* 3.6 26.5 - - + -
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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