Contacts of the strand formed by residues 614 - 618 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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611D LYS* 5.7 1.1 - - + -
612D LYS 3.2 14.2 + - - +
613D HIS* 1.3 71.3 - - - +
615D LEU* 1.3 67.8 + - - +
626D ILE* 3.7 16.6 - - + -
627D PHE 3.7 2.2 - - - +
628D ILE* 3.9 15.5 - - + -
638D ILE* 3.8 13.0 - - + -
639D SER* 4.2 17.0 - - - +
683D LYS* 2.7 42.2 + - + +
684D ILE* 3.5 37.0 - - + +
722D LEU* 3.4 31.6 - - + -
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Residues in contact with LEU 615 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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613D HIS 5.2 0.4 - - - -
614D LEU* 1.3 83.5 - - - +
616D LEU* 1.3 60.8 + - - +
626D ILE* 3.4 5.8 - - - +
627D PHE* 2.6 50.5 + - + +
628D ILE 4.9 0.4 - - - -
629D LYS* 3.7 36.8 - - + +
719D GLY* 5.9 0.9 - - - -
565F TYR* 3.7 44.9 - - + +
574F LEU* 5.3 2.7 - - + -
579F MET* 4.1 9.2 - - - -
581F VAL* 3.2 36.1 - - + -
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Residues in contact with LEU 616 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110D MET* 4.5 13.2 - - + -
614D LEU 4.4 0.6 + - - -
615D LEU* 1.3 72.2 - - - +
617D ALA* 1.3 62.9 + - - +
624D TRP* 3.4 39.0 - - + -
625D GLY 3.6 15.9 - - - +
626D ILE* 4.9 5.8 - - + -
683D LYS* 5.4 4.2 - - + +
686D PHE* 4.2 27.6 - - + -
565F TYR* 3.4 6.6 - - - +
566F PHE* 3.0 41.6 + - + +
567F HIS 3.4 25.6 - - - +
568F SER* 3.8 18.4 - - - +
571F CYS* 4.9 0.9 - - - -
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Residues in contact with ALA 617 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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616D LEU* 1.3 74.5 - - - +
618D PRO* 1.3 75.3 - - + +
624D TRP* 3.2 16.0 - - - -
625D GLY 2.9 29.0 + - - +
627D PHE* 3.3 21.6 - - + -
563F ARG* 4.0 11.0 - - + +
564F LEU 3.7 13.9 - - - +
565F TYR* 3.8 9.9 - - + -
566F PHE* 4.2 1.3 - - - -
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Residues in contact with PRO 618 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108D PRO* 4.1 24.0 - - + -
617D ALA* 1.3 91.5 - - + +
619D SER* 1.3 66.1 + - - +
620D ASP* 3.7 9.9 - - - +
623D GLY 3.4 11.9 - - - +
624D TRP* 4.1 6.3 - - + -
627D PHE* 3.8 7.4 - - - -
563F ARG* 4.9 2.0 + - + -
564F LEU 4.4 1.3 - - - +
566F PHE* 3.7 24.5 - - + -
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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
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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