Contacts of the strand formed by residues 720 - 724 (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 GLU 720 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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627D PHE* 4.1 1.3 - - - -
628D ILE* 3.1 26.8 + - - +
694D ASN* 4.1 3.1 + - - -
714D ARG* 3.0 43.0 + - - -
715D ALA 4.2 0.5 - - - +
716D ILE* 3.4 15.3 - - + -
717D GLN* 3.0 53.9 + - + +
718D THR 3.2 3.2 + - - +
719D GLY* 1.3 77.0 - - - +
721D GLU* 1.3 65.8 + - - +
722D LEU* 3.7 1.6 + - - +
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Residues in contact with GLU 721 (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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619D SER* 2.7 27.0 + - - -
620D ASP* 3.4 24.5 + - - +
625D GLY* 3.8 2.4 - - - -
626D ILE 3.6 10.8 - - - +
627D PHE* 3.3 37.2 - - + -
688D ASN* 3.7 7.8 + - - -
694D ASN* 2.5 30.6 + - - +
719D GLY 3.9 0.2 + - - -
720D GLU* 1.3 73.7 + - - +
722D LEU* 1.3 60.1 + - - +
723D PHE* 3.0 37.6 - - + -
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Residues in contact with LEU 722 (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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614D LEU* 3.4 32.8 - - + -
626D ILE* 2.9 29.2 + - + +
628D ILE* 4.1 20.0 - - + +
638D ILE* 4.0 17.9 - - + -
684D ILE* 4.1 10.8 - - + -
686D PHE 4.7 0.5 - - - +
687D ALA* 3.5 24.2 - - + -
688D ASN 3.6 3.8 + - - -
694D ASN* 3.7 4.9 - - - +
695D CYS* 3.5 25.1 - - - -
710D ILE* 6.4 0.4 - - + -
716D ILE* 3.9 19.7 - - + -
720D GLU 4.3 4.5 - - - +
721D GLU* 1.3 77.5 - - - +
723D PHE* 1.3 64.4 + - - +
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Residues in contact with PHE 723 (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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620D ASP* 6.3 0.7 - - + -
621D VAL* 3.7 29.4 - - + -
687D ALA* 4.5 1.1 - - - -
688D ASN* 3.3 41.5 - - + +
689D HIS 3.5 13.9 - - - -
690D SER* 3.6 22.4 - - - -
692D ASN 5.8 0.9 - - - -
693D PRO* 3.4 6.4 - - + +
694D ASN* 3.4 17.0 + - - +
695D CYS* 3.3 26.0 + - - +
721D GLU* 3.0 44.2 - - + -
722D LEU* 1.3 74.6 - - - +
724D PHE* 1.3 69.3 + - - +
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Residues in contact with PHE 724 (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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641D TYR* 3.7 34.5 - + - -
667D PHE* 3.5 34.1 - + - -
687D ALA* 3.6 35.4 - - + -
688D ASN 3.2 4.4 + - - +
689D HIS* 3.6 5.4 - - - -
690D SER 3.5 4.9 - - - -
693D PRO* 3.4 8.3 - - - -
695D CYS* 3.4 19.1 - - + +
696D TYR* 4.6 5.4 - - - -
697D ALA* 4.5 18.2 - - + +
710D ILE* 4.5 17.9 - - + -
723D PHE* 1.3 77.2 - - - +
725D ASP* 1.3 83.2 + - - +
726D TYR* 3.1 29.9 - + - -
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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