Contacts of the strand formed by residues 823 - 827 (chain B) in PDB entry 1LV5
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 HIS 823 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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491B ALA* 4.5 17.6 - - + +
643B SER* 4.9 2.7 - - - -
644B GLU* 6.1 0.4 - - - -
647B TRP* 4.3 11.2 - + - -
815B LEU* 4.9 2.7 - - - -
821B GLN 3.9 7.6 + - - +
822B ALA* 1.3 77.4 - - - +
824B LEU* 1.3 73.4 + - - +
825B LEU* 3.8 6.7 - - + +
834B LEU* 3.2 19.2 - - - +
835B GLU* 2.7 51.7 + - + +
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Residues in contact with LEU 824 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484B ILE* 4.1 14.6 - - + -
488B MET* 3.6 31.4 - - + +
491B ALA* 4.6 2.8 - - - +
808B MET* 4.1 42.0 - - + +
811B LEU* 4.6 10.8 - - + -
812B ASN* 5.1 9.0 - - + +
815B LEU* 5.0 8.6 - - + +
823B HIS* 1.3 79.8 - - - +
825B LEU* 1.3 65.0 + - - +
826B LEU 5.1 1.1 - - - +
832B LEU* 4.4 18.4 - - + -
833B ILE 3.9 6.7 - - - +
834B LEU* 4.0 31.1 - - + +
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Residues in contact with LEU 825 (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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488B MET* 3.3 28.3 - - - +
491B ALA* 4.4 6.3 - - + -
492B GLY 2.9 29.1 - - - +
493B VAL* 4.0 24.0 - - + +
606B PHE* 4.3 3.5 - - - -
641B VAL 6.2 0.2 - - - +
649B ILE* 4.4 10.5 - - + -
823B HIS* 3.8 26.9 - - - +
824B LEU* 1.3 77.4 - - - +
826B LEU* 1.3 75.2 + - + +
833B ILE* 3.0 17.1 + - + +
834B LEU* 4.2 4.0 - - - -
835B GLU* 3.7 37.0 - - + +
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Residues in contact with LEU 826 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488B MET* 3.5 8.9 - - - +
493B VAL* 3.7 24.7 - - + -
604B THR* 4.3 3.6 - - + -
606B PHE* 3.9 17.0 - - + -
623B LEU* 3.6 44.4 - - + +
640B PHE* 6.0 0.4 - - + -
824B LEU* 5.1 0.3 - - - +
825B LEU* 1.3 91.2 - - + +
827B GLN* 1.3 61.0 + - - +
828B VAL* 4.9 2.5 - - + -
832B LEU* 3.8 3.1 - - - +
833B ILE* 2.8 53.2 + - + +
872B TRP* 4.4 25.4 - - + -
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Residues in contact with GLN 827 (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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485B LEU* 6.0 0.4 - - + -
488B MET* 3.9 7.0 - - + +
606B PHE* 3.5 15.5 - - + -
616B LEU* 4.0 28.3 - - + +
624B GLN* 3.0 28.1 + - - +
804B ILE* 3.7 29.1 - - + +
805B LYS* 5.4 3.0 - - - +
808B MET* 3.8 18.5 - - + -
826B LEU* 1.3 74.4 - - - +
828B VAL* 1.3 65.3 + - - +
829B HIS* 2.7 34.2 + - - +
831B GLU 3.4 14.6 - - - +
832B LEU* 3.8 18.2 - - + -
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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