Contacts of the helix formed by residues 680 - 691 (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 ASP 680 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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655B SER* 5.4 0.3 + - - -
656B GLN* 3.3 14.5 + - - +
678B ASP 3.9 1.3 + - - +
679B LEU* 1.3 73.0 - - - +
681B ILE* 1.3 59.6 + - - +
682B HIS* 2.9 11.6 + - - +
683B THR* 2.8 64.8 + - + +
684B LYS* 3.1 14.4 + - - +
702B ARG* 3.0 25.8 + - - -
863B LYS* 5.3 6.7 + - - +
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Residues in contact with ILE 681 (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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656B GLN* 2.7 19.6 + - - +
659B LEU* 3.4 22.7 - - + -
671B LEU* 3.9 14.6 - - + -
674B ALA* 3.2 35.4 - - + -
675B PHE* 4.0 6.5 - - + -
679B LEU* 5.1 4.7 - - + +
680B ASP* 1.3 71.8 - - - +
682B HIS* 1.3 62.9 + - - +
684B LYS* 3.6 25.1 + - + +
685B THR* 3.2 22.5 + - - +
709B ASN* 4.2 9.4 - - - +
739B TYR* 4.6 6.1 - - - +
743B PHE* 4.3 21.1 - - + -
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Residues in contact with HIS 682 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B DCP 3.1 38.6 + - - -
656B GLN* 4.0 12.2 + - + -
659B LEU* 3.2 28.0 - - + +
680B ASP* 2.9 7.1 + - - +
681B ILE* 1.3 74.1 - - - +
683B THR* 1.3 61.0 + - - +
685B THR* 3.0 1.9 + - - -
686B ALA 2.9 23.6 + - - -
702B ARG* 4.2 26.9 - - + +
705B ALA* 3.2 11.5 - - - +
706B LYS* 3.9 17.4 - - + +
709B ASN* 2.5 34.0 + - + +
710B PHE* 3.5 21.5 - + - -
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Residues in contact with THR 683 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
680B ASP* 2.8 54.7 + - + +
682B HIS* 1.3 72.1 - - - +
684B LYS* 1.3 62.6 + - - +
686B ALA* 3.1 8.7 + - - +
687B MET* 2.9 31.5 + - - +
694B GLU* 5.2 17.9 + - + +
697B VAL* 5.0 8.9 - - + +
702B ARG* 3.4 27.1 - - + +
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Residues in contact with LYS 684 (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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670B ASN* 5.7 2.2 + - - -
674B ALA* 5.8 1.0 - - - +
679B LEU* 5.3 14.1 - - + +
680B ASP 3.1 14.0 + - - +
681B ILE* 3.7 26.0 - - + +
683B THR* 1.3 82.4 + - - +
685B THR* 1.3 60.8 + - - +
687B MET* 3.6 20.9 + - + +
688B ASP* 3.3 21.1 + - - +
743B PHE* 5.4 7.4 - - + -
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Residues in contact with THR 685 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
681B ILE* 3.2 12.1 + - - +
682B HIS 3.0 9.0 + - - -
684B LYS* 1.3 74.5 - - - +
686B ALA* 1.3 66.2 + - - +
687B MET 3.1 0.2 - - - -
688B ASP* 3.2 5.8 + - - +
689B ILE* 2.9 44.1 + - + +
705B ALA* 3.8 17.9 - - + +
708B VAL* 4.2 10.5 - - + -
709B ASN* 2.5 31.2 + - - +
735B PHE* 4.4 8.3 - - + -
739B TYR* 3.8 9.7 + - - -
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Residues in contact with ALA 686 (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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682B HIS 2.9 8.6 + - - +
683B THR* 3.1 8.7 + - - +
685B THR* 1.3 75.5 - - - +
687B MET* 1.3 62.9 + - - +
689B ILE* 4.5 0.2 - - - -
690B PHE* 2.8 37.7 + - - +
692B VAL* 4.1 2.1 - - - +
697B VAL* 4.1 13.9 - - + -
701B MET* 3.4 32.8 - - + +
702B ARG* 4.0 5.4 - - - +
705B ALA* 3.4 12.0 - - + +
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Residues in contact with MET 687 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
683B THR* 2.9 19.5 + - - +
684B LYS* 3.7 20.4 - - + +
685B THR 3.1 0.2 - - - -
686B ALA* 1.3 77.6 - - - +
688B ASP* 1.3 57.6 + - - +
691B GLN* 2.9 28.4 + - - -
692B VAL* 3.4 31.8 + - - +
693B SER 4.6 0.2 - - - -
694B GLU* 3.8 35.7 - - - +
697B VAL* 4.0 15.5 - - + -
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Residues in contact with ASP 688 (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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684B LYS 3.3 11.0 + - - +
685B THR* 3.2 9.2 + - - +
687B MET* 1.3 79.0 - - - +
689B ILE* 1.3 57.1 + - - +
691B GLN* 2.3 27.3 + - - +
735B PHE* 3.0 37.1 - - + -
738B ARG* 4.3 18.3 + - - -
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Residues in contact with ILE 689 (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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685B THR* 2.9 34.0 + - + +
686B ALA* 3.9 2.7 - - - +
688B ASP* 1.3 79.4 - - - +
690B PHE* 1.3 85.7 + - + +
691B GLN* 3.5 8.9 + - - -
705B ALA* 5.8 0.7 - - + -
708B VAL* 4.8 8.3 - - + -
725B LEU* 4.1 29.6 - - + -
727B ILE* 6.1 1.6 - - + -
735B PHE* 3.3 45.8 - - + -
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Residues in contact with PHE 690 (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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686B ALA* 2.8 33.4 + - - +
689B ILE* 1.3 93.3 - - + +
691B GLN* 1.3 76.3 + - - +
692B VAL* 3.3 12.4 - - + +
701B MET* 3.3 51.8 - - + -
704B GLN* 3.7 45.8 - - + -
705B ALA* 5.1 2.0 - - + -
725B LEU* 5.7 0.2 - - + -
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Residues in contact with GLN 691 (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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687B MET 2.9 7.7 + - - +
688B ASP* 2.3 31.6 + - - +
689B ILE 3.9 9.1 + - - -
690B PHE* 1.3 82.3 - - - +
692B VAL* 1.3 56.4 + - - +
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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