Contacts of the helix formed by residues 533 - 539 (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 GLN 533 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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526B PHE* 4.0 11.6 - - + +
527B ASN* 3.1 43.9 + - - +
530B SER* 2.9 21.5 + - - +
532B LYS* 1.3 91.5 - - - +
534B LEU* 1.3 58.8 + - - +
535B GLY 2.8 4.7 - - - -
536B VAL* 2.8 24.3 + - - +
537B ILE* 2.9 17.4 - - + +
12F C 2.7 28.5 + - - +
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Residues in contact with LEU 534 (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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526B PHE* 3.3 31.5 - - + -
527B ASN 4.3 0.2 + - - -
528B ILE* 3.8 29.8 - - + +
530B SER 3.9 10.8 + - - +
531B PRO* 5.3 0.4 - - + -
533B GLN* 1.3 77.7 - - - +
535B GLY* 1.3 56.0 + - - +
536B VAL 3.2 0.2 - - - -
537B ILE* 3.5 4.0 - - - +
538B LEU* 2.7 49.4 + - + +
556B THR* 3.0 31.4 - - + +
561B LEU* 5.5 0.2 - - + -
574B ILE* 3.9 30.7 - - + -
578B ARG* 4.0 11.7 - - - +
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Residues in contact with GLY 535 (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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531B PRO 6.0 0.2 - - - -
532B LYS* 3.3 11.9 + - - -
533B GLN 2.8 2.8 + - - -
534B LEU* 1.3 87.8 - - - +
536B VAL* 1.3 57.4 + - - +
539B PHE* 2.7 53.6 + - - +
554B TYR* 4.5 12.1 - - - -
556B THR* 5.6 2.2 - - - -
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Residues in contact with VAL 536 (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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532B LYS* 3.9 17.5 - - + +
533B GLN* 2.8 14.5 + - - +
535B GLY* 1.3 76.5 - - - +
537B ILE* 1.3 65.0 + - + +
538B LEU 3.3 0.2 - - - -
540B GLU* 3.0 39.2 - - - +
541B LYS* 3.0 25.5 + - - +
554B TYR* 5.8 3.8 - - + -
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Residues in contact with ILE 537 (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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522B ALA* 3.3 33.9 - - + -
524B GLN* 3.5 27.4 - - - +
526B PHE* 3.6 32.5 - - + -
533B GLN* 2.9 31.0 - - + +
534B LEU 3.2 6.5 + - - +
535B GLY 3.2 0.4 - - - -
536B VAL* 1.3 88.7 - - + +
538B LEU* 1.3 56.7 + - - +
541B LYS* 3.6 18.6 - - + +
542B LEU* 3.0 29.3 + - + +
570B ILE* 5.1 2.5 - - + -
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Residues in contact with LEU 538 (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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534B LEU* 2.7 29.1 + - + +
535B GLY* 4.2 2.2 - - - +
537B ILE* 1.3 80.3 - - + +
539B PHE* 1.3 99.7 + - + +
540B GLU 3.1 8.8 + - - -
542B LEU* 3.5 14.5 - - + +
544B LEU* 3.2 53.2 + - + +
561B LEU* 4.5 17.3 - - + -
564B LEU* 4.2 15.9 - - + -
570B ILE* 6.0 2.2 - - + -
571B VAL* 6.0 1.3 - - + -
574B ILE* 5.9 5.8 - - + -
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Residues in contact with PHE 539 (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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535B GLY* 2.7 26.4 + - - +
538B LEU* 1.3 100.8 - - + +
540B GLU* 1.3 63.6 + - - +
543B GLN 5.7 0.2 - - - -
544B LEU 3.7 8.3 - - - -
545B PRO 2.9 24.2 - - - -
546B VAL* 3.3 29.8 - - + +
547B LEU 4.6 1.8 - - - -
548B LYS 5.2 1.1 - - - -
554B TYR* 3.3 64.0 + + + -
555B SER 4.2 21.5 - - - -
556B THR* 4.5 6.5 - - - -
560B VAL* 4.6 9.9 - - + -
561B LEU* 5.0 0.9 - - + -
564B LEU* 4.4 4.5 - - + -
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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