Contacts of the helix formed by residues 496 - 520 (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 496 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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495B VAL* 1.3 76.4 - - - +
497B THR* 1.3 66.5 + - - +
498B LYS* 3.7 11.3 + - - +
499B ARG* 3.2 41.6 + - + +
500B LEU* 3.2 8.7 + - - +
600B LYS* 3.4 10.2 + - - +
638B GLN 4.6 0.7 - - - +
639B ALA* 2.5 31.1 + - - +
641B VAL* 4.4 17.3 - - + +
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Residues in contact with THR 497 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495B VAL* 5.3 1.3 - - + -
496B ASP* 1.3 72.8 - - - +
498B LYS* 1.3 67.3 + - - +
500B LEU* 2.7 33.2 + - + +
501B GLU* 2.9 22.5 + - - +
592B LEU* 4.1 13.5 - - + -
595B VAL* 4.1 31.6 - - + -
600B LYS* 3.4 31.9 + - + +
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Residues in contact with LYS 498 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496B ASP* 3.4 9.1 + - - +
497B THR* 1.3 87.8 + - - +
499B ARG* 1.3 61.5 + - - +
501B GLU* 3.5 17.3 + - - +
502B GLN* 3.2 20.8 + - - +
600B LYS* 4.8 8.5 - - - +
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Residues in contact with ARG 499 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496B ASP* 3.2 28.1 + - - +
497B THR 3.1 0.8 - - - -
498B LYS* 1.3 78.4 - - - +
500B LEU* 1.3 62.0 + - - +
502B GLN* 3.2 36.6 + - - +
503B MET* 3.2 21.0 + - + +
638B GLN* 3.3 63.6 + - - +
639B ALA* 3.6 4.5 - - + +
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Residues in contact with LEU 500 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495B VAL* 3.6 25.8 - - + -
496B ASP 3.6 3.6 - - - +
497B THR* 2.7 20.6 + - + +
499B ARG* 1.3 71.5 - - - +
501B GLU* 1.3 59.6 + - - +
503B MET* 3.7 11.8 + - + -
504B GLY* 2.9 23.9 + - - -
588B ILE* 3.5 34.1 - - + +
591B LEU* 4.3 25.4 - - + -
592B LEU* 4.1 21.8 - - + +
595B VAL* 5.3 0.9 - - + -
636B ILE* 4.4 12.8 - - + -
639B ALA* 3.4 24.7 - - + -
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Residues in contact with GLU 501 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497B THR* 2.9 20.9 + - - +
498B LYS* 3.8 17.8 - - - +
500B LEU* 1.3 73.6 - - - +
502B GLN* 1.3 66.9 + - - +
504B GLY* 2.9 2.7 + - - +
505B LYS* 2.9 44.7 + - - +
592B LEU* 4.1 24.3 - - + +
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Residues in contact with GLN 502 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498B LYS 3.2 12.4 + - - +
499B ARG* 3.2 26.6 + - - +
501B GLU* 1.3 79.5 - - - +
503B MET* 1.3 82.6 + - - +
504B GLY 2.9 1.4 + - - -
505B LYS* 3.2 10.6 + - - +
506B GLU* 3.3 34.0 + - - +
635B LYS* 5.3 5.0 + - - -
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Residues in contact with MET 503 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499B ARG* 3.2 24.8 + - + +
500B LEU* 3.8 20.2 - - + +
502B GLN* 1.3 98.1 - - - +
504B GLY* 1.3 61.2 + - - +
506B GLU* 3.5 15.2 + - - +
507B LEU* 3.0 34.5 + - + +
588B ILE* 3.9 6.7 - - + -
632B GLU 5.8 0.4 - - - +
635B LYS* 3.6 41.3 - - - +
636B ILE* 3.4 36.6 - - + +
638B GLN* 4.8 2.2 - - - +
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Residues in contact with GLY 504 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500B LEU 2.9 15.9 + - - -
501B GLU* 3.2 7.2 - - - -
502B GLN 2.9 3.0 - - - -
503B MET* 1.3 76.7 - - - +
505B LYS* 1.3 61.1 + - - -
507B LEU 3.1 3.1 + - - -
508B ALA 3.0 8.8 + - - -
584B GLN* 2.7 40.4 + - - -
588B ILE* 4.0 4.9 - - - -
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Residues in contact with LYS 505 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501B GLU* 2.9 34.1 + - - +
502B GLN* 4.1 3.4 - - - +
504B GLY* 1.3 71.9 - - - +
506B GLU* 1.3 62.1 + - + +
508B ALA* 3.3 9.4 - - + +
509B GLU* 3.2 28.5 + - - +
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Residues in contact with GLU 506 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502B GLN* 3.3 36.5 + - - +
503B MET* 3.6 15.2 - - - +
504B GLY 3.1 0.6 - - - -
505B LYS* 1.3 76.2 - - + +
507B LEU* 1.3 63.8 + - + +
508B ALA 3.0 5.9 + - - -
509B GLU* 3.6 20.4 - - - +
510B GLN* 3.4 21.9 - - - +
635B LYS* 5.9 2.6 - - - -
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Residues in contact with LEU 507 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503B MET* 3.0 26.8 + - + +
504B GLY 3.7 3.6 - - - +
506B GLU* 1.3 77.1 - - + +
508B ALA* 1.3 57.9 + - - +
510B GLN* 4.1 9.1 - - - +
511B LEU* 3.2 33.5 + - + +
580B LEU* 3.7 31.4 - - + +
583B LEU* 3.5 42.2 - - + -
584B GLN* 4.2 23.1 - - + +
588B ILE* 4.4 7.6 - - + -
636B ILE* 5.7 1.3 - - + -
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Residues in contact with ALA 508 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504B GLY 3.0 11.0 + - - +
505B LYS* 3.3 15.7 - - + +
506B GLU 3.0 0.6 - - - -
507B LEU* 1.3 76.2 - - - +
509B GLU* 1.3 59.2 + - - +
510B GLN 2.9 10.0 + - - -
511B LEU* 3.3 14.5 + - - +
512B GLY* 3.7 7.4 + - - -
584B GLN* 3.9 9.4 - - - +
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Residues in contact with GLU 509 (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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505B LYS 3.2 14.5 + - - +
506B GLU* 3.6 19.0 - - - +
508B ALA* 1.3 75.2 - - - +
510B GLN* 1.3 59.7 + - + +
512B GLY* 4.4 2.6 - - - -
513B THR* 3.0 19.8 + - - -
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Residues in contact with GLN 510 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506B GLU* 3.4 18.5 - - - +
507B LEU* 4.2 8.9 - - - +
508B ALA 2.9 0.8 - - - -
509B GLU* 1.3 81.5 - - + +
511B LEU* 1.3 54.9 + - - +
512B GLY 2.9 4.7 - - - -
513B THR* 2.7 28.0 + - - -
514B VAL* 2.9 24.9 + - + +
576B HIS* 3.5 29.1 + - - -
580B LEU* 3.6 21.7 - - + +
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Residues in contact with LEU 511 (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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507B LEU 3.2 21.6 + - - +
508B ALA* 3.3 7.2 + - - +
510B GLN* 1.3 76.9 - - - +
512B GLY* 1.3 57.0 + - - +
514B VAL* 4.1 5.4 - - - -
515B GLU* 3.4 9.9 + - - +
577B TYR* 3.0 56.7 + - + +
580B LEU* 3.2 37.2 - - + +
581B GLY* 3.3 28.3 - - - +
584B GLN* 4.2 15.9 - - + -
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Residues in contact with GLY 512 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508B ALA 3.7 8.5 + - - -
509B GLU* 5.0 2.0 - - - -
510B GLN 2.9 1.2 - - - +
511B LEU* 1.3 78.9 - - - +
513B THR* 1.3 61.3 + - - +
514B VAL 3.3 0.2 - - - -
515B GLU* 3.7 7.6 + - - +
516B GLN* 2.9 35.8 + - - +
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Residues in contact with THR 513 (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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509B GLU 3.0 19.1 + - - -
510B GLN* 2.7 12.0 + - - -
512B GLY* 1.3 79.6 - - - +
514B VAL* 1.3 59.6 + - + +
515B GLU 3.4 0.2 - - - -
516B GLN* 3.2 24.4 - - + +
517B ARG* 3.7 6.4 + - - +
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Residues in contact with VAL 514 (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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510B GLN* 2.9 20.8 + - + +
511B LEU* 4.5 1.1 - - - +
513B THR* 1.3 77.2 - - + +
515B GLU* 1.3 57.1 + - - +
516B GLN 2.9 9.4 + - - -
517B ARG* 3.2 12.7 + - - +
518B ILE* 3.0 22.9 + - + +
573B ASN* 3.8 20.0 - - - +
576B HIS* 3.2 54.3 - - + +
577B TYR* 4.1 11.9 - - + +
580B LEU* 3.6 14.6 - - + -
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Residues in contact with GLU 515 (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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511B LEU 3.4 16.9 + - - +
512B GLY* 4.0 9.0 - - - +
513B THR 3.4 0.6 - - - -
514B VAL* 1.3 77.5 - - - +
516B GLN* 1.3 62.9 + - - +
518B ILE* 3.9 12.3 - - + -
519B TYR* 2.5 74.5 + - + +
528B ILE* 3.2 11.7 - - + +
529B ASN* 4.9 1.9 + - - -
577B TYR* 2.7 33.2 + - + -
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Residues in contact with GLN 516 (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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512B GLY* 2.9 27.4 + - - +
513B THR* 3.2 16.6 - - + +
514B VAL 2.9 0.4 - - - -
515B GLU* 1.3 86.8 + - - +
517B ARG* 1.3 56.9 + - - +
518B ILE 3.0 7.4 + - - -
519B TYR* 3.5 8.3 + - - +
520B GLU* 3.1 34.4 + - - +
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Residues in contact with ARG 517 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513B THR 3.7 6.8 + - - +
514B VAL* 3.2 7.0 + - - +
516B GLN* 1.3 77.1 - - - +
518B ILE* 1.3 56.7 + - - +
520B GLU* 2.9 29.5 + - - -
521B LEU* 3.1 58.7 - - - +
569B GLU* 2.6 30.6 + - - -
573B ASN* 2.9 40.9 + - - +
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Residues in contact with ILE 518 (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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514B VAL 3.0 23.1 + - - +
515B GLU* 3.9 10.1 - - + +
516B GLN 3.0 0.6 - - - -
517B ARG* 1.3 78.6 - - - +
519B TYR* 1.3 67.7 + - + +
520B GLU 3.4 0.2 - - - -
521B LEU 3.8 0.2 + - - -
522B ALA* 3.4 8.7 + - - +
526B PHE* 4.6 3.1 - - + -
528B ILE* 3.6 22.7 - - + -
570B ILE* 3.3 21.2 - - + +
573B ASN* 2.8 40.4 - - + +
574B ILE* 3.4 26.5 - - + -
577B TYR* 3.4 32.5 - - + -
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Residues in contact with TYR 519 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515B GLU* 2.5 59.2 + - + +
516B GLN* 3.5 10.5 + - - +
518B ILE* 1.3 76.5 - - + +
520B GLU* 1.3 57.1 + - - +
522B ALA* 4.5 0.7 - - - -
523B GLY* 2.7 33.1 + - - +
524B GLN 3.1 27.9 - - - +
525B GLU* 3.3 33.3 + - + +
526B PHE* 2.8 38.4 + + - -
527B ASN* 4.6 1.0 - - - -
528B ILE* 3.0 22.7 - - + +
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Residues in contact with GLU 520 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516B GLN* 3.1 24.6 + - - +
517B ARG* 2.9 48.8 + - - +
519B TYR* 1.3 73.1 - - - +
521B LEU* 1.3 70.9 + - + +
522B ALA 3.0 9.5 + - - -
523B GLY* 3.2 11.1 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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