Contacts of the strand formed by residues 498 - 506 (chain B) in PDB entry 1L9N
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 VAL 498 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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492B LEU* 3.9 12.1 - - + -
493B ALA 6.1 0.2 - - - +
496B LYS 4.7 0.2 - - - +
497B GLU* 1.3 74.5 - - - +
499B ASN* 1.3 63.9 + - - +
500B LEU* 3.9 17.7 - - + -
552B ILE 3.4 0.9 - - - +
553B LYS* 3.3 7.4 - - - +
554B ILE* 2.7 50.1 + - + +
559B TYR* 3.9 20.9 - - + -
569B ILE* 4.2 8.1 - - + -
589B ILE* 3.7 23.6 - - + -
591B LEU* 3.9 28.3 - - + -
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Residues in contact with ASN 499 (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 VAL* 3.9 3.1 - - - +
489B ALA* 2.7 56.3 + - + +
491B MET 5.5 0.6 + - - -
492B LEU* 4.4 4.4 - - - +
497B GLU* 2.9 40.1 + - - +
498B VAL* 1.3 73.9 - - - +
500B LEU* 1.3 62.7 + - - +
552B ILE 3.5 1.6 - - - +
553B LYS* 2.6 37.2 + - - +
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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
----------------------------------------------------------
486B LEU* 5.2 5.6 - - + -
487B LYS 3.2 15.5 - - - +
488B VAL* 3.6 34.1 - - + -
489B ALA* 4.1 1.1 - - - +
492B LEU* 5.2 0.7 - - + -
498B VAL* 3.9 19.3 - - + -
499B ASN* 1.3 77.0 - - - +
501B VAL* 1.3 73.3 + - - +
551B PRO* 3.8 1.0 - - - +
552B ILE* 2.9 44.5 + - + +
571B ILE* 3.4 43.7 - - + -
587B ARG* 5.3 4.0 - - + -
589B ILE* 4.1 15.3 - - + -
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Residues in contact with VAL 501 (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 LYS 3.5 0.7 - - - +
486B LEU* 3.6 4.1 - - - -
487B LYS* 2.9 40.2 + - + +
489B ALA* 4.4 15.7 - - + -
500B LEU* 1.3 83.3 - - - +
502B LEU* 1.3 68.1 + - - +
503B LEU* 3.5 4.9 + - + +
549B GLU* 3.7 42.4 - - + +
550B HIS 3.7 8.5 - - - +
551B PRO* 4.6 9.2 - - + -
552B ILE* 5.1 0.4 - - - -
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Residues in contact with LEU 502 (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 LYS 3.6 13.5 - - - +
486B LEU* 3.9 24.8 - - + +
501B VAL* 1.3 71.6 - - - +
503B LEU* 1.3 60.3 + - - +
504B LEU* 3.7 32.2 + - + +
516B VAL* 3.5 32.1 - - + -
518B MET* 4.0 6.7 - - - -
549B GLU* 3.4 4.7 - - - -
550B HIS* 3.0 41.6 + - + +
552B ILE* 4.7 5.7 - - + +
573B ALA* 3.8 16.6 - - + -
575B CYS* 4.3 1.1 - - - -
585B VAL* 4.0 15.3 - - + -
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Residues in contact with LEU 503 (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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483B ILE* 3.9 0.6 - - + +
484B GLY* 3.0 6.4 - - - -
485B LYS* 2.7 54.0 + - + +
487B LYS* 4.4 28.9 - - + +
501B VAL* 3.5 5.5 + - + +
502B LEU* 1.3 70.9 - - - +
504B LEU* 1.3 78.2 + - - +
505B LYS* 4.6 5.6 - - + +
547B GLU* 4.3 20.4 - - + +
548B ALA 3.7 6.7 - - - +
549B GLU* 4.6 18.4 - - + +
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Residues in contact with LEU 504 (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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482B ILE* 4.1 10.1 - - + -
483B ILE 3.5 3.6 - - - +
484B GLY* 3.7 15.3 - - - -
502B LEU* 3.9 23.3 - - + +
503B LEU* 1.3 88.3 - - - +
505B LYS* 1.3 62.8 + - - +
514B VAL* 4.5 9.6 - - + -
516B VAL* 3.7 17.3 - - + -
540B MET* 3.3 36.1 - - + -
542B LEU* 4.3 11.7 - - + -
547B GLU* 3.3 4.5 - - - -
548B ALA* 2.9 35.9 + - + +
575B CYS* 3.9 18.2 - - - -
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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
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481B SER 3.6 1.2 - - - +
482B ILE* 3.5 9.0 - - - +
483B ILE* 3.1 46.1 + - + +
503B LEU* 4.8 4.7 - - + -
504B LEU* 1.3 77.6 - - - +
506B ASN* 1.3 65.1 + - - +
507B LEU* 3.6 16.0 + - + +
542B LEU* 4.6 0.7 - - - -
545B GLU* 3.4 45.7 + - - +
546B GLU 3.4 11.9 - - - +
547B GLU* 3.4 30.2 + - + +
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Residues in contact with ASN 506 (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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481B SER* 3.3 14.8 - - - -
482B ILE* 3.7 12.6 - - + +
505B LYS* 1.3 72.5 - - - +
507B LEU* 1.3 58.6 + - - +
508B SER* 3.1 21.5 + - - -
510B ASP 3.1 24.2 + - - -
512B LYS* 3.7 8.3 - - - +
542B LEU* 3.3 22.6 + - + +
543B ASP 3.1 27.8 + - - +
544B PRO* 3.6 4.8 - - - +
545B GLU* 2.6 35.5 + - - +
546B GLU 3.2 6.9 + - - -
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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