Contacts of the strand formed by residues 543 - 549 (chain B) in PDB entry 4P3N
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 LYS 543 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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498B LEU* 3.4 6.7 - - - +
499B SER* 2.9 56.4 + - - +
519B LEU* 4.7 1.8 - - - +
536B ASP 4.3 9.3 + - - -
537B GLY* 4.5 8.5 - - - -
538B ALA* 4.6 6.4 - - + +
542B PRO* 1.3 76.2 - - - +
544B ILE* 1.3 65.5 + - - +
545B ASP* 2.6 35.1 + - - +
560B THR* 4.8 3.8 - - - +
561B ILE 3.3 10.5 - - - +
562B GLN* 3.5 24.9 - - + +
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Residues in contact with ILE 544 (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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476B ILE* 3.8 28.5 - - + -
480B LEU* 4.9 3.1 - - + -
496B LEU* 4.6 7.6 - - + -
497B ASN 3.5 10.8 - - - +
498B LEU* 4.4 5.4 - - + -
519B LEU* 3.8 20.2 - - + +
523B LEU* 4.0 40.6 - - + -
543B LYS* 1.3 75.7 - - - +
545B ASP* 1.3 70.0 + - - +
546B ILE* 3.7 12.3 - - + +
560B THR* 3.3 5.0 + - - -
561B ILE* 2.8 57.1 + - + +
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Residues in contact with ASP 545 (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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495B LYS 3.8 0.5 - - - +
496B LEU* 3.4 5.0 - - - -
497B ASN* 3.0 56.5 + - - +
499B SER* 4.3 0.7 + - - -
543B LYS* 2.6 37.2 + - - +
544B ILE* 1.3 73.7 - - - +
546B ILE* 1.3 64.0 + - - +
547B GLN* 5.9 0.4 - - - -
557B GLN* 3.4 24.0 + - - +
559B ALA 4.1 0.7 - - - -
560B THR* 3.0 24.4 + - - -
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Residues in contact with ILE 546 (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 LEU* 3.6 22.7 - - + -
487B TYR* 4.1 17.5 - - + -
494B PHE* 3.9 30.1 - - + -
495B LYS 3.4 8.5 - - - +
496B LEU* 3.5 21.1 - - + -
544B ILE* 3.7 19.7 - - + +
545B ASP* 1.3 79.5 - - - +
547B GLN* 1.3 64.7 + - - +
548B ILE* 5.3 0.2 - - + -
557B GLN* 2.9 20.7 + - - -
558B CYS* 3.1 13.2 + - - +
559B ALA* 3.2 31.2 + - + +
560B THR* 4.1 2.9 - - - -
561B ILE* 4.1 10.1 - - + -
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Residues in contact with GLN 547 (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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494B PHE* 3.1 7.7 - - - +
495B LYS* 2.5 69.0 + - + +
497B ASN* 5.5 4.9 - - - +
545B ASP 4.3 0.2 - - - -
546B ILE* 1.3 73.9 - - - +
548B ILE* 1.3 63.4 + - - +
549B LYS 4.2 0.2 + - - -
555B TYR* 3.9 32.1 + - + +
556B HIS 3.3 4.0 - - - +
557B GLN* 3.8 38.7 - - - +
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Residues in contact with ILE 548 (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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487B TYR* 3.5 56.1 - - + +
492B PHE* 3.5 49.1 - - + -
493B SER 3.8 0.7 - - - +
494B PHE* 3.6 14.8 - - + -
546B ILE* 5.3 0.4 - - + -
547B GLN* 1.3 73.7 - - - +
549B LYS* 1.3 61.6 + - - +
554B ARG 3.3 1.6 - - - +
555B TYR* 3.2 7.3 - - - -
556B HIS* 2.9 47.2 + - + +
558B CYS* 4.5 13.9 - - + -
600B MET* 6.3 1.6 - - - -
603B ILE* 5.3 2.2 - - + -
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Residues in contact with LYS 549 (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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491B GLY 5.1 0.3 - - - +
492B PHE* 3.2 16.7 - - - -
493B SER* 2.8 46.4 + - - +
548B ILE* 1.3 72.4 - - - +
550B ASP* 1.3 75.2 + - - +
551B ALA* 5.1 4.6 + - - +
553B GLY* 3.7 33.9 - - - +
554B ARG 3.2 2.5 - - - +
555B TYR* 3.6 31.2 - - + +
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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