Contacts of the strand formed by residues 602 - 605 (chain F) in PDB entry 5JLH
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 602 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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484F ILE* 5.9 2.4 - - - +
583F GLN* 3.4 28.2 + - - +
585F PRO* 5.3 12.7 - - - +
590F ASP* 6.0 0.4 + - - -
595F SER* 3.4 25.2 + - - -
596F VAL 3.4 6.5 - - - +
597F LEU* 3.5 19.5 - - + +
601F GLY* 1.3 71.8 - - - -
603F VAL* 1.3 64.7 + - - +
604F ASP* 3.5 16.3 - - - +
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Residues in contact with VAL 603 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482F PHE* 4.0 20.6 - - + -
483F GLU 5.5 1.3 - - - +
484F ILE* 4.7 14.8 - - + -
488F ASN* 3.3 26.2 - - - +
496F ASN* 4.5 4.3 - - - +
595F SER* 3.1 20.1 - - - -
596F VAL 3.0 13.4 + - - +
598F HIS* 3.6 30.3 - - + +
601F GLY 4.0 4.5 - - - +
602F LYS* 1.3 77.9 - - - +
604F ASP* 1.3 73.0 + - - +
605F TYR* 3.9 20.4 - - + +
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Residues in contact with ASP 604 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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486F GLN 5.3 4.9 - - - +
487F LEU 3.7 2.0 - - - +
488F ASN* 3.0 32.8 + - - +
590F ASP* 5.8 0.2 - - - +
592F ALA* 3.4 22.5 - - + +
595F SER* 2.7 27.1 + - - +
602F LYS* 3.5 17.3 - - - +
603F VAL* 1.3 80.1 - - - +
605F TYR* 1.3 62.5 + - - +
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Residues in contact with TYR 605 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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488F ASN* 3.6 19.5 - - + -
489F SER 4.1 5.8 - - - -
492F GLN 4.6 0.2 - - - -
493F LEU* 3.6 34.9 - - + +
496F ASN* 3.1 24.1 + - - -
592F ALA* 3.3 4.7 - - - +
593F ASP* 2.8 28.6 + - - -
594F PHE* 2.9 48.7 + + + +
596F VAL* 3.5 27.1 - - + -
598F HIS* 2.9 25.5 + - - -
603F VAL* 3.9 18.8 - - + +
604F ASP* 1.3 77.8 - - - +
606F LYS* 1.3 56.7 + - - +
607F ALA 4.1 0.3 + - - -
610F TRP* 4.0 18.2 - + + -
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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