Contacts of the strand formed by residues 585 - 591 (chain C) in PDB entry 4OQB
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 ILE 585 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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572C LEU* 4.3 9.4 - - + -
573C GLN 3.3 17.0 - - - +
574C LEU* 4.3 8.1 - - + -
584C TRP* 1.3 73.7 - - - +
586C PHE* 1.3 60.1 + - - +
587C ARG* 4.9 9.6 - - - +
600C LYS 3.7 2.2 - - - +
601C LEU* 3.9 2.4 - - - +
602C GLU* 2.9 43.1 + - + +
604C MET* 3.9 13.4 - - + +
610C ALA 4.1 3.1 - - - +
613C HIS* 3.8 32.3 - - + +
614C PHE* 3.5 45.3 - - + +
617C LEU* 4.2 4.9 - - + -
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Residues in contact with PHE 586 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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534C ASP* 3.4 33.9 - - + -
536C ASP* 3.6 15.7 - - + -
537C SER* 3.5 41.1 - - - -
571C LYS* 4.9 3.1 - - + -
572C LEU* 3.5 5.9 - - - +
573C GLN* 3.0 51.4 + - + +
574C LEU* 5.1 0.2 - - - +
575C LEU* 4.5 10.3 - - + +
585C ILE* 1.3 74.3 - - - +
587C ARG* 1.3 63.6 + - - +
588C SER* 3.8 14.6 - - - -
599C ASN* 3.8 26.2 - - + -
600C LYS 3.8 0.4 - - - -
601C LEU* 3.8 30.3 - - + -
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Residues in contact with ARG 587 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570C TYR* 3.2 28.5 - - + +
571C LYS 3.7 3.4 - - - -
572C LEU* 3.6 18.6 - - + -
585C ILE* 4.9 5.3 - - + +
586C PHE* 1.3 74.9 - - - +
588C SER* 1.3 59.9 + - - +
589C TRP* 3.7 16.2 - - + -
599C ASN* 3.3 5.7 - - - +
600C LYS* 2.9 68.4 + - + +
602C GLU* 3.2 25.9 + - - +
613C HIS* 3.9 8.5 + - - -
617C LEU* 3.5 36.1 - - + +
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Residues in contact with SER 588 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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534C ASP* 4.2 4.5 + - - -
536C ASP* 4.1 14.9 + - - -
569C TYR* 3.8 15.2 + - - -
570C TYR* 3.3 7.1 - - - -
571C LYS* 2.8 49.2 + - - +
586C PHE* 3.8 19.0 - - - -
587C ARG* 1.3 74.2 - - - +
589C TRP* 1.3 65.3 + - - +
598C SER 4.0 7.1 + - - -
599C ASN* 4.2 4.3 + - - +
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Residues in contact with TRP 589 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A MET* 2.8 30.8 + - + +
44A PHE* 3.9 16.5 - - + +
569C TYR* 3.2 24.2 + - - +
570C TYR* 3.6 23.3 - + + -
587C ARG* 3.7 21.1 - - + -
588C SER* 1.3 79.0 + - - +
590C GLY* 1.3 59.9 + - - +
598C SER* 2.9 59.7 + - - +
599C ASN* 3.6 32.1 - - - -
600C LYS* 3.6 16.2 - - + -
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Residues in contact with GLY 590 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A ASP* 4.0 12.6 - - - -
568C SER* 3.3 7.0 - - - -
569C TYR* 2.9 36.8 + - - -
589C TRP* 1.3 81.2 - - - +
591C ARG* 1.3 60.9 + - - -
596C ILE 3.4 12.1 - - - -
597C GLY* 3.5 7.0 - - - -
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Residues in contact with ARG 591 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A GLN* 5.1 4.3 - - - -
45A ASP* 3.2 35.9 + - + +
565C GLY 2.8 30.3 + - - -
566C THR* 3.6 1.6 - - - +
567C ASN* 3.2 39.6 - - + +
569C TYR* 3.7 4.3 - - - -
590C GLY* 1.3 70.6 - - - -
592C VAL* 1.3 64.7 + - - +
593C GLY 3.3 1.9 + - - -
594C THR* 2.7 36.9 + - - +
596C ILE* 3.0 17.9 + - + -
744C PHE* 5.3 0.6 - - - +
745C GLY 2.8 20.3 + - - +
746C MET* 3.6 25.3 + - - +
747C LYS 3.0 32.1 + - - +
749C PRO* 4.5 1.0 - - - +
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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