Contacts of the strand formed by residues 585 - 591 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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572F LEU* 4.3 8.5 - - + -
573F GLN 3.3 17.0 - - - +
574F LEU* 4.3 7.2 - - + -
584F TRP* 1.3 73.7 - - - +
586F PHE* 1.3 60.3 + - - +
587F ARG* 4.9 9.2 - - - +
600F LYS 3.8 2.1 - - - +
601F LEU* 3.9 2.4 - - - +
602F GLU* 2.9 44.2 + - + +
604F MET* 3.9 13.6 - - + +
610F ALA 4.1 3.4 - - - +
613F HIS* 3.8 33.7 - - + +
614F PHE* 3.5 45.1 - - + +
617F LEU* 4.2 5.2 - - + -
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Residues in contact with PHE 586 (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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534F ASP* 3.4 32.5 - - + -
536F ASP* 3.6 15.7 - - + -
537F SER* 3.5 40.2 - - - -
571F LYS* 4.9 3.1 - - + -
572F LEU* 3.5 6.1 - - - +
573F GLN* 3.0 51.1 + - + +
575F LEU* 4.5 10.1 - - + +
584F TRP 4.5 0.2 + - - -
585F ILE* 1.3 74.5 - - - +
587F ARG* 1.3 64.2 + - - +
588F SER* 3.8 14.8 - - - -
599F ASN* 3.8 24.9 - - + -
600F LYS 3.8 0.4 - - - -
601F LEU* 3.8 29.4 - - + -
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Residues in contact with ARG 587 (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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570F TYR* 3.1 27.6 - - + +
571F LYS 3.7 3.4 - - - -
572F LEU* 3.6 18.8 - - + -
585F ILE* 4.9 5.5 - - + +
586F PHE* 1.3 77.0 - - - +
588F SER* 1.3 58.9 + - - +
589F TRP* 3.7 15.8 - - + -
599F ASN* 3.3 5.0 - - - +
600F LYS* 2.9 67.7 + - + +
602F GLU* 3.2 26.5 + - - +
613F HIS* 3.9 9.0 + - - -
617F LEU* 3.5 37.1 - - + +
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Residues in contact with SER 588 (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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534F ASP* 4.2 4.2 + - - -
536F ASP* 4.1 15.1 + - - -
569F TYR* 3.8 14.8 + - - -
570F TYR* 3.3 6.9 - - - -
571F LYS* 2.8 47.8 + - - +
586F PHE* 3.8 19.0 - - - -
587F ARG* 1.3 73.9 - - - +
589F TRP* 1.3 66.2 + - - +
598F SER 4.0 6.5 + - - -
599F ASN* 4.2 4.9 + - - +
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Residues in contact with TRP 589 (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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43D MET* 2.6 33.2 + - + +
44D PHE* 3.9 17.2 - - + +
569F TYR* 3.2 23.6 + - - +
570F TYR* 3.6 23.1 - + + -
587F ARG* 3.7 21.3 - - + -
588F SER* 1.3 79.6 + - - +
590F GLY* 1.3 60.2 + - - +
598F SER* 2.9 56.9 + - - +
599F ASN* 3.6 32.1 - - - -
600F LYS* 3.6 16.2 - - + -
638F PHE* 6.5 0.2 - - + -
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Residues in contact with GLY 590 (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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45D ASP* 4.1 13.7 - - - -
568F SER* 3.3 7.2 - - - -
569F TYR* 2.9 35.8 + - - -
589F TRP* 1.3 82.0 - - - +
591F ARG* 1.3 60.2 + - - -
596F ILE 3.4 12.1 - - - -
597F GLY* 3.5 6.5 - - - -
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Residues in contact with ARG 591 (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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40D GLN* 5.4 3.8 - - - -
45D ASP* 3.4 28.3 + - + +
565F GLY* 2.8 29.5 + - - -
566F THR* 3.6 1.2 - - - +
567F ASN* 3.2 44.5 - - + +
569F TYR* 3.7 3.7 - - - -
590F GLY* 1.3 70.3 - - - -
592F VAL* 1.3 65.8 + - - +
593F GLY 3.3 1.7 + - - -
594F THR* 2.7 37.2 + - - +
596F ILE* 3.0 19.7 + - + +
744F PHE* 5.3 0.8 - - - +
745F GLY 2.8 20.3 + - - +
746F MET* 3.6 25.0 + - - +
747F LYS 3.0 32.5 + - - +
749F 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