Contacts of the strand formed by residues 660 - 667 (chain B) in PDB entry 6RKU
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 PHE 660 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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620B LEU* 3.2 54.3 - - + +
621B SER 3.5 20.0 - - - -
622B ASP 4.0 3.6 - - - -
623B GLU* 3.5 46.7 - - + -
626B VAL* 4.5 15.8 - - + +
651B VAL* 5.7 5.4 - - + -
652B HIS 4.1 3.1 - - - +
653B THR* 3.4 32.5 - - + -
657B GLN 5.0 1.6 - - - -
658B ASN* 3.5 22.9 - - + +
659B LEU* 1.3 72.7 - - - +
661B GLU* 1.3 60.4 + - - +
662B PRO* 4.1 5.3 - - - +
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Residues in contact with GLU 661 (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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620B LEU* 5.3 2.5 - - + -
626B VAL* 5.4 1.6 - - - -
651B VAL* 5.6 1.1 - - - +
652B HIS* 3.4 34.4 + - + +
654B ASN* 4.5 24.2 + - - +
659B LEU* 3.3 18.1 + - + +
660B PHE* 1.3 75.5 - - - +
662B PRO* 1.3 68.8 - - - +
663B ILE* 3.7 7.8 + - + +
676B PRO* 5.5 2.5 - - + +
677B LEU 3.2 14.8 - - - +
678B ASP* 2.9 34.3 - - - +
679B HIS* 4.2 17.5 + - + +
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Residues in contact with PRO 662 (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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615B LEU* 5.8 2.5 - - + -
620B LEU* 6.4 0.2 - - + -
626B VAL* 3.6 30.5 - - + -
629B TRP* 3.9 28.5 - - + -
630B VAL* 5.0 11.9 - - + -
650B ASP 4.0 5.8 - - - +
651B VAL* 5.3 1.8 - - + -
660B PHE 4.1 5.2 - - - +
661B GLU* 1.3 85.1 - - - +
663B ILE* 1.3 62.5 + - - +
664B VAL* 6.0 1.1 - - + -
677B LEU* 3.1 50.8 + - + +
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Residues in contact with ILE 663 (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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630B VAL* 4.7 2.2 - - - +
649B PHE* 3.9 1.6 - - - +
650B ASP* 2.8 68.3 + - + +
652B HIS* 3.7 25.4 - - + -
661B GLU* 4.0 6.7 - - + +
662B PRO* 1.3 81.3 - - - +
664B VAL* 1.3 65.9 + - - +
665B ARG* 5.9 2.2 - - + +
674B ASP* 4.0 27.8 - - + +
675B TYR 4.0 7.9 - - - +
676B PRO* 3.8 24.0 - - + -
677B LEU* 4.7 0.2 - - - -
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Residues in contact with VAL 664 (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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605B MET* 4.6 15.9 - - - -
630B VAL* 4.9 10.5 - - + -
633B LEU* 4.5 20.9 - - + -
634B VAL* 5.2 6.1 - - + -
637B LEU* 5.3 2.9 - - + -
647B TRP* 3.8 34.8 - - + -
648B LYS 3.8 9.2 - - - +
649B PHE* 4.8 0.2 - - - +
662B PRO* 5.7 1.1 - - + -
663B ILE* 1.3 78.9 - - - +
665B ARG* 1.3 63.9 + - - +
666B VAL* 4.6 0.7 - - + +
673B THR 3.7 2.1 - - - +
674B ASP* 3.3 8.3 - - - +
675B TYR* 3.2 40.1 + - + +
677B LEU* 5.0 6.7 - - + -
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Residues in contact with ARG 665 (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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647B TRP* 3.6 0.7 - - - -
648B LYS* 2.6 71.3 + - + +
649B PHE 4.6 8.7 + - - +
650B ASP* 4.7 18.7 + - + +
663B ILE* 4.1 2.7 + - + +
664B VAL* 1.3 73.5 - - - +
666B VAL* 1.3 60.1 + - - +
667B ARG* 4.3 0.8 + - + -
672B ASP* 3.0 39.0 + - + -
673B THR 4.0 4.9 - - - +
674B ASP* 4.8 13.4 - - + +
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Residues in contact with VAL 666 (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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602B PRO* 5.6 2.2 - - + -
645B SER* 3.8 11.4 - - - +
646B GLN 3.3 19.7 - - - +
647B TRP* 3.5 36.6 - - + -
664B VAL* 4.0 0.6 - - + -
665B ARG* 1.3 74.3 - - - +
667B ARG* 1.3 65.6 + - - +
668B THR* 4.0 6.6 + - + +
672B ASP* 3.2 6.2 - - - +
673B THR* 3.1 41.3 + - - +
675B TYR* 4.2 17.9 - - + -
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Residues in contact with ARG 667 (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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493A GLY 5.4 5.3 + - - -
495A ALA* 5.3 11.1 - - - +
644B GLY 4.7 0.2 - - - +
645B SER* 3.3 19.2 + - - -
646B GLN* 3.5 40.0 + - + +
648B LYS* 5.1 18.7 - - + +
665B ARG* 4.3 0.9 + - + -
666B VAL* 1.3 75.9 - - - +
668B THR* 1.3 73.4 + - - +
669B HIS 5.5 2.4 + - - -
670B GLY* 5.7 4.0 + - - -
671B VAL 5.1 3.4 - - - +
672B ASP* 4.4 13.9 - - + +
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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