Contacts of the strand formed by residues 561 - 567 (chain U) in PDB entry 6FF7
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 VAL 561 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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559U HIS 3.5 4.7 + - - +
560U ASP* 1.3 73.3 - - - +
562U CYS* 1.3 62.4 + - - +
595U CYS 3.2 10.8 - - - +
596U GLU* 4.4 3.1 - - + +
658U ARG* 4.7 1.4 - - - +
659U ARG* 4.5 19.2 + - - +
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Residues in contact with CYS 562 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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560U ASP 3.9 2.5 + - - +
561U VAL* 1.3 76.3 - - - +
563U PHE* 1.3 63.0 + - - +
594U GLY* 3.5 2.4 - - - -
595U CYS* 2.8 37.8 + - + +
597U ILE* 6.1 1.1 - - + +
656U ILE* 5.5 5.6 - - + -
657U MET 3.3 17.0 - - - +
658U ARG* 4.7 6.1 - - + -
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Residues in contact with PHE 563 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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480U GLU 4.6 3.6 - - - +
483U GLN* 4.7 2.5 - - + -
484U ASP* 2.8 35.4 - - + +
562U CYS* 1.3 75.2 - - - +
564U LEU* 1.3 58.4 + - - +
593U ARG 3.4 2.9 - - - +
594U GLY* 4.4 2.2 - - - -
656U ILE* 3.3 7.4 - - - +
657U MET* 2.9 41.0 + - + +
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Residues in contact with LEU 564 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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484U ASP* 2.5 23.7 - - - +
485U ILE* 2.8 3.1 + - - +
488U SER* 4.9 0.2 - - - -
562U CYS 4.2 0.4 + - - -
563U PHE* 1.3 70.0 - - - +
565U ILE* 1.3 53.3 + - - +
591U TYR* 4.4 0.7 - - - +
592U VAL* 3.5 0.3 - - - -
593U ARG* 2.6 36.1 + - + +
594U GLY 5.1 2.6 - - - +
595U CYS* 5.7 4.7 - - + +
653U PHE* 4.4 17.3 - - + -
655U ILE 3.6 4.7 - - - -
656U ILE* 4.8 2.9 - - + +
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Residues in contact with ILE 565 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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484U ASP 1.4 46.3 + - - +
485U ILE* 1.7 57.2 - - - +
486U GLU 2.6 2.9 - - - +
487U ASP 2.7 3.4 - - - +
488U SER* 2.7 20.8 - - - +
489U VAL 2.4 24.3 + - - -
564U LEU* 1.3 62.1 - - - +
566U THR* 1.3 49.8 + - - -
653U PHE* 4.3 3.3 - - - +
654U ASN 3.0 12.5 + - - -
655U ILE 2.8 8.9 + - - -
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Residues in contact with THR 566 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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485U ILE* 2.1 34.7 + - - +
489U VAL* 2.9 4.3 - - - -
565U ILE 1.3 67.6 - - - -
567U VAL* 1.3 61.5 + - - +
589U LEU* 3.8 0.5 - - - -
590U VAL* 2.8 33.2 + - - +
591U TYR* 3.3 17.6 + - - -
649U VAL 5.7 0.2 - - - -
652U THR* 3.9 31.0 - - - -
653U PHE* 4.4 1.6 - - - -
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Residues in contact with VAL 567 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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486U GLU* 4.1 12.6 - - - +
489U VAL* 2.1 39.2 - - + +
490U SER* 3.8 17.7 - - - +
494U PRO* 4.7 4.0 - - + -
502U VAL* 4.8 9.4 - - - +
566U THR* 1.3 70.3 - - - +
568U ARG* 1.3 59.7 + - - +
569U PRO 3.7 2.5 - - - -
587U VAL* 3.6 20.9 - - + +
588U GLY 3.3 6.5 - - - +
590U VAL* 5.4 0.2 - - - -
654U ASN* 5.3 1.7 - - - +
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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