Contacts of the strand formed by residues 556 - 566 (chain E) in PDB entry 3E20
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 ALA 556 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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502E MET* 4.2 12.4 - - + +
503E PRO* 3.6 31.0 - - + -
554E VAL 3.9 0.6 + - - -
555E HIS* 1.3 76.8 - - - +
557E THR* 1.3 68.4 + - - +
628E PRO* 4.6 2.7 - - + -
629E VAL 3.6 16.2 - - - +
630E CYS* 3.8 7.0 - - - -
631E MET* 4.5 0.9 - - - +
660E ILE* 4.5 1.1 - - - +
662E ASP* 3.1 14.7 - - - +
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Residues in contact with THR 557 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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556E ALA* 1.3 80.6 - - - +
558E THR* 1.3 69.5 + - - +
559E ARG 2.8 31.8 + - - +
560E PHE* 4.5 0.8 - - + -
625E THR* 3.7 3.8 + - - -
628E PRO* 3.3 6.9 - - - +
629E VAL* 3.0 25.1 + - - +
631E MET* 3.9 31.0 - - + +
660E ILE* 3.7 15.9 - - + -
661E LEU 3.2 13.3 + - - -
662E ASP* 3.7 11.9 + - - -
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Residues in contact with THR 558 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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557E THR* 1.3 75.9 + - - +
559E ARG* 1.3 72.0 + - - +
560E PHE* 4.3 2.9 - - - -
623E LEU 3.4 0.8 - - - +
624E GLU* 2.9 12.5 - - - +
625E THR* 2.9 51.6 + - - +
626E GLN 4.7 1.6 - - - +
627E THR* 3.4 27.1 - - - -
628E PRO* 3.4 11.4 - - + -
662E ASP* 5.4 0.4 + - - -
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Residues in contact with ARG 559 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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557E THR* 2.8 18.9 + - - +
558E THR* 1.3 93.5 + - - +
560E PHE* 1.3 63.1 + - - +
594E LYS* 5.4 1.2 - - - +
622E GLU* 2.9 27.2 + - - +
623E LEU 3.3 2.9 - - - -
624E GLU* 3.5 37.5 + - + +
661E LEU* 2.9 44.5 + - + +
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Residues in contact with PHE 560 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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557E THR* 4.4 3.4 - - + -
558E THR* 4.9 1.3 - - - -
559E ARG* 1.3 80.0 - - - +
561E ILE* 1.3 63.9 + - - +
562E ALA* 4.1 5.8 - - + -
581E MET* 3.0 36.6 - - + -
590E VAL* 4.7 0.2 - - + -
621E ALA 4.1 0.2 - - - +
622E GLU* 3.4 3.8 - - - +
623E LEU* 2.8 67.4 + - + +
625E THR* 4.4 16.8 - - + -
631E MET* 3.6 41.1 - - + -
643E PHE* 3.8 14.8 - + - -
657E VAL* 4.1 11.9 - - + -
659E LYS 3.3 15.0 - - - +
660E ILE* 4.4 4.5 - - + -
661E LEU* 4.2 3.9 - - - +
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Residues in contact with ILE 561 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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560E PHE* 1.3 76.2 - - - +
562E ALA* 1.3 56.6 + - - +
596E LEU* 3.7 27.8 - - + -
620E ILE* 4.1 12.8 - - + -
621E ALA 3.2 17.3 - - - +
622E GLU* 4.2 8.7 - - + +
657E VAL* 3.7 1.6 - - - +
658E VAL* 2.7 46.9 + - + +
659E LYS* 2.8 25.4 + - + +
661E LEU* 4.2 30.1 - - + -
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Residues in contact with ALA 562 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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560E PHE* 4.1 8.5 + - + -
561E ILE* 1.3 77.0 - - - +
563E GLN* 1.3 67.0 + - - +
564E ILE* 3.7 7.9 + - + +
620E ILE* 3.5 3.5 - - - -
621E ALA 3.1 29.8 + - - +
623E LEU* 4.9 2.9 - - + +
643E PHE* 3.7 20.2 - - + -
656E LYS 3.1 19.5 - - - +
657E VAL* 3.7 9.2 - - - -
658E VAL* 3.8 4.7 - - - -
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Residues in contact with GLN 563 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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562E ALA* 1.3 74.3 - - - +
564E ILE* 1.3 66.8 + - - +
599E LEU* 3.7 28.8 - - + +
603E ASN* 4.2 17.5 + - - +
618E LYS* 6.1 4.8 - - + +
619E ILE 3.8 4.0 - - - -
620E ILE* 4.3 17.3 - - + -
655E GLY* 3.2 19.5 - - - -
656E LYS* 3.1 43.0 + - + +
658E VAL* 4.4 9.9 - - + +
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Residues in contact with ILE 564 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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562E ALA 3.7 10.3 - - - +
563E GLN* 1.3 83.9 - - - +
565E ALA* 1.3 61.3 + - - +
566E ILE* 3.5 13.0 + - + -
592E PHE* 3.4 35.2 - - + -
599E LEU* 5.7 0.2 - - - +
618E LYS* 3.7 3.2 - - - +
619E ILE* 2.8 45.0 + - + +
621E ALA* 5.0 3.8 - - + +
623E LEU* 3.9 23.6 - - + -
643E PHE* 4.3 8.5 - - + -
645E LEU* 4.0 6.7 - - + -
653E ALA* 3.5 22.9 - - + -
654E VAL 3.4 11.7 - - - +
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Residues in contact with ALA 565 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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564E ILE* 1.3 72.5 - - - +
566E ILE* 1.3 65.5 + - - +
567E LEU* 3.1 8.4 - - + +
617E MET 4.3 3.8 - - - -
618E LYS* 4.6 16.4 - - + +
653E ALA* 3.2 1.0 - - - -
654E VAL* 2.9 46.7 + - + +
655E GLY* 4.6 0.6 - - - -
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Residues in contact with ILE 566 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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564E ILE* 3.8 12.8 - - + +
565E ALA* 1.3 73.5 - - - +
567E LEU* 1.3 64.7 + - - +
569E LEU* 3.8 28.7 - - + -
573E LEU* 4.8 10.8 - - + -
592E PHE* 6.0 1.6 - - + -
613E ALA* 4.3 15.0 - - + -
614E THR 3.4 28.7 - - - +
615E LYS* 3.4 13.5 - - - -
616E GLY* 2.9 23.9 + - - -
617E MET 3.4 10.3 + - - +
619E ILE* 3.1 35.9 - - + -
652E VAL 3.7 2.7 - - - -
653E ALA* 3.9 7.0 - - + -
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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