Contacts of the strand formed by residues 647 - 654 (chain A) in PDB entry 3S3J
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 GLU 647 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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608A SER* 4.0 17.9 + - - -
609A LEU 3.5 13.7 - - - +
610A GLN* 4.1 24.3 + - + +
642A VAL* 4.2 0.7 - - - +
645A GLY 4.0 1.8 + - - -
646A GLU* 1.3 105.2 + - - +
648A VAL* 1.3 76.4 + - - +
649A LYS* 3.0 32.6 - - + -
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Residues in contact with VAL 648 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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607A VAL 3.7 0.9 - - - +
608A SER* 3.1 21.1 - - - -
609A LEU* 3.0 25.5 + - + +
620A CYS* 5.7 0.4 - - + -
622A PHE* 4.0 22.2 - - + -
638A ILE* 3.4 33.9 - - + -
642A VAL* 4.1 25.8 - - + -
647A GLU* 1.3 84.0 - - - +
649A LYS* 1.3 64.4 + - - +
668A PHE* 4.7 4.9 - - + -
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Residues in contact with LYS 649 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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592A ARG* 5.9 1.0 - - - +
606A GLU* 3.1 39.1 + - + +
607A VAL 3.5 2.9 - - - +
608A SER* 3.5 21.1 + - - -
622A PHE* 5.6 0.2 - - - -
638A ILE* 5.2 0.5 - - - +
647A GLU* 3.0 26.0 - - + +
648A VAL* 1.3 76.9 - - - +
650A VAL* 1.3 71.1 + - - +
651A ARG* 4.3 19.7 - - - +
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Residues in contact with VAL 650 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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607A VAL* 2.9 53.4 + - + +
622A PHE* 4.1 17.0 - - + -
624A VAL* 5.9 0.9 - - + -
636A VAL* 3.8 44.0 - - + -
638A ILE* 4.1 19.3 - - + -
649A LYS* 1.3 81.6 - - - +
651A ARG* 1.3 72.3 + - - +
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Residues in contact with ARG 651 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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594A LEU* 5.6 4.0 - - + +
604A VAL* 4.1 17.5 - - + -
605A ALA 3.0 11.0 - - - +
606A GLU* 2.8 41.7 + - + +
607A VAL* 5.1 0.7 - - - -
636A VAL* 5.8 2.1 - - - +
649A LYS* 4.3 20.0 - - - +
650A VAL* 1.3 89.1 - - - +
652A MET* 1.3 61.6 + - - +
653A ASP* 5.1 0.5 - - - +
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Residues in contact with MET 652 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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604A VAL* 4.4 3.1 - - - -
605A ALA* 2.7 41.7 + - + +
607A VAL* 5.7 2.0 - - + +
624A VAL* 5.2 14.1 - - + -
634A LYS* 4.8 18.8 - - + -
651A ARG* 1.3 76.2 - - - +
653A ASP* 1.3 67.3 + - - +
654A LEU* 3.4 19.0 - - + +
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Residues in contact with ASP 653 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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603A LEU 3.6 6.5 - - - +
604A VAL* 4.5 10.0 - - + +
630A THR* 5.0 3.5 - - - -
651A ARG 4.4 0.7 - - - +
652A MET* 1.3 72.1 - - - +
654A LEU* 1.3 69.1 + - - +
655A LEU* 4.1 10.8 - - + +
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Residues in contact with LEU 654 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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593A ILE* 5.8 5.6 - - + -
602A LYS* 4.0 5.0 - - - +
603A LEU* 2.7 40.6 + - + +
604A VAL 4.9 1.3 - - - -
605A ALA* 3.6 24.2 - - + +
624A VAL* 5.5 0.7 - - + -
629A LEU* 4.0 23.1 - - + +
630A THR* 4.3 22.9 - - + -
652A MET* 3.4 26.0 - - + +
653A ASP* 1.3 84.3 - - - +
655A LEU* 1.3 70.2 + - - +
656A PRO* 3.8 4.0 - - + -
664A LEU* 3.8 24.2 - - + -
682A VAL* 6.1 1.3 - - + -
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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