Contacts of the strand formed by residues 587 - 598 (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 VAL 587 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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543E THR 5.5 1.0 + - - -
580E VAL* 3.7 22.2 - - + -
581E MET 3.5 2.7 - - - -
582E HIS* 3.1 37.0 - - + +
584E HIS 5.4 1.1 - - - +
585E THR 4.3 1.3 + - - +
586E ALA* 1.3 80.1 - - - +
588E GLU* 1.3 79.1 + - - +
648E GLN* 5.3 0.4 - - - +
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Residues in contact with GLU 588 (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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580E VAL* 4.6 3.8 - - - -
581E MET* 2.7 48.5 + - + +
586E ALA* 5.5 2.2 - - + -
587E VAL* 1.3 89.6 - - - +
589E GLU* 1.3 83.1 + - - +
590E VAL 3.6 0.2 + - - -
625E THR* 4.4 8.5 - - + -
626E GLN* 4.8 1.2 - - - +
627E THR* 3.0 29.4 + - - +
628E PRO 6.0 0.2 - - - -
629E VAL* 4.1 32.0 - - + +
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Residues in contact with GLU 589 (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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578E SER* 4.1 14.2 + - - -
579E CYS 3.7 6.5 - - - +
580E VAL* 4.6 4.7 - - + +
588E GLU* 1.3 82.9 - - - +
590E VAL* 1.3 62.9 + - - +
591E SER* 6.0 0.5 - - - -
625E THR* 3.8 19.8 - - - +
626E GLN* 2.2 51.5 + - + +
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Residues in contact with VAL 590 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
577E TYR 4.2 0.2 - - - +
578E SER* 3.2 3.1 + - - -
579E CYS* 2.6 64.7 + - - +
581E MET* 3.9 31.6 - - + -
588E GLU 3.6 0.2 + - - -
589E GLU* 1.3 78.3 + - - +
591E SER* 1.3 63.9 + - - +
592E PHE* 5.6 1.6 - - + -
623E LEU* 4.0 27.4 - - + -
624E GLU 3.4 14.8 - - - +
625E THR* 3.5 16.6 - - + -
645E LEU* 4.5 8.5 - - + -
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Residues in contact with SER 591 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
576E GLY 4.3 5.4 - - - -
577E TYR 3.1 13.0 - - - -
578E SER* 4.0 12.1 - - - -
589E GLU* 6.0 0.9 - - - -
590E VAL* 1.3 76.2 - - - +
592E PHE* 1.3 65.6 + - - +
623E LEU* 3.5 6.9 - - - +
624E GLU* 2.9 42.8 + - - +
626E GLN* 5.9 1.0 + - - -
399H MET* 6.4 0.4 - - - -
403H LYS* 4.8 13.3 + - - -
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Residues in contact with PHE 592 (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* 3.4 28.0 - - + -
566E ILE* 6.0 2.0 - - + -
573E LEU* 3.8 24.0 - - + -
575E THR* 2.1 47.0 - - - +
577E TYR* 2.8 49.2 + + + -
579E CYS* 4.8 4.5 - - - -
590E VAL* 5.6 1.6 - - + -
591E SER* 1.3 77.3 + - - +
593E ALA* 1.3 62.4 + - - +
594E LYS 4.9 1.3 - - - +
595E LEU* 5.2 4.3 - - + -
619E ILE* 5.1 3.8 - - + -
621E ALA* 3.9 16.2 - - + -
622E GLU 3.7 2.7 - - - -
623E LEU* 3.3 17.9 - - + -
645E LEU* 3.6 30.5 - - + -
653E ALA* 5.9 0.2 - - + -
403H LYS* 5.7 3.3 - - - +
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Residues in contact with ALA 593 (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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575E THR* 3.1 28.4 + - - +
591E SER 3.6 2.6 + - - -
592E PHE* 1.3 71.4 - - - +
594E LYS* 1.3 69.7 + - + +
622E GLU* 2.6 38.0 + - + +
624E GLU* 3.6 30.0 - - + +
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Residues in contact with LYS 594 (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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559E ARG* 5.4 1.2 - - - +
575E THR* 4.0 5.8 - - - -
592E PHE* 5.2 0.8 - - - -
593E ALA* 1.3 88.6 + - - +
595E LEU* 1.3 64.6 + - - +
596E LEU* 3.9 21.5 - - + +
621E ALA* 3.0 6.2 - - - +
622E GLU* 2.7 62.6 + - - +
624E GLU* 4.8 3.0 + - - -
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Residues in contact with LEU 595 (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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573E LEU* 4.0 11.4 - - + +
574E THR* 4.3 3.6 - - - -
575E THR* 3.4 35.0 + - - +
592E PHE* 5.2 4.0 - - + -
594E LYS* 1.3 77.5 - - - +
596E LEU* 1.3 63.2 + - - +
597E HIS 3.7 0.2 - - - -
609E PRO* 3.3 20.1 - - - +
610E PRO* 3.8 38.6 - - + +
611E MET 5.0 3.8 - - - +
612E PHE* 4.1 3.1 - - - -
613E ALA* 4.0 32.1 - - + +
619E ILE* 4.0 18.2 - - + -
620E ILE 4.3 0.2 - - - -
621E ALA* 3.9 5.8 - - + -
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Residues in contact with LEU 596 (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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561E ILE* 3.7 41.7 - - + -
594E LYS* 4.1 26.2 - - + -
595E LEU* 1.3 77.9 - - - +
597E HIS* 1.3 91.0 + - + +
609E PRO* 2.9 19.9 - - - +
620E ILE* 2.9 19.9 + - + +
621E ALA* 4.4 8.7 - - - -
622E GLU* 4.7 3.8 - - + +
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Residues in contact with HIS 597 (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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596E LEU* 1.3 103.2 + - + +
598E LYS* 1.3 68.3 + - - +
605E LYS* 3.3 43.6 - - + +
606E SER 3.5 17.9 - - - +
607E LYS* 4.2 11.9 - - + +
610E PRO* 3.1 12.9 - - - +
619E ILE* 3.1 13.0 - - - +
620E ILE* 3.1 43.8 + - + +
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Residues in contact with LYS 598 (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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597E HIS* 1.3 77.5 - - - +
599E LEU* 1.3 73.5 + - - +
600E ASP* 5.5 6.5 - - - +
604E ARG 3.2 1.7 - - - +
606E SER* 2.8 48.6 + - - +
610E PRO* 3.4 21.0 - - + +
612E PHE 6.0 0.2 - - - +
617E MET* 3.9 30.3 - - + -
618E LYS 3.6 16.8 - - - +
619E ILE* 4.2 0.7 - - - +
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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