Contacts of the helix formed by residues 594 - 610 (chain C) in PDB entry 4IVE
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 SER 594 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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590C TYR* 3.0 31.0 + - - -
591C MSE 3.1 9.5 + - - +
592C LEU 3.6 0.4 - - - -
593C GLU* 1.3 80.7 - - - +
595C PRO* 1.4 66.6 - - - +
596C GLU* 3.2 7.2 + - - +
597C SER* 3.2 28.2 + - - -
598C LEU 3.0 18.4 + - - -
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Residues in contact with PRO 595 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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568C MSE 4.8 3.7 - - + +
591C MSE 4.7 0.7 - - - +
592C LEU 5.7 1.8 - - - +
593C GLU 3.8 7.0 - - - +
594C SER* 1.4 84.7 - - - +
596C GLU* 1.3 67.3 + - + +
598C LEU* 3.5 9.7 + - + +
599C ARG* 3.0 30.2 + - - +
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Residues in contact with GLU 596 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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594C SER* 3.2 6.0 - - - +
595C PRO* 1.3 86.6 - - + +
597C SER* 1.4 58.0 + - - +
599C ARG* 3.4 9.7 + - - +
600C SER* 3.1 27.0 + - - -
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Residues in contact with SER 597 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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587C GLU* 5.4 1.6 - - - -
590C TYR* 3.4 22.3 - - - -
591C MSE 3.6 15.5 - - - +
594C SER* 3.1 31.9 + - - -
596C GLU* 1.4 74.7 - - - +
598C LEU* 1.4 64.7 + - - +
600C SER* 3.0 20.4 + - - -
601C LYS* 3.2 17.0 + - - +
612D HIS* 5.6 4.3 - - - -
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Residues in contact with LEU 598 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
561C LEU* 3.7 27.4 - - + -
564C LEU* 3.8 40.2 - - + -
565C ILE* 4.2 5.6 - - + -
568C MSE 3.9 17.0 - - + -
580C LEU* 4.2 4.0 - - + -
591C MSE 3.5 39.7 - - + +
592C LEU* 5.4 0.2 - - + -
594C SER 3.0 9.9 + - - +
595C PRO* 3.8 7.2 - - + +
597C SER* 1.4 75.6 + - - +
599C ARG* 1.3 58.3 + - - +
601C LYS* 3.2 2.9 + - - +
602C VAL* 2.9 45.7 + - + +
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Residues in contact with ARG 599 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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568C MSE 3.7 52.2 + - + +
569C HIS* 5.4 4.6 + - - -
595C PRO 3.0 17.8 + - - +
596C GLU* 3.5 8.7 - - - +
597C SER 3.3 0.2 - - - -
598C LEU* 1.3 76.3 - - - +
600C SER* 1.3 57.1 + - - +
602C VAL* 3.3 1.9 + - - +
603C ASP* 3.0 55.3 + - - +
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Residues in contact with SER 600 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596C GLU 3.1 13.5 + - - -
597C SER* 3.0 18.7 + - - -
599C ARG* 1.3 76.8 - - - +
601C LYS* 1.3 59.5 + - - +
603C ASP* 3.5 10.5 + - - +
604C GLU* 3.1 34.1 + - - +
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Residues in contact with LYS 601 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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580C LEU* 3.8 10.6 - - + +
583C ILE* 4.2 7.4 - - + -
587C GLU* 4.8 9.0 - - - +
591C MSE 3.7 35.2 - - + -
597C SER* 3.2 15.1 + - - +
598C LEU 3.6 6.7 - - - +
600C SER* 1.3 73.3 - - - +
602C VAL* 1.3 61.6 + - - +
604C GLU* 3.3 19.6 + - - +
605C ALA* 2.9 28.8 + - - +
607D ALA 3.1 13.9 + - - -
608D VAL* 2.8 28.2 + - + +
610D GLN 2.7 28.9 + - - -
611D ALA* 5.4 1.6 - - - +
612D HIS* 5.5 0.9 - - - +
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Residues in contact with VAL 602 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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565C ILE* 3.8 28.9 - - + -
568C MSE 3.8 22.0 - - + -
569C HIS* 3.5 32.8 - - + +
576C ILE* 4.2 18.8 - - + -
580C LEU* 4.0 6.3 - - + -
598C LEU* 2.9 28.4 + - + +
599C ARG 3.6 4.9 - - - +
601C LYS* 1.3 76.3 - - - +
603C ASP* 1.4 57.3 + - - +
605C ALA* 3.1 3.8 + - - +
606C VAL* 2.9 32.1 + - - +
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Residues in contact with ASP 603 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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569C HIS* 4.4 12.1 + - - -
599C ARG* 3.0 46.2 + - - +
600C SER* 3.6 8.5 - - - +
602C VAL* 1.4 77.0 - - - +
604C GLU* 1.3 57.3 + - + +
606C VAL* 3.4 9.1 + - - +
607C ALA* 3.1 27.2 + - - +
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Residues in contact with GLU 604 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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600C SER* 3.1 18.7 + - - +
601C LYS* 3.3 40.7 + - - +
603C ASP* 1.3 75.4 - - - +
605C ALA* 1.4 62.2 + - - +
607C ALA* 3.3 8.7 + - - +
608C VAL* 3.2 24.9 + - - +
604D GLU* 5.2 1.7 - - - +
607D ALA* 3.5 32.9 - - + +
608D VAL* 3.8 12.7 - - + +
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Residues in contact with ALA 605 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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576C ILE* 3.8 25.4 - - + -
579C MSE 3.8 23.0 - - + +
580C LEU* 3.9 13.9 - - + -
601C LYS 2.9 14.0 + - - +
602C VAL 3.4 7.9 - - - +
604C GLU* 1.4 72.0 - - - +
606C VAL* 1.4 64.9 + - - +
608C VAL* 3.1 6.5 + - - +
609C LEU* 3.1 27.8 + - - +
608D VAL* 4.1 2.4 - - - +
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Residues in contact with VAL 606 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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569C HIS* 3.7 36.1 - - + +
572C LEU* 4.7 12.9 - - + +
576C ILE* 3.7 20.2 - - + -
602C VAL 2.9 19.2 + - - +
603C ASP* 3.5 11.9 - - - +
605C ALA* 1.4 74.6 - - - +
607C ALA* 1.4 62.7 + - - +
609C LEU* 3.3 11.0 + - - +
610C GLN* 3.1 22.7 + - + +
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Residues in contact with ALA 607 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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603C ASP 3.1 13.3 + - - +
604C GLU* 3.5 11.7 - - - +
605C ALA 3.3 0.4 - - - -
606C VAL* 1.4 74.5 - - - +
608C VAL* 1.4 54.2 + - - +
610C GLN* 3.4 20.9 + - - +
601D LYS* 2.8 27.7 + - - -
604D GLU* 3.4 19.4 - - + +
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Residues in contact with VAL 608 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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579C MSE 3.8 25.6 - - + -
604C GLU 3.2 15.8 + - - +
605C ALA 3.1 8.6 + - - +
607C ALA* 1.4 75.0 - - - +
609C LEU* 1.3 59.0 + - - +
580D LEU* 3.7 29.6 - - + -
583D ILE* 3.4 11.4 - - + +
601D LYS* 3.1 28.2 + - + +
604D GLU* 3.6 40.8 - - + -
605D ALA* 4.0 2.2 - - + +
608D VAL* 3.9 11.4 - - + -
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Residues in contact with LEU 609 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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572C LEU* 4.2 24.2 - - + -
575C LYS* 3.9 23.6 - - + +
576C ILE* 3.8 28.7 - - + -
579C MSE 3.7 21.1 - - + -
605C ALA 3.1 15.7 + - - +
606C VAL* 3.3 7.8 + - - +
608C VAL* 1.3 74.7 - - - +
610C GLN* 1.4 62.1 + - - +
611C ALA* 3.4 3.8 + - - +
582D GLU* 3.7 31.4 - - + +
583D ILE* 3.9 22.6 - - + +
584D ASP 5.5 0.7 + - - -
587D GLU* 5.2 0.3 - - - +
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Residues in contact with GLN 610 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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606C VAL* 3.1 14.0 + - + +
607C ALA* 3.5 20.6 - - - +
608C VAL 3.4 0.6 - - - -
609C LEU* 1.4 73.8 - - - +
611C ALA* 1.3 72.5 + - - +
613C GLN 5.6 0.9 - - - +
587D GLU* 4.6 0.7 - - - +
601D LYS* 2.8 32.1 + - - -
604D GLU* 5.7 0.5 - - - +
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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