Contacts of the helix formed by residues 594 - 610 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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590D TYR* 3.0 33.2 + - - -
591D MSE 3.3 10.2 + - - +
592D LEU 3.6 0.2 - - - -
593D GLU* 1.3 78.3 - - - +
595D PRO* 1.4 65.5 - - - +
596D GLU* 4.2 2.9 + - - +
597D SER* 3.2 28.2 + - - -
598D LEU 3.0 17.7 + - - -
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Residues in contact with PRO 595 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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568D MSE 3.8 11.9 - - + +
591D MSE 5.0 0.2 - - - +
593D GLU 3.6 7.9 - - - +
594D SER* 1.4 85.3 - - - +
596D GLU* 1.3 70.1 + - + +
598D LEU* 3.5 6.6 + - + +
599D ARG* 2.9 34.8 + - - +
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Residues in contact with GLU 596 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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594D SER* 3.3 2.8 + - - +
595D PRO* 1.3 81.9 - - + +
597D SER* 1.4 61.1 + - - +
599D ARG* 3.1 42.9 + - - +
600D SER* 3.1 28.1 + - - -
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Residues in contact with SER 597 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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612C HIS* 5.0 3.9 - - - +
587D GLU* 5.4 1.6 - - - -
590D TYR* 3.3 30.6 + - - -
591D MSE 4.5 7.6 - - - -
594D SER* 3.2 24.3 + - - -
596D GLU* 1.4 72.9 - - - +
598D LEU* 1.3 64.4 + - - +
600D SER* 3.0 20.7 + - - -
601D LYS* 3.1 19.1 + - - +
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Residues in contact with LEU 598 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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561D LEU* 4.5 12.6 - - + +
564D LEU* 3.7 43.1 - - + -
565D ILE* 4.1 9.4 - - + -
568D MSE 4.2 15.0 - - + -
580D LEU* 3.9 13.7 - - + -
591D MSE 3.6 49.4 - - + +
594D SER 3.0 8.6 + - - +
595D PRO* 3.8 6.3 - - + +
597D SER* 1.3 76.1 - - - +
599D ARG* 1.3 56.4 + - - +
601D LYS* 3.2 2.4 + - - +
602D VAL* 2.9 40.6 + - + +
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Residues in contact with ARG 599 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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568D MSE 3.4 52.6 - - + +
595D PRO* 2.9 21.0 + - - +
596D GLU* 3.1 39.5 + - - +
597D SER 3.3 0.2 - - - -
598D LEU* 1.3 75.9 - - - +
600D SER* 1.3 58.0 + - - +
602D VAL* 3.3 2.6 + - - +
603D ASP* 3.0 47.7 + - - +
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Residues in contact with SER 600 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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596D GLU 3.1 14.3 + - - -
597D SER* 3.0 17.8 + - - -
599D ARG* 1.3 75.5 - - - +
601D LYS* 1.3 61.4 + - - +
603D ASP* 3.5 10.6 + - - +
604D GLU* 3.0 37.2 + - - +
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Residues in contact with LYS 601 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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607C ALA 2.8 27.7 + - - -
608C VAL* 3.1 20.9 + - - +
610C GLN* 2.8 26.5 + - - +
611C ALA 5.8 0.4 - - - -
580D LEU* 3.8 14.4 - - + +
583D ILE* 4.5 2.7 - - + -
587D GLU* 4.7 11.4 - - - -
591D MSE 3.9 30.5 - - + -
597D SER* 3.1 19.8 + - - +
598D LEU 3.2 6.5 + - - +
600D SER* 1.3 76.9 + - - +
602D VAL* 1.4 57.9 + - - +
604D GLU* 3.3 17.1 + - - +
605D ALA* 2.9 28.8 + - - +
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Residues in contact with VAL 602 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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565D ILE* 3.8 35.4 - - + -
568D MSE 4.1 15.5 - - + -
569D HIS* 3.7 29.8 - - + -
576D ILE* 4.1 23.3 - - + -
580D LEU* 3.9 9.4 - - + -
598D LEU* 2.9 24.6 + - + +
599D ARG 3.6 6.1 - - - +
601D LYS* 1.4 74.2 - - - +
603D ASP* 1.3 57.0 + - - +
605D ALA* 3.2 3.8 + - - +
606D VAL* 2.9 32.9 + - - +
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Residues in contact with ASP 603 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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569D HIS* 4.0 19.6 + - - -
599D ARG* 3.0 36.0 + - - +
600D SER* 3.6 9.1 - - - +
602D VAL* 1.3 75.1 - - - +
604D GLU* 1.3 57.7 + - + +
606D VAL* 3.4 10.0 + - - +
607D ALA* 3.1 27.0 + - - +
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Residues in contact with GLU 604 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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604C GLU* 5.2 1.0 - - - +
607C ALA* 3.4 25.0 - - + +
608C VAL* 3.6 15.0 - - + -
610C GLN* 5.7 0.3 - - - +
600D SER* 3.0 24.2 + - - +
601D LYS* 3.3 40.6 + - - +
603D ASP* 1.3 75.9 - - + +
605D ALA* 1.4 61.1 + - - +
607D ALA* 3.3 9.1 + - - +
608D VAL* 3.1 24.9 + - - +
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Residues in contact with ALA 605 (chain D).
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 5.9 0.2 - - - -
608C VAL* 4.0 5.3 - - + +
576D ILE* 3.8 22.9 - - + -
579D MSE 3.7 18.6 - - + +
580D LEU* 4.1 11.7 - - + -
601D LYS 2.9 14.3 + - - +
602D VAL 3.2 8.3 + - - +
604D GLU* 1.4 71.5 - - - +
606D VAL* 1.4 65.0 + - - +
608D VAL* 3.1 12.9 + - - +
609D LEU* 3.1 27.2 + - - +
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Residues in contact with VAL 606 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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569D HIS* 4.6 16.4 - - + +
572D LEU* 4.6 16.2 - - + -
576D ILE* 3.7 22.2 - - + -
602D VAL* 2.9 25.4 + - + +
603D ASP* 3.5 11.9 - - - +
605D ALA* 1.4 74.8 - - - +
607D ALA* 1.4 61.6 + - - +
609D LEU* 3.2 21.2 + - - +
610D GLN* 3.2 15.0 + - + +
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Residues in contact with ALA 607 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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601C LYS* 3.1 14.9 + - - -
604C GLU* 3.5 20.6 - - - +
603D ASP 3.1 13.6 + - - +
604D GLU* 3.3 12.5 + - - +
606D VAL* 1.4 74.1 - - - +
608D VAL* 1.4 62.4 + - - +
610D GLN* 3.3 16.1 + - - +
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Residues in contact with VAL 608 (chain D).
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 4.7 5.4 - - - +
580C LEU* 3.8 29.2 - - + -
583C ILE* 3.4 16.0 - - + +
601C LYS* 2.8 25.4 + - + +
604C GLU* 3.8 29.4 - - + -
605C ALA* 4.1 1.6 - - - +
608C VAL* 3.9 18.8 - - + -
579D MSE 3.6 19.5 - - + -
604D GLU 3.1 16.9 + - - +
605D ALA* 3.1 8.3 + - - +
607D ALA* 1.4 75.7 - - - +
609D LEU* 1.3 56.2 + - - +
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Residues in contact with LEU 609 (chain D).
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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582C GLU* 3.6 31.4 - - + +
583C ILE* 4.1 16.5 - - + +
584C ASP* 5.1 6.8 + - - +
572D LEU* 4.5 22.2 - - + -
575D LYS* 4.1 18.4 - - + -
576D ILE* 4.3 16.6 - - + -
579D MSE 3.7 34.5 - - + -
605D ALA 3.1 15.0 + - - +
606D VAL* 3.2 9.1 + - - +
608D VAL* 1.3 73.5 - - - +
610D GLN* 1.3 63.9 + - - +
611D ALA* 3.4 4.3 + - - +
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Residues in contact with GLN 610 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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583C ILE* 6.2 0.2 - - - -
587C GLU* 5.4 0.7 - - - -
601C LYS* 2.7 28.4 + - - -
606D VAL* 3.2 14.4 + - + +
607D ALA* 3.3 16.2 + - - +
609D LEU* 1.3 73.5 - - - +
611D ALA* 1.3 87.1 + - - +
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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