Contacts of the helix formed by residues 592 - 607 (chain J) in PDB entry 4E2I
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 ILE 592 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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362J THR* 4.1 12.6 - - + +
365J PHE* 3.7 32.3 - - + -
366J ASN* 3.4 31.6 - - - +
369J LEU* 4.5 4.0 - - + -
588J PHE* 3.6 12.8 - - + -
589J ALA* 3.0 40.2 + - + +
591J SER* 1.3 80.0 - - - +
593J GLN* 1.3 58.4 + - - +
594J SER 3.0 2.7 - - - -
595J ARG* 2.8 28.8 + - + +
596J ILE* 3.0 25.1 + - + +
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Residues in contact with GLN 593 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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585J VAL* 3.1 43.4 - - + +
586J ALA* 4.3 8.4 + - - +
588J PHE* 3.6 9.8 + - + +
589J ALA 2.9 18.1 + - - +
590J GLN* 3.1 40.4 + - - +
591J SER 3.7 0.2 - - - -
592J ILE* 1.3 78.0 - - - +
594J SER* 1.3 58.1 + - - +
596J ILE* 3.8 3.8 - - - -
597J VAL* 3.1 31.2 + - - +
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Residues in contact with SER 594 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
590J GLN 5.0 2.3 + - - -
591J SER 5.6 4.5 - - - -
592J ILE 3.0 1.2 - - - +
593J GLN* 1.3 80.1 - - - +
595J ARG* 1.3 58.8 + - - +
597J VAL* 4.1 6.2 + - - +
598J GLU* 3.1 28.2 + - - +
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Residues in contact with ARG 595 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366J ASN* 3.2 41.6 + - - +
369J LEU* 3.2 28.4 - - + +
370J ASP* 3.1 36.7 + - - +
373J ASP* 2.8 28.3 + - - -
592J ILE* 2.8 16.6 + - + +
594J SER* 1.3 79.0 - - - +
596J ILE* 1.3 65.1 + - - +
597J VAL 3.3 0.7 - - - -
598J GLU* 3.1 35.6 - - - +
599J TRP* 3.6 15.4 + - + +
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Residues in contact with ILE 596 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365J PHE* 5.6 1.3 - - + -
369J LEU* 4.7 8.3 - - + -
576J LEU* 6.0 0.4 - - + -
580J ILE* 3.6 24.9 - - + +
585J VAL* 4.1 7.6 - - + -
588J PHE* 3.4 59.9 - - + -
592J ILE* 3.0 35.2 + - + +
593J GLN* 3.8 6.5 - - - +
594J SER 3.5 0.2 - - - -
595J ARG* 1.3 78.8 - - - +
597J VAL* 1.3 61.7 + - - +
598J GLU 3.3 0.3 + - - -
599J TRP* 3.4 2.5 + - - -
600J LYS* 3.2 39.7 + - - +
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Residues in contact with VAL 597 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
585J VAL* 3.7 22.9 - - + -
593J GLN 3.1 18.4 + - - +
594J SER* 4.3 7.0 - - - +
595J ARG 3.3 0.4 - - - -
596J ILE* 1.3 73.4 - - - +
598J GLU* 1.3 66.0 + - - +
600J LYS* 3.1 21.2 + - + +
601J GLU* 3.1 29.5 + - + +
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Residues in contact with GLU 598 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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594J SER* 3.1 17.7 + - - +
595J ARG* 3.1 36.2 - - - +
596J ILE 3.1 0.6 - - - -
597J VAL* 1.3 79.1 - - - +
599J TRP* 1.3 67.8 + - + +
601J GLU* 3.3 22.8 + - - +
602J ARG* 3.4 10.9 + - - +
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Residues in contact with TRP 599 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369J LEU* 3.8 28.1 - - + +
372J MET* 3.6 47.6 - - + -
373J ASP* 3.2 33.1 + - - -
376J PHE* 3.9 19.7 - + + -
384J ILE* 5.1 4.5 - - + -
577J LEU* 4.9 0.2 - - + -
580J ILE* 4.1 21.1 - - + -
595J ARG* 3.6 20.3 - - + +
596J ILE 3.4 2.2 + - - +
598J GLU* 1.3 78.8 + - + +
600J LYS* 1.3 56.7 + - - +
601J GLU 2.9 5.6 - - - -
602J ARG* 3.6 30.5 - - + -
603J LEU* 2.9 58.8 + - + +
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Residues in contact with LYS 600 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
580J ILE* 2.7 36.6 + - + +
581J TRP 4.2 7.9 + - - -
582J TYR 4.6 1.2 + - - -
583J ARG 3.2 24.2 + - - -
584J PRO* 4.2 2.5 - - - +
585J VAL* 3.4 36.3 - - + +
596J ILE* 3.2 25.5 + - - +
597J VAL* 3.1 16.5 + - + +
599J TRP* 1.3 77.5 - - - +
601J GLU* 1.3 58.5 + - + +
603J LEU* 5.0 3.1 - - - -
604J ASP* 2.6 35.2 - - - +
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Residues in contact with GLU 601 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597J VAL* 3.1 28.9 - - + +
598J GLU* 3.5 16.2 - - - +
599J TRP 2.9 0.6 - - - -
600J LYS* 1.3 81.1 - - + +
602J ARG* 1.3 60.1 + - - +
603J LEU 3.4 0.2 - - - -
604J ASP* 4.0 3.2 - - - +
605J LYS* 3.0 30.1 + - - +
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Residues in contact with ARG 602 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376J PHE* 3.5 31.9 + - - +
384J ILE* 4.6 17.1 - - + +
598J GLU 3.4 9.6 + - - +
599J TRP* 3.2 41.1 + - + +
601J GLU* 1.3 77.7 - - - +
603J LEU* 1.3 66.7 + - + +
605J LYS* 3.2 14.7 + - - +
606J GLU* 3.0 54.9 + - + +
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Residues in contact with LEU 603 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384J ILE* 4.9 8.3 - - + -
388J MET* 3.7 16.4 - - + -
577J LEU* 3.6 35.2 - - + +
580J ILE* 5.0 6.7 - - + -
581J TRP* 3.6 37.4 - - + +
599J TRP* 2.9 57.2 + - + +
600J LYS* 5.0 2.5 - - - -
602J ARG* 1.3 81.4 - - + +
604J ASP* 1.3 58.2 + - - +
606J GLU* 4.1 3.5 - - - +
607J PHE* 2.8 36.1 + - - +
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Residues in contact with ASP 604 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
581J TRP* 5.1 9.6 - - - -
600J LYS* 2.6 29.1 + - - +
601J GLU* 3.7 4.4 + - - +
602J ARG 3.4 0.2 - - - -
603J LEU* 1.3 80.3 - - - +
605J LYS* 1.3 60.5 + - - +
607J PHE 3.3 18.5 - - - +
608J SER* 4.4 4.9 + - - -
609J LEU* 4.4 18.0 - - - +
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Residues in contact with LYS 605 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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601J GLU 3.0 20.6 + - - +
602J ARG* 3.4 15.3 - - - +
603J LEU 3.1 0.2 - - - -
604J ASP* 1.3 80.1 - - - +
606J GLU* 1.3 72.7 + - - +
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Residues in contact with GLU 606 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384J ILE* 4.6 14.9 - - + +
602J ARG* 3.0 48.0 + - + +
603J LEU* 4.1 2.2 - - - +
605J LYS* 1.3 92.0 - - + +
607J PHE* 1.3 83.6 + - + +
608J SER 4.3 0.2 - - - -
611J VAL* 5.5 2.6 - - - +
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Residues in contact with PHE 607 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384J ILE* 4.1 13.7 - - + -
385J GLU* 3.4 53.2 - - + -
388J MET* 4.2 16.8 - - + -
581J TRP* 3.8 20.1 - - + -
603J LEU* 2.8 26.5 + - - +
604J ASP* 3.3 15.8 - - - +
605J LYS 5.2 0.2 - - - -
606J GLU* 1.3 98.0 - - + +
608J SER* 1.3 65.6 + - - +
611J VAL* 3.5 33.7 - - + -
612J TYR* 5.1 1.3 - - + +
615J MET* 4.2 20.6 - - + -
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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