Contacts of the helix formed by residues 592 - 607 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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362D THR* 4.1 11.0 - - + +
365D PHE* 3.7 33.0 - - + -
366D ASN* 3.4 33.0 - - - +
369D LEU* 4.5 4.3 - - + -
588D PHE* 3.6 13.0 - - + -
589D ALA* 3.0 39.7 + - + +
591D SER* 1.3 80.8 + - - +
593D GLN* 1.3 58.6 + - - +
594D SER* 3.0 2.9 - - - -
595D ARG* 2.8 28.1 + - + +
596D ILE* 3.0 24.2 + - + +
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Residues in contact with GLN 593 (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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585D VAL* 3.1 44.5 + - + +
586D ALA* 4.3 8.7 + - - +
588D PHE 3.6 9.2 + - - +
589D ALA 2.9 18.0 + - - +
590D GLN* 3.1 40.9 - - - +
591D SER 3.7 0.4 - - - -
592D ILE* 1.3 79.0 - - - +
594D SER* 1.3 57.4 + - - +
596D ILE* 4.0 3.4 - - - -
597D VAL* 3.1 31.1 + - - +
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Residues in contact with SER 594 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
590D GLN 5.0 2.9 + - - -
591D SER 5.5 4.5 - - - -
592D ILE 3.0 1.5 - - - -
593D GLN* 1.3 77.2 - - - +
595D ARG* 1.3 57.8 + - - +
597D VAL* 4.1 7.1 + - - +
598D GLU* 3.1 27.6 + - - +
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Residues in contact with ARG 595 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366D ASN* 3.2 41.0 + - - +
369D LEU* 3.2 28.4 - - + +
370D ASP* 3.1 37.0 + - - +
373D ASP* 2.8 28.1 + - - -
591D SER 5.9 0.2 - - - +
592D ILE* 2.8 16.8 + - + +
594D SER* 1.3 78.8 - - - +
596D ILE* 1.3 65.1 + - - +
597D VAL 3.3 0.2 - - - -
598D GLU* 3.1 35.8 - - - +
599D TRP* 3.6 14.8 + - + +
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Residues in contact with ILE 596 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365D PHE* 5.6 1.3 - - + -
369D LEU* 4.8 8.5 - - + -
576D LEU* 6.0 0.9 - - + -
580D ILE* 3.6 23.6 - - + +
585D VAL* 4.0 7.2 - - + -
588D PHE* 3.4 60.8 - - + -
592D ILE* 3.0 34.5 + - + +
593D GLN* 3.8 7.2 - - - +
594D SER 3.5 0.2 - - - -
595D ARG* 1.3 79.1 - - - +
597D VAL* 1.3 62.0 + - - +
598D GLU 3.3 0.3 + - - -
599D TRP 3.4 2.9 + - - -
600D LYS* 3.2 43.9 + - - +
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Residues in contact with VAL 597 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
585D VAL* 3.7 23.3 - - + -
593D GLN 3.1 18.3 + - - +
594D SER* 4.3 7.2 - - - +
595D ARG 3.3 0.2 - - - -
596D ILE* 1.3 74.4 - - - +
598D GLU* 1.3 65.5 + - - +
600D LYS* 3.1 20.9 + - + +
601D GLU* 3.1 29.4 + - + +
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Residues in contact with GLU 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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594D SER* 3.1 18.9 + - - +
595D ARG* 3.1 34.1 - - - +
596D ILE 3.1 0.4 - - - -
597D VAL* 1.3 79.9 - - + +
599D TRP* 1.3 68.9 + - + +
601D GLU* 3.3 23.0 + - - +
602D ARG* 3.3 10.6 + - - +
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Residues in contact with TRP 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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369D LEU* 3.8 28.5 - - + +
372D MET* 3.6 47.8 - - + -
373D ASP* 3.2 32.0 + - - -
376D PHE* 3.9 19.7 - + + -
384D ILE* 5.0 4.0 - - + -
580D ILE* 4.1 20.0 - - + -
595D ARG* 3.6 21.2 - - + +
596D ILE 3.4 2.5 + - - +
597D VAL 3.3 0.2 - - - -
598D GLU* 1.3 79.1 + - + +
600D LYS* 1.3 56.7 + - - +
601D GLU 2.9 6.3 - - - -
602D ARG* 3.6 28.5 - - + -
603D LEU* 2.9 61.4 + - + +
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Residues in contact with LYS 600 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
580D ILE* 2.7 35.8 + - + +
581D TRP 4.2 7.7 + - - -
582D TYR 4.6 1.2 + - - -
583D ARG 3.2 23.4 + - - -
584D PRO* 4.4 2.7 - - - +
585D VAL* 3.4 35.7 - - + +
596D ILE* 3.2 25.7 + - - +
597D VAL* 3.1 16.9 + - + +
599D TRP* 1.3 76.4 - - - +
601D GLU* 1.3 58.4 + - + +
603D LEU* 5.0 2.9 - - - -
604D ASP* 2.6 36.2 - - - +
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Residues in contact with GLU 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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597D VAL* 3.1 30.3 + - + +
598D GLU* 3.5 16.1 - - - +
599D TRP 2.9 0.2 - - - -
600D LYS* 1.3 81.9 - - + +
602D ARG* 1.3 59.3 + - - +
603D LEU 3.4 0.2 - - - -
604D ASP* 4.0 2.8 - - - +
605D LYS* 3.0 30.9 + - - +
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Residues in contact with ARG 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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376D PHE* 3.5 31.4 + - - +
384D ILE* 4.6 17.1 - - + +
598D GLU 3.3 9.6 + - - +
599D TRP* 3.2 41.5 + - + +
601D GLU* 1.3 77.0 - - - +
603D LEU* 1.3 67.1 + - + +
605D LYS* 3.2 14.5 + - - +
606D GLU* 3.1 54.6 + - + +
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Residues in contact with LEU 603 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384D ILE* 4.9 8.1 - - + -
388D MET* 3.7 16.2 - - + -
577D LEU* 3.7 34.3 - - + +
580D ILE* 5.0 7.9 - - + -
581D TRP* 3.6 37.8 - - + +
599D TRP* 2.9 57.7 + - + +
600D LYS* 5.0 2.9 - - - -
602D ARG* 1.3 81.8 - - + +
604D ASP* 1.3 56.9 + - - +
606D GLU* 3.4 3.6 + - - +
607D PHE* 2.8 36.3 + - - +
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Residues in contact with ASP 604 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
581D TRP* 5.1 8.9 - - - -
600D LYS* 2.6 29.3 + - - +
601D GLU* 3.7 4.4 + - - +
602D ARG 3.4 0.4 - - - -
603D LEU* 1.3 79.6 - - - +
605D LYS* 1.3 60.2 + - - +
607D PHE 3.3 18.7 - - - +
608D SER* 4.4 5.0 + - - -
609D LEU* 4.4 18.0 - - - +
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Residues in contact with LYS 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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601D GLU 3.0 20.2 + - - +
602D ARG* 3.4 15.9 - - - +
603D LEU 3.1 0.4 - - - -
604D ASP* 1.3 81.0 - - - +
606D GLU* 1.3 71.7 + - - +
607D PHE 5.2 0.2 - - - -
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Residues in contact with GLU 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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384D ILE* 4.6 13.6 - - + +
602D ARG* 3.1 50.2 + - + +
603D LEU* 4.1 2.2 - - - +
605D LYS* 1.3 92.0 - - + +
607D PHE* 1.3 83.6 + - + +
608D SER 4.4 0.2 + - - -
611D VAL* 5.5 2.3 - - - +
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Residues in contact with PHE 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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384D ILE* 4.1 13.9 - - + -
385D GLU* 3.4 52.5 - - + -
388D MET* 4.2 17.5 - - + -
581D TRP* 3.8 19.7 - - + -
603D LEU* 2.8 29.1 + - - +
604D ASP* 3.3 15.6 - - - +
605D LYS 5.2 0.2 - - - -
606D GLU* 1.3 95.0 - - + +
608D SER* 1.3 66.3 + - - +
611D VAL* 3.5 32.8 - - + -
612D TYR* 5.1 1.3 - - + +
615D MET* 4.2 21.1 - - + -
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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