Contacts of the helix formed by residues 592 - 607 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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362K THR* 4.1 11.7 - - + +
365K PHE* 3.7 33.2 - - + -
366K ASN* 3.4 31.9 - - - +
369K LEU* 4.5 3.6 - - + -
588K PHE* 3.6 13.9 - - + -
589K ALA* 3.0 40.0 + - + +
591K SER* 1.3 81.0 + - - +
593K GLN* 1.3 59.6 + - - +
594K SER 3.0 2.9 - - - -
595K ARG* 2.8 27.9 + - + +
596K ILE* 3.0 23.6 + - + +
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Residues in contact with GLN 593 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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585K VAL* 3.1 44.1 + - + +
586K ALA* 4.2 9.2 + - - +
588K PHE 3.6 9.0 + - - +
589K ALA 2.9 18.3 + - - +
590K GLN* 3.1 41.7 + - + +
591K SER 3.7 0.4 - - - -
592K ILE* 1.3 77.9 - - - +
594K SER* 1.3 58.7 + - - +
596K ILE* 3.5 4.4 + - - -
597K VAL* 3.1 30.5 + - - +
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Residues in contact with SER 594 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
590K GLN 5.0 2.7 + - - -
591K SER 5.5 4.7 - - - -
592K ILE* 3.0 1.8 - - - +
593K GLN* 1.3 78.7 - - - +
595K ARG* 1.3 59.9 + - - +
597K VAL* 4.1 6.2 + - - +
598K GLU* 3.1 27.3 + - - +
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Residues in contact with ARG 595 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366K ASN* 3.2 40.8 + - - +
369K LEU* 3.2 28.3 - - + +
370K ASP* 3.1 36.2 + - - +
373K ASP* 2.8 28.5 + - - -
592K ILE* 2.8 17.0 + - + +
594K SER* 1.3 80.9 - - - +
596K ILE* 1.3 64.9 + - - +
597K VAL 3.3 0.4 - - - -
598K GLU* 3.1 35.0 + - - +
599K TRP* 3.6 15.5 + - + +
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Residues in contact with ILE 596 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365K PHE* 5.7 1.1 - - + -
369K LEU* 4.8 9.0 - - + -
576K LEU* 6.0 0.4 - - + -
580K ILE* 3.6 24.4 - - + +
585K VAL* 4.1 6.7 - - + -
588K PHE* 3.4 61.5 - - + -
592K ILE* 3.0 34.7 + - + +
593K GLN* 3.8 6.7 - - - +
594K SER 3.5 0.4 - - - -
595K ARG* 1.3 78.3 - - - +
597K VAL* 1.3 61.3 + - - +
598K GLU 3.3 0.3 + - - -
599K TRP* 3.4 3.0 + - - -
600K LYS* 3.2 44.6 + - + +
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Residues in contact with VAL 597 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
585K VAL* 3.7 23.3 - - + -
593K GLN 3.1 19.0 + - - +
594K SER* 4.3 6.5 - - - +
595K ARG 3.3 0.2 - - - -
596K ILE* 1.3 72.7 - - - +
598K GLU* 1.3 66.7 + - - +
600K LYS* 3.1 21.0 + - + +
601K GLU* 3.1 28.4 + - + +
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Residues in contact with GLU 598 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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594K SER* 3.1 18.6 + - - +
595K ARG* 3.1 33.5 - - - +
597K VAL* 1.3 79.9 - - - +
599K TRP* 1.3 69.0 + - + +
601K GLU* 3.3 21.6 + - - +
602K ARG* 3.4 11.3 + - - +
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Residues in contact with TRP 599 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369K LEU* 3.8 27.6 - - + +
372K MET* 3.6 47.1 - - + -
373K ASP* 3.2 32.5 + - - -
376K PHE* 3.9 20.2 - + + -
384K ILE* 5.0 4.5 - - + -
577K LEU* 4.9 0.2 - - + -
580K ILE* 4.1 21.5 - - + -
595K ARG* 3.6 20.4 - - + +
596K ILE 3.4 2.0 + - - +
597K VAL 3.3 0.4 - - - -
598K GLU* 1.3 79.7 + - + +
600K LYS* 1.3 56.7 + - - +
601K GLU 2.9 6.3 - - - -
602K ARG* 3.6 28.5 - - + -
603K LEU* 2.9 60.8 + - + +
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Residues in contact with LYS 600 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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580K ILE* 2.7 35.6 + - + +
581K TRP 4.2 7.5 + - - -
582K TYR 4.6 1.4 + - - -
583K ARG 3.2 24.1 + - - -
584K PRO* 4.4 2.4 - - - +
585K VAL* 3.4 36.1 - - + +
596K ILE* 3.2 25.3 + - - +
597K VAL* 3.1 17.3 + - + +
599K TRP* 1.3 76.3 - - - +
601K GLU* 1.3 58.4 + - + +
603K LEU* 5.0 2.2 - - - -
604K ASP* 2.6 36.3 - - - +
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Residues in contact with GLU 601 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597K VAL* 3.1 29.8 - - + +
598K GLU* 3.5 16.6 - - - +
599K TRP 2.9 0.4 - - - -
600K LYS* 1.3 82.6 - - + +
602K ARG* 1.3 59.0 + - - +
603K LEU 3.4 0.2 - - - -
604K ASP* 3.9 3.2 - - - +
605K LYS* 3.0 30.8 + - - +
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Residues in contact with ARG 602 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376K PHE* 3.5 31.7 + - - +
384K ILE* 4.6 16.8 - - + +
598K GLU 3.4 9.4 + - - +
599K TRP* 3.2 41.9 + - + +
601K GLU* 1.3 77.7 - - - +
603K LEU* 1.3 68.9 + - + +
605K LYS* 3.2 14.1 + - - +
606K GLU* 3.0 56.1 + - + +
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Residues in contact with LEU 603 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384K ILE* 4.9 7.9 - - + -
388K MET* 3.7 17.0 - - + -
577K LEU* 3.7 35.0 - - + +
580K ILE* 5.0 6.7 - - + -
581K TRP* 3.6 37.8 - - + +
599K TRP* 2.9 58.1 + - + +
600K LYS* 5.0 2.7 - - - -
602K ARG* 1.3 81.1 - - + +
604K ASP* 1.3 58.0 + - - +
606K GLU* 4.1 3.3 - - - +
607K PHE* 2.8 35.9 + - - +
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Residues in contact with ASP 604 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
581K TRP* 5.1 9.5 - - - -
600K LYS* 2.6 30.1 + - - +
601K GLU* 3.7 3.7 + - - +
602K ARG 3.4 0.4 - - - -
603K LEU* 1.3 80.6 - - - +
605K LYS* 1.3 60.9 + - - +
607K PHE 3.3 20.1 - - - +
608K SER* 4.4 4.9 + - - -
609K LEU* 4.4 17.7 - - - +
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Residues in contact with LYS 605 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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601K GLU 3.0 19.5 + - - +
602K ARG* 3.3 15.9 - - - +
603K LEU 3.1 0.2 - - - -
604K ASP* 1.3 81.7 - - - +
606K GLU* 1.3 72.5 + - - +
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Residues in contact with GLU 606 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384K ILE* 4.6 14.2 - - + +
602K ARG* 3.0 47.4 + - + +
603K LEU* 4.1 2.2 - - - +
605K LYS* 1.3 92.4 - - + +
607K PHE* 1.3 84.5 + - + +
608K SER 4.4 0.2 + - - -
611K VAL* 5.5 2.1 - - - +
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Residues in contact with PHE 607 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384K ILE* 4.1 13.0 - - + -
385K GLU* 3.4 52.7 - - + -
388K MET* 4.2 18.2 - - + -
581K TRP* 3.8 20.2 - - + -
603K LEU* 2.8 26.3 + - - +
604K ASP* 3.3 15.7 - - - +
606K GLU* 1.3 99.3 - - + +
608K SER* 1.3 65.6 + - - +
611K VAL* 3.5 34.1 - - + -
612K TYR* 5.1 1.6 - - + +
615K MET* 4.2 21.1 - - + -
626K LEU* 5.5 0.2 - - + -
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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