Contacts of the helix formed by residues 592 - 607 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362I THR* 4.1 11.9 - - + +
365I PHE* 3.7 33.2 - - + -
366I ASN* 3.4 31.4 - - - +
369I LEU* 4.5 3.8 - - + -
588I PHE* 3.6 12.1 - - + -
589I ALA* 3.0 41.1 + - + +
591I SER* 1.3 80.5 - - - +
593I GLN* 1.3 58.1 + - - +
594I SER 3.0 3.4 - - - -
595I ARG* 2.8 27.6 + - + +
596I ILE* 3.0 24.0 + - + +
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Residues in contact with GLN 593 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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585I VAL* 3.1 45.6 - - + +
586I ALA* 4.3 8.8 + - - +
588I PHE* 3.6 9.6 + - + +
589I ALA 2.9 19.1 + - - +
590I GLN* 3.1 40.8 + - - +
591I SER 3.7 0.4 - - - -
592I ILE* 1.3 78.4 - - - +
594I SER* 1.3 58.5 + - - +
596I ILE* 3.8 4.3 - - - -
597I VAL* 3.1 30.9 + - - +
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Residues in contact with SER 594 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
590I GLN 5.0 3.0 + - - -
591I SER 5.5 4.0 - - - -
592I ILE 3.0 1.4 - - - +
593I GLN* 1.3 79.1 - - - +
595I ARG* 1.3 57.9 + - - +
597I VAL* 4.1 6.1 + - - +
598I GLU* 3.1 27.5 + - - +
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Residues in contact with ARG 595 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366I ASN* 3.2 41.3 + - - +
369I LEU* 3.2 28.7 - - + +
370I ASP* 3.1 36.7 + - - +
373I ASP* 2.8 27.7 + - - -
592I ILE* 2.8 16.8 + - + +
594I SER* 1.3 80.5 - - - +
596I ILE* 1.3 63.7 + - - +
597I VAL 3.3 0.7 - - - -
598I GLU* 3.1 35.1 + - - +
599I TRP* 3.6 14.6 + - + +
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Residues in contact with ILE 596 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365I PHE* 5.6 0.9 - - + -
369I LEU* 4.8 8.5 - - + -
576I LEU* 6.0 0.9 - - + -
580I ILE* 3.6 24.3 - - + +
585I VAL* 4.1 6.5 - - + -
588I PHE* 3.4 60.6 - - + -
592I ILE* 3.2 34.5 - - + +
593I GLN* 3.8 6.7 - - - +
594I SER 3.5 0.2 - - - -
595I ARG* 1.3 79.2 - - - +
597I VAL* 1.3 62.9 + - - +
598I GLU 3.3 0.3 + - - -
599I TRP 3.4 2.9 + - - -
600I LYS* 3.2 39.6 + - - +
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Residues in contact with VAL 597 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
585I VAL* 3.7 23.6 - - + -
593I GLN 3.1 19.0 + - - +
594I SER* 4.3 7.2 - - - +
595I ARG 3.3 0.4 - - - -
596I ILE* 1.3 73.2 - - - +
598I GLU* 1.3 65.6 + - - +
600I LYS* 3.1 21.5 + - + +
601I GLU* 3.1 28.4 + - + +
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Residues in contact with GLU 598 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
594I SER* 3.1 18.4 + - - +
595I ARG* 3.1 33.0 - - - +
596I ILE 3.1 0.2 - - - -
597I VAL* 1.3 81.0 - - - +
599I TRP* 1.3 68.9 + - + +
601I GLU* 3.3 21.9 + - - +
602I ARG* 3.4 10.7 + - - +
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Residues in contact with TRP 599 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369I LEU* 3.8 28.1 - - + +
372I MET* 3.6 47.3 - - + -
373I ASP* 3.2 33.3 + - - -
376I PHE* 3.9 19.7 - + + -
384I ILE* 5.1 4.0 - - + -
577I LEU* 4.9 0.2 - - + -
580I ILE* 4.1 22.2 - - + -
595I ARG* 3.6 21.0 - - + +
596I ILE 3.4 2.5 + - - +
597I VAL 3.3 0.2 - - - -
598I GLU* 1.3 79.2 + - + +
600I LYS* 1.3 56.6 + - - +
601I GLU 2.9 6.1 - - - -
602I ARG* 3.6 30.1 - - + -
603I LEU* 2.9 57.7 + - + +
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Residues in contact with LYS 600 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
580I ILE* 2.7 35.1 + - + +
581I TRP 4.2 7.3 + - - -
582I TYR 4.6 1.2 + - - -
583I ARG 3.2 24.2 + - - -
584I PRO* 4.4 2.6 - - - +
585I VAL* 3.4 35.9 - - + +
596I ILE* 3.2 26.1 + - - +
597I VAL* 3.1 16.9 + - + +
599I TRP* 1.3 77.3 - - - +
601I GLU* 1.3 58.1 + - + +
603I LEU* 5.0 2.5 - - - -
604I ASP* 2.6 35.3 - - - +
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Residues in contact with GLU 601 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597I VAL* 3.1 29.6 + - + +
598I GLU* 3.5 15.4 - - - +
599I TRP 2.9 0.4 - - - -
600I LYS* 1.3 82.2 - - + +
602I ARG* 1.3 59.2 + - - +
603I LEU 3.4 0.2 - - - -
604I ASP* 4.0 3.5 - - - +
605I LYS* 3.0 30.1 + - - +
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Residues in contact with ARG 602 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376I PHE* 3.5 30.9 + - - +
384I ILE* 4.6 16.8 - - + +
598I GLU 3.4 9.8 + - - +
599I TRP* 3.2 41.1 + - + +
601I GLU* 1.3 77.2 - - - +
603I LEU* 1.3 68.9 + - + +
605I LYS* 3.2 14.5 + - - +
606I GLU* 3.0 55.7 + - + +
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Residues in contact with LEU 603 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384I ILE* 4.9 8.5 - - + -
388I MET* 3.7 16.4 - - + -
577I LEU* 3.6 35.7 - - + +
580I ILE* 5.0 7.0 - - + -
581I TRP* 3.6 37.8 - - + +
599I TRP* 2.9 57.9 + - + +
600I LYS* 5.0 2.5 - - - -
602I ARG* 1.3 81.5 - - + +
604I ASP* 1.3 58.3 + - - +
606I GLU* 3.4 3.7 + - - +
607I PHE* 2.8 35.4 + - - +
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Residues in contact with ASP 604 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
581I TRP* 5.1 9.3 - - - -
600I LYS* 2.6 28.9 + - - +
601I GLU* 3.7 4.2 + - - +
602I ARG 3.4 0.2 - - - -
603I LEU* 1.3 78.8 - - - +
605I LYS* 1.3 61.0 + - - +
607I PHE 3.3 19.2 - - - +
608I SER* 4.4 5.0 + - - -
609I LEU* 4.4 17.7 - - - +
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Residues in contact with LYS 605 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601I GLU 3.0 20.8 + - - +
602I ARG* 3.3 15.0 - - - +
603I LEU 3.1 0.2 - - - -
604I ASP* 1.3 80.8 - - - +
606I GLU* 1.3 72.1 + - - +
607I PHE 5.2 0.2 - - - -
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Residues in contact with GLU 606 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384I ILE* 4.6 14.0 - - + +
602I ARG* 3.0 48.4 + - + +
603I LEU* 4.1 2.0 - - - +
605I LYS* 1.3 93.1 - - + +
607I PHE* 1.3 85.8 + - + +
611I VAL* 5.5 2.3 - - - +
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Residues in contact with PHE 607 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384I ILE* 4.1 13.2 - - + -
385I GLU* 3.4 51.6 - - + -
388I MET* 4.2 17.3 - - + -
581I TRP* 3.8 20.6 - - + -
603I LEU* 2.8 28.7 + - - +
604I ASP* 3.3 16.2 - - - +
606I GLU* 1.3 96.2 - - + +
608I SER* 1.3 65.4 + - - +
611I VAL* 3.5 33.2 - - + -
612I TYR* 5.1 1.1 - - + +
615I MET* 4.2 21.3 - - + -
626I LEU* 5.6 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