Contacts of the helix formed by residues 592 - 607 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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362C THR* 4.1 11.2 - - + +
365C PHE* 3.7 32.3 - - + -
366C ASN* 3.4 32.5 - - - +
369C LEU* 4.5 4.3 - - + -
588C PHE* 3.6 13.0 - - + -
589C ALA* 3.0 39.7 + - + +
591C SER* 1.3 81.0 + - - +
593C GLN* 1.3 59.3 + - - +
594C SER 3.0 3.4 - - - -
595C ARG* 2.8 28.4 + - + +
596C ILE* 3.0 26.3 + - + +
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Residues in contact with GLN 593 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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585C VAL* 3.1 44.1 - - + +
586C ALA* 4.3 8.3 + - - +
588C PHE 3.6 9.8 + - - +
589C ALA 2.9 18.3 + - - +
590C GLN* 3.1 40.6 - - - +
591C SER 3.7 0.4 - - - -
592C ILE* 1.3 77.9 - - - +
594C SER* 1.3 59.3 + - - +
596C ILE* 3.5 4.2 + - - -
597C VAL* 3.1 30.9 + - - +
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Residues in contact with SER 594 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
590C GLN 5.0 2.1 + - - -
591C SER 5.5 4.3 - - - -
592C ILE 3.0 2.1 - - - +
593C GLN* 1.3 79.6 - - - +
595C ARG* 1.3 58.0 + - - +
597C VAL* 4.1 6.4 + - - +
598C GLU* 3.1 26.5 + - - +
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Residues in contact with ARG 595 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366C ASN* 3.2 41.2 + - - +
369C LEU* 3.2 27.5 - - + +
370C ASP* 3.2 37.6 + - - +
373C ASP* 2.8 28.1 + - - -
592C ILE* 2.8 17.0 + - + +
594C SER* 1.3 80.0 - - - +
596C ILE* 1.3 65.4 + - - +
597C VAL 3.3 0.4 - - - -
598C GLU* 3.1 36.2 - - - +
599C TRP* 3.6 15.2 + - + +
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Residues in contact with ILE 596 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365C PHE* 5.6 1.1 - - + -
369C LEU* 4.8 8.1 - - + -
576C LEU* 6.0 0.4 - - + -
580C ILE* 3.6 25.3 - - + +
585C VAL* 4.1 6.3 - - + -
588C PHE* 3.4 60.8 - - + -
592C ILE* 3.2 33.7 - - + +
593C GLN* 3.8 7.0 - - - +
594C SER 3.5 0.2 - - - -
595C ARG* 1.3 78.9 - - - +
597C VAL* 1.3 61.5 + - - +
598C GLU 3.3 0.2 + - - -
599C TRP* 3.4 3.2 + - - -
600C LYS* 3.2 43.5 + - - +
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Residues in contact with VAL 597 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
585C VAL* 3.7 23.1 - - + -
593C GLN 3.1 17.9 + - - +
594C SER* 4.3 7.4 - - - +
595C ARG 3.3 0.2 - - - -
596C ILE* 1.3 73.6 - - - +
598C GLU* 1.3 65.3 + - - +
600C LYS* 3.1 21.5 + - + +
601C GLU* 3.1 29.8 + - + +
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Residues in contact with GLU 598 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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594C SER* 3.1 18.5 + - - +
595C ARG* 3.1 34.5 - - - +
596C ILE 3.1 0.2 - - - -
597C VAL* 1.3 80.3 - - + +
599C TRP* 1.3 68.5 + - + +
601C GLU* 3.3 22.9 + - - +
602C ARG* 3.4 11.1 + - - +
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Residues in contact with TRP 599 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369C LEU* 3.8 28.5 - - + +
372C MET* 3.7 46.4 - - + -
373C ASP* 3.2 32.9 + - - -
376C PHE* 3.9 20.2 - + + -
384C ILE* 5.0 4.5 - - + -
580C ILE* 4.1 20.9 - - + -
595C ARG* 3.6 20.8 - - + +
596C ILE 3.4 2.7 + - - +
597C VAL 3.3 0.4 - - - -
598C GLU* 1.3 79.2 + - + +
600C LYS* 1.3 56.9 + - - +
601C GLU 2.9 6.5 - - - -
602C ARG* 3.6 29.8 - - + -
603C LEU* 2.9 60.0 + - + +
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Residues in contact with LYS 600 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
580C ILE* 2.7 36.1 + - + +
581C TRP 4.2 7.5 + - - -
582C TYR 4.6 1.4 + - - -
583C ARG 3.2 24.3 + - - -
584C PRO* 4.4 2.8 - - - +
585C VAL* 3.4 35.7 - - + +
596C ILE* 3.2 25.0 + - - +
597C VAL* 3.1 17.8 + - + +
599C TRP* 1.3 76.4 - - - +
601C GLU* 1.3 59.2 + - + +
603C LEU* 5.0 2.5 - - - -
604C ASP* 2.6 35.7 - - - +
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Residues in contact with GLU 601 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597C VAL* 3.1 29.5 - - + +
598C GLU* 3.5 15.9 - - - +
600C LYS* 1.3 82.4 - - + +
602C ARG* 1.3 59.1 + - - +
603C LEU 3.4 0.2 - - - -
604C ASP* 4.0 2.7 - - - +
605C LYS* 3.0 30.4 + - - +
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Residues in contact with ARG 602 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376C PHE* 3.5 31.3 + - - +
384C ILE* 4.6 17.0 - - + +
598C GLU 3.4 10.3 + - - +
599C TRP* 3.2 41.0 + - + +
601C GLU* 1.3 78.0 - - - +
603C LEU* 1.3 68.2 + - + +
605C LYS* 3.2 14.2 + - - +
606C GLU* 3.0 55.1 + - + +
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Residues in contact with LEU 603 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384C ILE* 4.9 8.7 - - + -
388C MET* 3.7 16.4 - - + -
577C LEU* 3.6 34.8 - - + +
580C ILE* 5.0 7.2 - - + -
581C TRP* 3.6 37.6 - - + +
599C TRP* 2.9 58.5 + - + +
600C LYS* 5.0 2.7 - - - -
602C ARG* 1.3 81.4 - - + +
604C ASP* 1.3 57.5 + - - +
606C GLU* 4.1 3.7 - - - +
607C PHE* 2.8 36.1 + - - +
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Residues in contact with ASP 604 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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581C TRP* 5.1 9.7 - - - -
600C LYS* 2.6 28.6 + - - +
601C GLU* 3.7 4.4 + - - +
602C ARG 3.4 0.2 - - - -
603C LEU* 1.3 80.0 - - - +
605C LYS* 1.3 60.7 + - - +
607C PHE 3.3 19.0 - - - +
608C SER* 4.4 5.4 + - - -
609C LEU* 4.4 18.2 - - - +
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Residues in contact with LYS 605 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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601C GLU 3.0 20.2 + - - +
602C ARG* 3.3 15.0 - - - +
603C LEU 3.1 0.4 - - - -
604C ASP* 1.3 80.1 - - - +
606C GLU* 1.3 73.2 + - - +
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Residues in contact with GLU 606 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384C ILE* 4.6 14.5 - - + +
602C ARG* 3.0 48.4 + - + +
603C LEU* 4.1 2.2 - - - +
605C LYS* 1.3 91.7 - - + +
607C PHE* 1.3 83.2 + - + +
608C SER 4.4 0.2 + - - -
611C VAL* 5.5 2.3 - - - +
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Residues in contact with PHE 607 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384C ILE* 4.1 13.7 - - + -
385C GLU* 3.4 51.8 - - + -
388C MET* 4.2 17.5 - - + -
581C TRP* 3.8 19.5 - - + -
603C LEU* 2.8 25.7 + - - +
604C ASP* 3.3 16.1 - - - +
606C GLU* 1.3 99.7 - - + +
608C SER* 1.3 65.3 + - - +
611C VAL* 3.5 33.4 - - + -
612C TYR* 5.2 1.8 - - + +
615C MET* 4.2 21.1 - - + -
626C LEU* 5.5 0.4 - - + -
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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