Contacts of the helix formed by residues 592 - 607 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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362L THR* 4.1 11.4 - - + +
365L PHE* 3.7 33.0 - - + -
366L ASN* 3.4 32.5 - - - +
369L LEU* 4.5 3.8 - - + -
588L PHE* 3.6 12.8 - - + -
589L ALA* 3.0 40.6 + - + +
591L SER* 1.3 81.5 + - - +
593L GLN* 1.3 58.8 + - - +
594L SER 3.0 3.4 - - - -
595L ARG* 2.8 28.9 + - + +
596L ILE* 3.0 23.9 + - + +
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Residues in contact with GLN 593 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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585L VAL* 3.1 44.7 - - + +
586L ALA* 4.3 8.3 + - - +
588L PHE 3.6 9.8 + - - +
589L ALA 2.9 17.8 + - - +
590L GLN* 3.1 42.1 + - - +
591L SER 3.7 0.6 - - - -
592L ILE* 1.3 78.3 - - - +
594L SER* 1.3 58.4 + - - +
596L ILE* 3.5 4.2 + - - -
597L VAL* 3.1 30.7 + - - +
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Residues in contact with SER 594 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
590L GLN 5.0 2.9 + - - -
591L SER 5.5 4.3 - - - -
592L ILE 3.0 1.5 - - - +
593L GLN* 1.3 78.9 - - - +
595L ARG* 1.3 58.3 + - - +
597L VAL* 4.1 6.9 + - - +
598L GLU* 3.1 27.3 + - - +
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Residues in contact with ARG 595 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366L ASN* 3.2 42.0 + - - +
369L LEU* 3.2 28.6 - - + +
370L ASP* 3.1 37.1 + - - +
373L ASP* 2.8 28.3 + - - -
592L ILE* 2.8 17.4 + - + +
594L SER* 1.3 79.5 - - - +
596L ILE* 1.3 66.0 + - - +
597L VAL 3.3 0.4 - - - -
598L GLU* 3.1 35.0 - - - +
599L TRP* 3.6 15.0 + - + +
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Residues in contact with ILE 596 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365L PHE* 5.6 1.1 - - + -
369L LEU* 4.8 9.0 - - + -
576L LEU* 6.0 0.9 - - + -
580L ILE* 3.6 24.9 - - + +
585L VAL* 4.1 6.5 - - + -
588L PHE* 3.4 61.2 - - + -
592L ILE* 3.0 35.1 + - + +
593L GLN* 3.8 7.0 - - - +
594L SER 3.5 0.2 - - - -
595L ARG* 1.3 79.0 - - - +
597L VAL* 1.3 61.0 + - - +
598L GLU 3.3 0.3 + - - -
599L TRP 3.4 2.8 + - - -
600L LYS* 3.2 44.0 + - - +
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Residues in contact with VAL 597 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
585L VAL* 3.7 23.3 - - + -
593L GLN 3.1 18.4 - - - +
594L SER* 4.3 6.7 - - - +
595L ARG 3.3 0.4 - - - -
596L ILE* 1.3 73.4 - - - +
598L GLU* 1.3 66.4 + - - +
600L LYS* 3.1 21.2 + - + +
601L GLU* 3.1 28.5 + - + +
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Residues in contact with GLU 598 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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594L SER* 3.1 19.0 + - - +
595L ARG* 3.1 34.4 - - - +
596L ILE 3.1 0.2 - - - -
597L VAL* 1.3 80.5 - - - +
599L TRP* 1.3 69.0 + - + +
601L GLU* 3.3 21.9 + - - +
602L ARG* 3.4 11.4 + - - +
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Residues in contact with TRP 599 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369L LEU* 3.8 29.4 - - + +
372L MET* 3.6 48.2 - - + -
373L ASP* 3.2 32.2 + - - -
376L PHE* 3.9 19.7 - + + -
384L ILE* 5.0 3.8 - - + -
577L LEU* 4.9 0.2 - - + -
580L ILE* 4.1 19.7 - - + -
595L ARG* 3.6 20.3 - - + +
596L ILE 3.4 2.7 + - - +
597L VAL 3.3 0.2 - - - -
598L GLU* 1.3 79.5 + - + +
600L LYS* 1.3 56.7 + - - +
601L GLU 2.9 5.8 - - - -
602L ARG* 3.6 30.1 - - + -
603L LEU* 2.9 60.6 + - + +
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Residues in contact with LYS 600 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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580L ILE* 2.7 36.3 + - + +
581L TRP 4.2 7.5 + - - -
582L TYR 4.6 1.4 + - - -
583L ARG 3.2 23.8 + - - -
584L PRO* 4.4 2.8 - - - +
585L VAL* 3.4 36.1 - - + +
596L ILE* 3.2 25.0 + - - +
597L VAL* 3.1 16.9 + - + +
599L TRP* 1.3 76.8 - - - +
601L GLU* 1.3 58.0 + - + +
603L LEU* 5.0 2.9 - - - -
604L ASP* 2.6 35.8 - - - +
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Residues in contact with GLU 601 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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597L VAL* 3.1 29.6 - - + +
598L GLU* 3.5 16.2 - - - +
599L TRP 2.9 0.6 - - - -
600L LYS* 1.3 82.1 - - + +
602L ARG* 1.3 58.6 + - - +
603L LEU 3.4 0.2 - - - -
604L ASP* 3.9 2.8 - - - +
605L LYS* 3.0 30.6 + - - +
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Residues in contact with ARG 602 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376L PHE* 3.5 32.2 + - - +
384L ILE* 4.6 16.6 - - + +
598L GLU 3.4 9.2 + - - +
599L TRP* 3.2 41.7 + - + +
601L GLU* 1.3 78.2 - - - +
603L LEU* 1.3 68.3 + - + +
605L LYS* 3.2 13.7 + - - +
606L GLU* 3.0 56.1 + - + +
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Residues in contact with LEU 603 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384L ILE* 4.9 8.1 - - + -
388L MET* 3.7 16.4 - - + -
577L LEU* 3.6 34.5 - - + +
580L ILE* 5.0 7.2 - - + -
581L TRP* 3.6 37.7 - - + +
599L TRP* 2.9 58.4 + - + +
600L LYS* 5.0 2.9 - - - -
602L ARG* 1.3 81.2 - - + +
604L ASP* 1.3 57.1 + - - +
606L GLU* 3.4 3.3 + - - +
607L PHE* 2.8 36.2 + - - +
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Residues in contact with ASP 604 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
581L TRP* 5.1 9.9 - - - -
600L LYS* 2.6 29.4 + - - +
601L GLU* 3.7 3.7 + - - +
602L ARG 3.4 0.4 - - - -
603L LEU* 1.3 80.4 - - - +
605L LYS* 1.3 61.4 + - - +
607L PHE 3.3 18.6 - - - +
608L SER* 4.4 5.0 + - - -
609L LEU* 4.4 17.8 - - - +
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Residues in contact with LYS 605 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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601L GLU 3.0 19.3 + - - +
602L ARG* 3.3 16.4 - - - +
604L ASP* 1.3 81.0 - - - +
606L GLU* 1.3 72.1 + - - +
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Residues in contact with GLU 606 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384L ILE* 4.6 14.2 - - + +
602L ARG* 3.0 48.3 + - + +
603L LEU* 4.1 2.2 - - - +
605L LYS* 1.3 92.1 - - + +
607L PHE* 1.3 85.7 + - + +
611L VAL* 5.5 2.6 - - - +
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Residues in contact with PHE 607 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384L ILE* 4.1 13.7 - - + -
385L GLU* 3.4 51.8 - - + -
388L MET* 4.2 17.0 - - + -
581L TRP* 3.8 20.6 - - + -
603L LEU* 2.8 29.6 + - - +
604L ASP* 3.3 15.9 - - - +
605L LYS 5.2 0.2 - - - -
606L GLU* 1.3 95.7 - - + +
608L SER* 1.3 65.1 + - - +
611L VAL* 3.5 34.1 - - + -
612L TYR* 5.2 1.1 - - + +
615L MET* 4.2 21.1 - - + -
626L 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