Contacts of the helix formed by residues 592 - 607 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362B THR* 4.1 11.4 - - + +
365B PHE* 3.7 32.5 - - + -
366B ASN* 3.4 33.4 - - - +
369B LEU* 4.5 3.8 - - + -
588B PHE* 3.6 12.8 - - + -
589B ALA* 3.0 40.2 + - + +
591B SER* 1.3 81.2 - - - +
593B GLN* 1.3 59.3 + - - +
594B SER 3.0 3.1 - - - -
595B ARG* 2.8 29.0 + - + +
596B ILE* 3.0 24.3 + - + +
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Residues in contact with GLN 593 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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585B VAL* 3.1 45.2 - - + +
586B ALA* 4.3 8.6 + - - +
588B PHE 3.6 9.8 + - - +
589B ALA 2.9 18.5 + - - +
590B GLN* 3.1 40.8 - - - +
591B SER 3.7 0.4 - - - -
592B ILE* 1.3 77.2 - - - +
594B SER* 1.3 58.4 + - - +
596B ILE* 3.8 3.8 - - - -
597B VAL* 3.1 31.2 + - - +
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Residues in contact with SER 594 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
590B GLN 5.0 2.5 + - - -
591B SER 5.5 4.0 - - - -
592B ILE 3.0 1.7 - - - +
593B GLN* 1.3 79.3 - - - +
595B ARG* 1.3 59.7 + - - +
597B VAL* 4.1 6.2 + - - +
598B GLU* 3.1 26.5 + - - +
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Residues in contact with ARG 595 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366B ASN* 3.2 42.0 + - - +
369B LEU* 3.2 27.3 - - + +
370B ASP* 3.1 35.9 + - - +
373B ASP* 2.8 28.1 + - - -
592B ILE* 2.8 17.4 + - + +
594B SER* 1.3 79.6 - - - +
596B ILE* 1.3 64.8 + - - +
597B VAL 3.3 0.4 - - - -
598B GLU* 3.1 35.1 + - - +
599B TRP* 3.6 15.3 + - + +
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Residues in contact with ILE 596 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365B PHE* 5.6 1.1 - - + -
369B LEU* 4.8 8.5 - - + -
576B LEU* 6.0 0.7 - - + -
580B ILE* 3.6 24.9 - - + +
585B VAL* 4.0 6.3 - - + -
588B PHE* 3.4 60.6 - - + -
592B ILE* 3.2 34.1 - - + +
593B GLN* 3.8 6.7 - - - +
594B SER 3.5 0.2 - - - -
595B ARG* 1.3 78.5 - - - +
597B VAL* 1.3 62.3 + - - +
598B GLU 3.3 0.2 + - - -
599B TRP* 3.4 2.6 + - - -
600B LYS* 3.2 40.6 + - - +
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Residues in contact with VAL 597 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
585B VAL* 3.7 23.6 - - + -
593B GLN 3.1 18.4 + - - +
594B SER* 4.3 7.0 - - - +
595B ARG 3.3 0.2 - - - -
596B ILE* 1.3 73.8 - - - +
598B GLU* 1.3 65.5 + - - +
600B LYS* 3.1 20.7 + - + +
601B GLU* 3.1 29.4 + - + +
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Residues in contact with GLU 598 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
594B SER* 3.1 18.6 + - - +
595B ARG* 3.1 34.7 - - - +
596B ILE 3.1 0.2 - - - -
597B VAL* 1.3 81.1 - - + +
599B TRP* 1.3 66.4 + - + +
601B GLU* 3.3 23.7 + - - +
602B ARG* 3.4 10.6 + - - +
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Residues in contact with TRP 599 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369B LEU* 3.8 28.3 - - + +
372B MET* 3.6 46.7 - - + -
373B ASP* 3.2 33.4 + - - -
376B PHE* 3.9 19.7 - + + -
384B ILE* 5.0 4.3 - - + -
577B LEU* 4.9 0.2 - - + -
580B ILE* 4.1 21.1 - - + -
595B ARG* 3.6 20.6 - - + +
596B ILE 3.4 2.2 + - - +
597B VAL 3.3 0.2 - - - -
598B GLU* 1.3 79.6 + - + +
600B LYS* 1.3 57.4 + - - +
601B GLU 2.9 5.6 - - - -
602B ARG* 3.6 31.0 - - + -
603B LEU* 2.9 59.8 + - + +
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Residues in contact with LYS 600 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
580B ILE* 2.7 35.4 + - + +
581B TRP 4.2 7.9 + - - -
582B TYR 4.6 1.4 + - - -
583B ARG 3.2 24.5 + - - -
584B PRO* 4.4 2.4 - - - +
585B VAL* 3.4 36.3 - - + +
596B ILE* 3.2 25.5 + - - +
597B VAL* 3.1 16.5 + - + +
599B TRP* 1.3 76.6 - - - +
601B GLU* 1.3 59.1 + - + +
603B LEU* 5.0 3.1 - - - -
604B ASP* 2.6 35.7 - - - +
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Residues in contact with GLU 601 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597B VAL* 3.1 29.4 - - + +
598B GLU* 3.5 15.7 - - - +
599B TRP 2.9 0.4 - - - -
600B LYS* 1.3 82.5 - - - +
602B ARG* 1.3 58.8 + - - +
603B LEU 3.4 0.2 - - - -
604B ASP* 4.0 2.8 - - - +
605B LYS* 3.0 31.0 + - - +
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Residues in contact with ARG 602 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376B PHE* 3.5 31.1 + - - +
384B ILE* 4.6 17.5 - - + +
598B GLU 3.4 9.5 + - - +
599B TRP* 3.2 40.6 + - + +
601B GLU* 1.3 79.2 - - - +
603B LEU* 1.3 67.4 + - + +
605B LYS* 3.2 14.1 + - - +
606B GLU* 3.0 56.0 + - + +
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Residues in contact with LEU 603 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384B ILE* 4.9 8.5 - - + -
388B MET* 3.7 16.2 - - + -
577B LEU* 3.7 34.1 - - + +
580B ILE* 5.0 6.7 - - + -
581B TRP* 3.6 38.9 - - + +
599B TRP* 2.9 58.4 + - + +
600B LYS* 5.0 2.5 - - - -
602B ARG* 1.3 81.8 - - + +
604B ASP* 1.3 58.5 + - - +
606B GLU* 4.1 3.0 - - - +
607B PHE* 2.8 35.9 + - - +
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Residues in contact with ASP 604 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
581B TRP* 5.1 9.3 - - - -
600B LYS* 2.6 29.1 + - - +
601B GLU* 3.7 4.2 + - - +
602B ARG 3.4 0.4 - - - -
603B LEU* 1.3 80.6 - - - +
605B LYS* 1.3 60.8 + - - +
607B PHE 3.3 18.7 - - - +
608B SER* 4.4 5.5 + - - -
609B LEU* 4.4 18.0 - - - +
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Residues in contact with LYS 605 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601B GLU 3.0 20.6 + - - +
602B ARG* 3.3 15.5 - - - +
603B LEU 3.1 0.2 - - - -
604B ASP* 1.3 80.7 - - - +
606B GLU* 1.3 72.6 + - - +
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Residues in contact with GLU 606 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384B ILE* 4.6 14.2 - - + +
602B ARG* 3.0 49.2 + - + +
603B LEU* 4.1 1.8 - - - +
605B LYS* 1.3 93.4 - - + +
607B PHE* 1.3 84.9 + - + +
608B SER 4.4 0.2 + - - -
611B VAL* 5.5 2.3 - - - +
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Residues in contact with PHE 607 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384B ILE* 4.1 13.5 - - + -
385B GLU* 3.4 51.8 - - + -
388B MET* 4.2 16.6 - - + -
581B TRP* 3.8 20.1 - - + -
603B LEU* 2.8 29.8 + - - +
604B ASP* 3.3 16.3 - - - +
605B LYS 5.2 0.2 - - - -
606B GLU* 1.3 95.3 - - + +
608B SER* 1.3 65.4 + - - +
611B VAL* 3.5 34.1 - - + -
612B TYR* 5.1 1.6 - - + +
615B MET* 4.2 20.0 - - + -
626B 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
------------------------------------------------------------
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