Contacts of the helix formed by residues 594 - 610 (chain B) in PDB entry 4IVE
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 SER 594 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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590B TYR* 2.8 52.3 + - - -
591B MSE 3.0 16.9 - - - +
592B LEU 5.2 0.2 - - - -
593B GLU* 1.4 73.1 - - - +
595B PRO* 1.4 65.7 - - - +
596B GLU* 3.7 10.7 + - - +
597B SER* 3.4 16.7 + - - -
598B LEU 3.2 10.4 + - - -
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Residues in contact with PRO 595 (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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568B MSE 5.2 5.2 - - + +
591B MSE 5.0 0.4 - - - +
593B GLU 3.6 10.1 - - - +
594B SER* 1.4 81.8 - - - +
596B GLU* 1.4 58.9 + - + +
598B LEU* 3.9 8.0 - - + +
599B ARG* 3.0 40.5 + - - +
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Residues in contact with GLU 596 (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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590B TYR* 4.5 7.6 + - - -
594B SER* 3.7 11.7 + - - +
595B PRO* 1.4 77.9 - - + +
597B SER* 1.3 66.2 + - - +
599B ARG* 3.5 4.8 + - - +
600B SER* 3.2 23.3 + - - -
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Residues in contact with SER 597 (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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612A HIS* 4.2 9.1 - - - +
587B GLU* 4.0 6.1 + - - -
590B TYR* 3.5 33.6 - - - -
591B MSE 3.9 16.4 - - - +
594B SER* 3.4 8.2 + - - -
596B GLU* 1.3 80.8 - - - +
598B LEU* 1.4 56.3 + - - +
600B SER* 3.0 20.4 + - - -
601B LYS* 3.0 30.0 + - - +
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Residues in contact with LEU 598 (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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561B LEU* 3.8 25.8 - - + -
564B LEU* 3.8 41.7 - - + -
565B ILE* 4.2 3.8 - - + -
568B MSE 3.8 18.6 - - + -
580B LEU* 4.1 4.0 - - + -
591B MSE 3.5 37.6 - - + +
594B SER 3.2 10.8 + - - +
595B PRO* 3.9 7.6 - - + +
596B GLU 3.3 0.4 - - - -
597B SER* 1.4 75.3 - - - +
599B ARG* 1.4 52.0 + - - +
601B LYS* 3.2 2.9 + - - +
602B VAL* 2.9 50.7 + - + +
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Residues in contact with ARG 599 (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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568B MSE 3.8 49.0 - - - +
595B PRO* 3.0 24.2 + - - +
596B GLU* 3.8 5.6 - - - +
598B LEU* 1.4 73.9 - - - +
600B SER* 1.4 57.4 + - - +
602B VAL* 3.3 2.6 + - - +
603B ASP* 3.0 48.0 + - - +
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Residues in contact with SER 600 (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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596B GLU* 3.2 12.6 + - - +
597B SER* 3.0 21.0 + - - -
599B ARG* 1.4 77.8 - - - +
601B LYS* 1.4 59.0 + - - +
603B ASP* 3.5 10.3 + - - +
604B GLU* 3.0 36.5 + - - +
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Residues in contact with LYS 601 (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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607A ALA 3.1 21.0 + - - -
608A VAL* 3.2 20.7 + - + +
610A GLN* 2.8 28.2 + - - +
611A ALA 5.7 0.2 - - - -
612A HIS* 5.8 1.8 - - - +
580B LEU* 3.8 11.5 - - + +
583B ILE* 4.4 3.4 - - + -
587B GLU* 4.8 7.6 - - - -
591B MSE 3.8 36.8 - - + -
597B SER* 3.0 26.2 + - - +
598B LEU 3.7 3.6 - - - +
600B SER* 1.4 74.4 - - - +
602B VAL* 1.3 60.9 + - - +
604B GLU* 3.2 18.9 + - - +
605B ALA* 2.9 29.3 + - - +
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Residues in contact with VAL 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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565B ILE* 3.8 30.1 - - + -
568B MSE 4.1 23.1 - - + -
569B HIS* 3.9 29.2 - - + -
576B ILE* 4.0 21.1 - - + -
580B LEU* 4.0 9.6 - - + -
598B LEU* 2.9 24.2 + - + +
599B ARG 3.6 4.9 - - - +
601B LYS* 1.3 74.9 - - - +
603B ASP* 1.3 58.3 + - - +
605B ALA* 3.2 3.8 + - - +
606B VAL* 2.9 32.1 + - - +
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Residues in contact with ASP 603 (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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569B HIS* 5.0 8.8 + - - -
599B ARG* 3.0 34.3 + - - +
600B SER* 3.6 9.1 - - - +
602B VAL* 1.3 80.8 - - - +
604B GLU* 1.3 59.6 + - - +
606B VAL* 3.3 9.8 + - - +
607B ALA* 3.1 22.0 + - - +
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Residues in contact with GLU 604 (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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604A GLU* 5.4 0.8 - - - +
607A ALA* 3.5 31.9 - - + +
608A VAL* 3.6 14.9 - - + +
600B SER* 3.0 23.0 + - - +
601B LYS* 3.2 40.0 + - - +
603B ASP* 1.3 75.3 - - + +
605B ALA* 1.4 60.5 + - - +
607B ALA* 3.3 10.0 + - - +
608B VAL* 3.2 25.3 + - - +
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Residues in contact with ALA 605 (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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608A VAL* 4.1 5.7 - - + +
576B ILE* 3.9 22.4 - - + -
579B MSE 3.3 31.6 - - + +
580B LEU* 4.1 12.3 - - + -
601B LYS 2.9 13.7 + - - +
602B VAL 3.2 8.5 + - - +
604B GLU* 1.4 72.5 - - - +
606B VAL* 1.4 65.4 + - - +
608B VAL* 3.1 6.0 + - - -
609B LEU* 3.1 21.5 + - - +
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Residues in contact with VAL 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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569B HIS* 3.5 39.3 - - + +
572B LEU* 6.4 2.9 - - + -
576B ILE* 3.7 18.2 - - + -
602B VAL 2.9 19.5 + - - +
603B ASP* 3.5 12.1 - - - +
604B GLU 3.3 0.2 - - - -
605B ALA* 1.4 74.8 - - - +
607B ALA* 1.4 60.8 + - - +
609B LEU* 3.3 12.3 + - + +
610B GLN* 3.2 24.9 + - + +
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Residues in contact with ALA 607 (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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601A LYS* 3.0 20.1 + - - -
604A GLU* 3.5 19.9 - - + +
603B ASP 3.1 12.8 + - - +
604B GLU* 3.4 11.9 - - - +
605B ALA 3.3 0.4 - - - -
606B VAL* 1.4 74.6 - - - +
608B VAL* 1.3 59.8 + - - +
610B GLN* 3.4 15.1 + - - +
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Residues in contact with VAL 608 (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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579A MSE 4.5 7.0 - - + +
580A LEU* 3.8 28.5 - - + -
583A ILE* 3.4 18.3 - - + +
601A LYS* 3.1 24.0 + - + +
604A GLU* 3.8 28.7 - - + -
605A ALA* 4.1 1.8 - - + +
608A VAL* 3.9 19.1 - - + -
579B MSE 3.7 17.7 - - + -
604B GLU 3.2 15.2 + - - +
605B ALA* 3.1 9.5 + - - +
607B ALA* 1.3 75.5 - - - +
609B LEU* 1.3 59.4 + - - +
610B GLN 4.0 0.2 - - - +
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Residues in contact with LEU 609 (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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582A GLU 3.6 30.3 - - - +
583A ILE* 3.9 19.9 - - + +
584A ASP* 4.6 6.9 + - - +
572B LEU* 4.3 20.9 - - + -
575B LYS* 4.1 22.2 - - + +
576B ILE* 4.2 15.0 - - + -
579B MSE 3.5 36.6 - - + -
605B ALA 3.1 11.0 + - - +
606B VAL* 3.6 11.7 - - + +
608B VAL* 1.3 74.9 - - - +
610B GLN* 1.3 61.8 + - - +
611B ALA* 3.3 3.6 + - - -
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Residues in contact with GLN 610 (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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587A GLU* 5.0 0.6 - - - +
601A LYS* 2.8 30.2 + - - +
606B VAL* 3.2 17.0 + - + +
607B ALA* 3.5 15.5 - - - +
608B VAL 3.3 0.8 - - - -
609B LEU* 1.3 72.5 - - - +
611B ALA* 1.4 83.0 + - - +
612B HIS* 4.8 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