Contacts of the helix formed by residues 594 - 610 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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590A TYR* 2.9 41.7 + - - -
591A MSE 3.2 7.9 + - - +
592A LEU 3.6 0.2 - - - -
593A GLU* 1.3 80.6 - - - +
595A PRO* 1.4 66.5 - - - +
596A GLU* 4.2 5.5 + - - +
597A SER* 3.0 24.2 + - - -
598A LEU 3.0 18.9 + - - -
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Residues in contact with PRO 595 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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568A MSE 4.7 4.7 - - + +
591A MSE 4.3 0.9 - - - +
592A LEU 5.8 1.1 - - - +
593A GLU 3.7 7.9 - - - +
594A SER* 1.4 85.3 - - - +
596A GLU* 1.3 56.1 + - - +
598A LEU* 3.5 9.1 + - + +
599A ARG* 3.1 30.2 + - - +
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Residues in contact with GLU 596 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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594A SER* 4.4 6.3 - - - +
595A PRO* 1.3 81.5 - - + +
597A SER* 1.3 56.2 + - - +
599A ARG* 3.5 5.6 + - - +
600A SER* 3.2 27.0 + - - -
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Residues in contact with SER 597 (chain A).
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* 5.3 1.8 - - - -
590A TYR* 3.1 28.8 + - - -
591A MSE 4.2 12.3 - - - -
594A SER* 3.0 23.2 + - - -
596A GLU* 1.3 74.3 - - - +
598A LEU* 1.3 65.4 + - - +
600A SER* 3.0 19.7 + - - -
601A LYS* 3.1 18.2 + - - +
612B HIS* 5.1 5.1 - - - +
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Residues in contact with LEU 598 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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561A LEU* 3.8 27.1 - - + -
564A LEU* 3.8 33.9 - - + -
565A ILE* 4.3 4.7 - - + -
568A MSE 3.7 22.7 - - + -
580A LEU* 4.0 11.4 - - + -
591A MSE 3.6 41.4 - - + +
594A SER 3.0 8.1 + - - +
595A PRO* 3.9 7.9 - - + +
597A SER* 1.3 77.6 - - - +
599A ARG* 1.4 50.4 - - - +
601A LYS* 3.2 3.4 + - - +
602A VAL* 2.9 42.3 + - + +
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Residues in contact with ARG 599 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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568A MSE 3.5 57.4 + - + +
569A HIS* 3.7 17.8 + - - -
595A PRO 3.1 18.1 + - - +
596A GLU* 3.8 6.5 - - - +
597A SER 3.3 0.2 - - - -
598A LEU* 1.4 76.6 - - - +
600A SER* 1.4 56.7 + - - +
602A VAL* 3.3 3.0 + - - +
603A ASP* 3.0 64.3 + - - +
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Residues in contact with SER 600 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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596A GLU 3.2 13.5 + - - -
597A SER* 3.0 17.3 + - - -
599A ARG* 1.4 76.9 - - - +
601A LYS* 1.3 59.0 + - - +
603A ASP* 3.5 10.7 + - - +
604A GLU* 3.0 36.0 + - - +
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Residues in contact with LYS 601 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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580A LEU* 3.8 10.8 - - + +
583A ILE* 4.3 7.4 - - + -
587A GLU* 4.7 13.0 - - - +
591A MSE 3.9 30.5 - - + -
597A SER* 3.1 22.1 + - - +
598A LEU 3.6 3.6 - - - +
600A SER* 1.3 75.2 - - - +
602A VAL* 1.4 61.9 + - - +
604A GLU* 3.2 20.4 + - - +
605A ALA* 2.9 28.6 + - - +
607B ALA 3.0 22.0 + - - -
608B VAL* 3.1 19.7 + - + +
610B GLN* 2.8 28.5 + - - +
612B HIS* 5.4 2.7 - - - +
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Residues in contact with VAL 602 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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565A ILE* 3.9 26.5 - - + -
568A MSE 3.8 24.2 - - + -
569A HIS* 3.5 31.9 - - + +
576A ILE* 4.0 20.0 - - + -
580A LEU* 3.9 11.4 - - + -
598A LEU* 2.9 23.4 + - + +
599A ARG* 3.3 6.0 + - - +
601A LYS* 1.4 74.0 - - - +
603A ASP* 1.3 51.1 + - - +
605A ALA* 3.1 4.3 + - - +
606A VAL* 2.8 37.3 + - - +
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Residues in contact with ASP 603 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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569A HIS* 4.2 10.4 + - - -
599A ARG* 3.0 54.2 + - - +
600A SER* 3.6 9.2 - - - +
601A LYS 3.3 0.2 - - - -
602A VAL* 1.3 74.3 - - - +
604A GLU* 1.3 57.3 + - + +
606A VAL* 3.4 8.8 + - - +
607A ALA* 3.1 26.5 + - - +
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Residues in contact with GLU 604 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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600A SER* 3.0 18.9 + - - +
601A LYS* 3.2 41.0 + - - +
603A ASP* 1.3 72.4 - - - +
605A ALA* 1.4 63.3 + - - +
607A ALA* 3.3 9.0 + - - +
608A VAL* 3.2 24.9 + - - +
604B GLU* 5.2 0.6 - - - +
607B ALA* 3.5 31.9 - - + +
608B VAL* 3.8 13.4 - - + +
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Residues in contact with ALA 605 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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576A ILE* 3.9 24.2 - - + +
579A MSE 3.6 27.7 - - + +
580A LEU* 4.0 11.0 - - + -
601A LYS 2.9 13.0 + - - +
602A VAL 3.4 8.3 - - - +
604A GLU* 1.4 72.3 - - - +
606A VAL* 1.4 65.6 + - - +
608A VAL* 3.1 6.7 + - - +
609A LEU* 3.1 26.8 + - - +
608B VAL* 4.1 1.9 - - + +
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Residues in contact with VAL 606 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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569A HIS* 3.9 33.0 - - + +
572A LEU* 4.6 12.7 - - + +
576A ILE* 3.7 24.9 - - + -
602A VAL 2.8 20.3 + - - +
603A ASP* 3.6 9.2 - - - +
604A GLU 3.3 0.2 - - - -
605A ALA* 1.4 75.7 - - - +
607A ALA* 1.3 61.4 + - - +
609A LEU* 3.3 11.0 + - - +
610A GLN* 3.2 21.9 + - + +
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Residues in contact with ALA 607 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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603A ASP 3.1 13.8 + - - +
604A GLU* 3.5 12.1 - - - +
605A ALA 3.3 0.2 - - - -
606A VAL* 1.3 77.4 - - - +
608A VAL* 1.4 61.6 + - - +
610A GLN* 3.3 18.5 + - - +
601B LYS* 3.1 16.6 + - - -
604B GLU* 3.5 19.8 - - - +
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Residues in contact with VAL 608 (chain A).
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 3.6 22.9 - - + -
604A GLU 3.2 16.3 + - - +
605A ALA 3.1 8.6 + - - +
607A ALA* 1.4 76.4 - - - +
609A LEU* 1.3 56.3 + - - +
580B LEU* 3.7 30.1 - - + -
583B ILE* 3.5 11.1 - - + +
601B LYS* 3.2 27.7 + - + +
604B GLU* 3.6 39.9 - - + -
605B ALA* 4.1 2.5 - - + +
608B VAL* 3.9 11.9 - - + -
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Residues in contact with LEU 609 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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572A LEU* 4.3 24.5 - - + -
575A LYS* 4.0 24.7 - - + +
576A ILE* 3.8 29.4 - - + +
579A MSE 3.7 19.3 - - + -
605A ALA 3.1 15.9 + - - +
606A VAL* 3.3 8.7 + - - +
608A VAL* 1.3 73.3 - - - +
610A GLN* 1.3 64.0 + - - +
611A ALA* 3.4 4.0 + - - +
582B GLU* 3.7 29.8 - - + +
583B ILE* 4.0 20.9 - - + +
584B ASP* 5.2 5.5 - - - +
587B GLU* 5.3 0.2 - - - +
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Residues in contact with GLN 610 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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606A VAL* 3.2 13.3 + - + +
607A ALA* 3.5 17.4 - - - +
608A VAL 3.3 1.2 - - - -
609A LEU* 1.3 73.9 - - - +
611A ALA* 1.3 75.3 + - - +
587B GLU* 5.0 0.7 - - - +
601B LYS* 2.8 31.2 + - - +
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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