Contacts of the helix formed by residues 572 - 581 (chain C) 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 LEU 572 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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569C HIS* 3.4 14.4 + - + +
571C THR* 1.3 86.7 - - + +
573C ALA* 1.3 53.2 - - - +
574C GLY 3.4 2.5 - - - -
575C LYS* 3.1 33.3 + - + +
576C ILE* 2.9 48.0 + - + +
606C VAL* 4.7 17.0 - - + +
609C LEU* 4.2 20.6 - - + -
701C CL 3.9 13.1 - - + +
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Residues in contact with ALA 573 (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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562C PHE* 3.7 17.9 - - + -
565C ILE* 3.8 11.1 - - + +
566C GLN* 3.6 27.6 - - + +
569C HIS 3.0 17.1 + - - +
570C PRO 3.8 10.5 - - - +
571C THR 3.5 2.4 - - - -
572C LEU* 1.3 75.0 - - - +
574C GLY* 1.3 55.0 + - - +
577C THR* 2.7 38.5 + - - -
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Residues in contact with GLY 574 (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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542B ALA 5.3 0.9 - - - -
546B ALA* 3.4 19.9 - - - +
553B GLN* 5.5 1.2 + - - -
562C PHE* 3.7 15.2 - - - -
571C THR 5.1 1.4 + - - -
572C LEU 3.4 0.8 - - - -
573C ALA* 1.3 76.9 - - - +
575C LYS* 1.3 57.2 + - - +
578C GLY* 3.1 23.7 + - - -
582D GLU* 4.4 2.2 - - - +
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Residues in contact with LYS 575 (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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584B ASP* 5.9 0.8 + - - -
571C THR 5.5 3.6 - - - +
572C LEU* 3.1 31.4 + - + +
574C GLY* 1.3 74.5 - - - +
576C ILE* 1.3 64.1 + - - +
578C GLY 3.5 0.7 + - - -
579C MSE 3.1 24.8 + - - +
609C LEU* 3.9 24.0 - - + +
582D GLU* 3.4 43.7 + - + +
584D ASP* 2.9 39.8 + - - +
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Residues in contact with ILE 576 (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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565C ILE* 3.7 23.8 - - + -
569C HIS* 3.8 17.3 - - + -
572C LEU* 2.9 36.3 + - + +
575C LYS* 1.3 70.4 - - - +
577C THR* 1.4 55.5 + - - +
579C MSE 3.2 6.4 + - - +
580C LEU* 2.8 49.5 + - + +
602C VAL* 4.2 11.0 - - + -
605C ALA* 3.8 22.0 - - + -
606C VAL* 3.7 24.7 - - + -
609C LEU* 3.8 17.7 - - + -
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Residues in contact with THR 577 (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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543B SER 5.3 0.7 - - - +
546B ALA* 4.0 17.3 - - + -
558C GLY* 4.1 22.2 - - - +
561C LEU* 4.5 5.6 - - + -
562C PHE* 3.6 22.0 - - + +
565C ILE* 3.4 21.7 - - - +
573C ALA 2.7 22.5 + - - -
574C GLY 3.9 4.0 - - - -
576C ILE* 1.4 75.4 - - - +
578C GLY* 1.3 64.0 - - - +
580C LEU* 3.3 2.9 + - - +
581C LEU* 3.0 43.0 + - + +
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Residues in contact with GLY 578 (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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546B ALA 3.1 25.4 + - - -
553B GLN* 5.8 0.2 - - - -
574C GLY 3.1 13.4 + - - -
575C LYS 3.5 0.2 + - - -
576C ILE 3.3 0.2 - - - -
577C THR* 1.3 76.7 - - - +
579C MSE 1.3 61.4 + - - +
581C LEU* 3.6 13.6 + - - +
582C GLU* 4.0 11.4 - - - +
579D MSE 5.9 0.2 - - - -
582D GLU* 3.5 18.7 - - - +
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Residues in contact with MSE 579 (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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575C LYS 3.1 12.9 + - - +
576C ILE 3.2 3.8 + - - +
578C GLY* 1.3 73.9 - - - +
580C LEU* 1.4 63.7 + - - +
582C GLU* 3.1 22.9 + - - +
583C ILE 4.5 0.3 + - - -
605C ALA* 3.8 22.4 - - + +
608C VAL* 3.8 36.3 - - + -
609C LEU* 3.7 40.8 - - + -
579D MSE 3.6 54.6 - - + +
582D GLU* 3.8 10.4 + - + -
583D ILE* 5.3 0.2 - - + -
605D ALA* 5.8 0.2 - - - -
608D VAL* 4.7 3.6 - - + -
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Residues in contact with LEU 580 (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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561C LEU* 5.0 4.3 - - + -
565C ILE* 3.8 24.2 - - + -
576C ILE* 2.8 25.8 + - + +
577C THR* 4.0 4.3 - - - +
579C MSE 1.4 67.4 - - - +
581C LEU* 1.3 56.4 + - - +
582C GLU 3.1 5.2 - - - -
583C ILE* 3.1 32.4 + - + +
588C LEU* 3.2 22.3 - - + +
591C MSE 3.9 18.6 - - + -
598C LEU* 4.2 3.1 - - + -
601C LYS* 3.8 18.8 - - + +
602C VAL* 4.0 19.5 - - + +
605C ALA* 3.9 10.3 - - + -
608D VAL* 3.8 25.6 - - + -
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Residues in contact with LEU 581 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546B ALA 4.2 2.0 - - - +
547B SER* 3.6 39.7 - - - +
554C LYS* 2.9 62.1 + - + +
557C LEU* 4.0 8.1 - - + -
558C GLY* 3.7 20.2 - - - +
561C LEU* 3.9 16.2 - - + -
577C THR* 3.0 28.7 + - + +
578C GLY 3.7 7.2 - - - +
579C MSE 3.2 0.8 - - - -
580C LEU* 1.3 75.3 - - - +
582C GLU* 1.3 58.9 + - - +
583C ILE 3.3 0.7 - - - -
588C LEU* 4.1 6.7 - - + -
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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