Contacts of the helix formed by residues 572 - 581 (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 LEU 572 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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569A HIS* 3.5 10.5 + - + +
571A THR* 1.3 89.4 - - + +
573A ALA* 1.4 53.2 - - - +
574A GLY 3.3 2.7 - - - -
575A LYS* 3.0 33.1 + - + +
576A ILE* 2.9 47.2 + - + +
606A VAL* 4.6 23.8 - - + +
609A LEU* 4.3 22.0 - - + -
701A CL 4.1 1.0 - - - +
584B ASP* 6.1 0.2 - - - +
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Residues in contact with ALA 573 (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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562A PHE* 3.6 20.4 - - + -
565A ILE* 3.8 10.9 - - + +
566A GLN* 3.7 23.8 - - + +
569A HIS 3.0 17.3 + - - +
570A PRO 3.6 12.5 + - - +
571A THR 3.4 2.2 - - - -
572A LEU* 1.4 74.8 - - - +
574A GLY* 1.3 55.9 + - - +
577A THR* 2.7 39.7 + - - -
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Residues in contact with GLY 574 (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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562A PHE* 3.7 14.8 - - - -
571A THR 5.2 1.0 + - - -
572A LEU 3.3 1.0 - - - -
573A ALA* 1.3 76.9 - - - +
575A LYS* 1.3 55.8 + - - +
578A GLY* 3.1 24.1 + - - -
582B GLU* 4.5 1.8 - - - +
542D ALA* 5.3 1.1 - - - -
546D ALA* 3.5 20.6 - - - +
553D GLN* 5.6 0.9 + - - -
586D SER* 6.0 0.9 + - - -
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Residues in contact with LYS 575 (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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571A THR 5.8 0.4 - - - +
572A LEU* 3.0 29.7 + - + +
574A GLY* 1.3 72.5 - - - +
576A ILE* 1.4 63.8 + - - +
578A GLY 3.4 1.4 + - - -
579A MSE 3.1 23.2 + - - +
609A LEU* 4.0 24.5 - - + +
582B GLU* 3.4 44.9 + - + +
583B ILE* 5.1 0.4 - - - +
584B ASP* 2.7 41.0 + - - +
584D ASP* 5.9 2.0 + - - -
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Residues in contact with ILE 576 (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* 3.7 22.0 - - + -
569A HIS* 3.7 19.7 - - + -
572A LEU* 2.9 38.1 + - + +
575A LYS* 1.4 67.7 - - - +
577A THR* 1.4 59.0 + - - +
579A MSE 3.2 7.0 + - - +
580A LEU* 2.9 39.2 + - + +
602A VAL* 4.0 16.8 - - + -
605A ALA* 3.9 20.4 - - + -
606A VAL* 3.7 25.8 - - + -
609A LEU* 3.8 17.3 - - + -
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Residues in contact with THR 577 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
558A GLY* 4.3 11.0 - - - +
561A LEU* 4.5 5.1 - - + +
562A PHE* 3.5 33.2 - - + +
565A ILE* 3.5 21.0 - - - +
573A ALA 2.7 22.5 + - - -
574A GLY 3.8 4.5 - - - -
576A ILE* 1.4 74.0 - - - +
578A GLY* 1.3 61.3 - - - +
579A MSE 3.3 0.2 + - - -
580A LEU* 3.3 2.1 + - - +
581A LEU* 3.0 44.1 + - + +
543D SER 5.3 0.2 - - - +
546D ALA* 3.9 18.4 - - + -
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Residues in contact with GLY 578 (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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554A LYS* 5.6 0.7 + - - -
574A GLY 3.1 12.5 + - - -
575A LYS 3.4 1.3 + - - -
576A ILE 3.4 0.2 - - - -
577A THR* 1.3 77.2 - - - +
579A MSE 1.4 59.7 + - - +
581A LEU* 3.5 13.9 + - - +
582A GLU* 3.9 12.6 - - - +
578B GLY 5.8 0.2 - - - +
579B MSE 5.7 0.4 - - - -
582B GLU* 3.4 21.7 - - - +
546D ALA 3.2 23.5 + - - -
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Residues in contact with MSE 579 (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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575A LYS 3.1 11.4 + - - +
576A ILE* 3.2 8.5 + - - +
578A GLY* 1.4 73.4 - - - +
580A LEU* 1.3 63.1 + - - +
582A GLU* 3.1 22.5 + - - +
583A ILE* 4.4 0.9 + - - +
605A ALA* 3.6 42.4 - - + +
608A VAL* 3.6 31.4 - - + -
609A LEU* 3.7 27.1 - - + -
579B MSE 3.6 48.6 - - + +
582B GLU* 3.9 7.3 + - + -
583B ILE* 5.2 0.4 - - + -
608B VAL* 4.5 9.4 - - + -
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Residues in contact with LEU 580 (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* 5.0 3.6 - - + -
565A ILE* 3.8 24.9 - - + -
576A ILE* 2.9 25.7 + - + +
577A THR 4.0 3.1 - - - +
579A MSE 1.3 71.8 - - - +
581A LEU* 1.3 56.1 + - - +
582A GLU 3.1 0.4 - - - -
583A ILE* 3.1 39.7 + - + +
588A LEU* 3.2 11.5 - - + +
591A MSE 3.8 21.1 - - + -
598A LEU* 4.0 3.6 - - + -
601A LYS* 3.8 16.2 - - + +
602A VAL* 3.9 23.6 - - + +
605A ALA* 4.0 8.1 - - + -
608B VAL* 3.8 26.2 - - + -
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Residues in contact with LEU 581 (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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554A LYS* 3.4 52.7 - - + +
557A LEU* 3.9 10.1 - - + -
558A GLY* 3.6 13.5 - - - +
561A LEU* 3.8 16.4 - - + -
577A THR* 3.0 33.4 + - + +
578A GLY 3.7 7.4 - - - +
579A MSE 3.2 1.0 - - - -
580A LEU* 1.3 74.8 - - - +
582A GLU* 1.3 60.0 + - - +
583A ILE 3.3 7.1 + - - +
585A ASN* 5.5 1.0 - - - +
588A LEU* 4.1 8.6 - - + +
546D ALA 3.9 5.8 - - - +
547D SER* 3.5 39.9 - - - +
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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