Contacts of the helix formed by residues 584 - 593 (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 ASP 584 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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582A GLU 3.8 1.0 + - - -
583A ILE* 1.4 77.5 - - - +
585A ASN* 1.3 65.9 + - - +
586A SER* 3.4 11.2 + - - +
587A GLU* 2.8 38.8 + - - +
588A LEU* 3.1 16.8 + - - +
575B LYS* 4.3 13.1 - - - +
609B LEU* 4.6 8.7 + - - +
611B ALA* 4.2 12.7 - - - +
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Residues in contact with ASN 585 (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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542A ALA* 5.7 4.7 - - + -
545A LEU* 4.1 18.4 - - + +
546A ALA 5.6 0.2 - - - +
553A GLN* 2.7 38.3 + - - +
554A LYS* 5.5 4.3 + - - +
557A LEU* 3.3 23.8 - - + +
581A LEU 5.5 1.0 - - - +
583A ILE 4.4 5.0 - - - +
584A ASP* 1.3 71.0 - - - +
586A SER* 1.3 57.0 + - - +
588A LEU* 3.3 9.6 + - - +
589A LEU* 2.9 35.2 + - + +
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Residues in contact with SER 586 (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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542A ALA* 3.8 21.3 - - - +
584A ASP* 3.3 8.9 + - - +
585A ASN* 1.3 76.2 - - - +
587A GLU* 1.3 61.8 + - - +
589A LEU* 3.4 10.2 + - - +
590A TYR* 3.1 21.8 + - - +
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Residues in contact with GLU 587 (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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583A ILE* 3.6 18.6 - - + -
584A ASP* 2.8 30.2 + - - +
586A SER* 1.3 69.6 - - - +
588A LEU* 1.3 60.3 + - - +
590A TYR* 3.3 13.0 + - - +
591A MSE 3.0 42.4 + - - +
597A SER* 5.3 0.9 - - - -
601A LYS* 4.7 6.9 - - - -
610B GLN 5.0 2.2 - - - +
611B ALA* 3.5 18.5 - - + +
612B HIS* 2.8 56.0 + - - +
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Residues in contact with LEU 588 (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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557A LEU* 3.7 31.4 - - + -
561A LEU* 3.8 20.9 - - + +
580A LEU 3.2 24.2 - - - +
581A LEU* 4.1 20.0 - - + +
583A ILE* 3.3 25.4 - - + +
584A ASP 3.1 11.7 + - - +
585A ASN* 3.3 10.3 + - - +
587A GLU* 1.3 76.3 - - - +
589A LEU* 1.4 56.4 + - - +
591A MSE 3.3 26.1 + - + +
592A LEU* 2.9 33.9 + - - +
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Residues in contact with LEU 589 (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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540A LEU* 3.3 42.6 - - + +
541A THR* 3.7 4.7 - - - -
542A ALA* 3.5 32.5 - - + +
545A LEU* 4.1 8.7 - - + -
557A LEU* 3.8 17.5 - - + -
585A ASN 2.9 23.6 + - - +
586A SER* 3.7 8.7 - - - +
587A GLU 3.4 0.4 - - - -
588A LEU* 1.4 71.4 - - - +
590A TYR* 1.3 66.1 + - - +
592A LEU* 3.4 18.4 + - + +
593A GLU* 3.5 21.7 + - - +
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Residues in contact with TYR 590 (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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586A SER 3.1 13.4 + - - +
587A GLU* 3.4 17.9 - - - +
589A LEU* 1.3 76.7 - - - +
591A MSE 1.4 58.0 + - - +
593A GLU* 3.0 11.3 + - + +
594A SER* 2.9 48.0 + - - -
597A SER* 3.1 28.4 + - - -
612B HIS* 3.4 54.4 + + + -
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Residues in contact with MSE 591 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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561A LEU* 4.9 2.2 - - + -
580A LEU* 3.8 26.7 - - + -
583A ILE* 4.0 12.3 - - + -
587A GLU* 3.0 45.9 + - - +
588A LEU* 3.6 28.0 - - + +
590A TYR* 1.4 76.4 - - - +
592A LEU* 1.4 60.2 + - - +
593A GLU 3.1 0.4 - - - -
594A SER* 3.2 24.6 + - - +
595A PRO* 4.8 0.3 - - - +
597A SER* 4.2 21.1 - - - +
598A LEU* 3.6 29.5 - - + +
601A LYS* 3.9 25.8 - - + -
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Residues in contact with LEU 592 (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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540A LEU* 4.9 2.7 - - + -
557A LEU* 3.8 31.2 - - + +
560A ARG* 3.6 47.1 - - + +
561A LEU* 3.7 25.4 - - + +
564A LEU* 4.1 21.7 - - + +
588A LEU 2.9 15.5 + - - +
589A LEU* 3.6 18.4 - - + +
590A TYR 3.2 0.4 - - - -
591A MSE 1.4 75.2 - - - +
593A GLU* 1.3 61.3 + - + +
594A SER 3.6 0.2 - - - -
595A PRO* 5.8 0.9 - - - +
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Residues in contact with GLU 593 (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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539A THR* 3.5 27.3 - - - +
540A LEU 5.1 2.1 - - - +
589A LEU* 3.5 15.5 + - - +
590A TYR* 3.0 10.9 + - + +
592A LEU* 1.3 80.4 - - + +
594A SER* 1.3 59.0 - - - +
595A PRO* 3.7 9.8 - - - +
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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