Contacts of the helix formed by residues 587 - 600 (chain A) in PDB entry 5I75
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 ILE 587 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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167A ILE* 5.4 4.3 - - + -
583A THR* 3.2 19.5 - - - +
584A SER* 3.4 29.4 - - - +
585A SER 3.4 1.5 - - - +
586A PHE* 1.3 78.1 - - - +
588A CYS* 1.3 57.4 + - + +
589A ILE 3.4 0.2 - - - -
590A PRO* 3.4 7.5 - - - +
591A THR* 2.7 37.9 + - + +
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Residues in contact with CYS 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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160A GLY* 3.4 8.6 - - - -
163A TYR* 4.0 16.4 - - + -
164A ALA* 3.4 41.1 - - - -
167A ILE* 4.4 10.1 - - + -
585A SER 3.7 10.3 - - - +
586A PHE* 3.0 0.8 - - - -
587A ILE* 1.3 82.2 - - + +
589A ILE* 1.3 67.2 + - - +
591A THR* 3.2 6.3 + - - -
592A TYR* 3.0 27.9 + - - +
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Residues in contact with ILE 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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157A ILE 4.1 3.2 - - - +
158A PHE* 4.5 11.4 - - + -
160A GLY* 4.0 18.8 - - - -
161A ILE* 3.7 19.1 - - + +
164A ALA* 5.0 2.9 - - + -
504A VAL* 6.0 1.3 - - + -
507A ILE* 3.7 37.9 - - + -
586A PHE* 3.0 37.7 + - + +
588A CYS* 1.3 82.0 - - - +
590A PRO* 1.3 66.7 - - + +
592A TYR* 3.9 2.1 - - - +
593A ILE* 3.1 33.0 + - + +
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Residues in contact with PRO 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 PHE* 3.0 30.7 - - + +
587A ILE* 3.4 8.1 - - - +
589A ILE* 1.3 84.9 - - + +
591A THR* 1.3 62.4 + - + +
593A ILE* 3.0 15.2 + - + +
594A ALA* 2.8 28.6 + - - +
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Residues in contact with THR 591 (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 ILE* 2.7 28.3 + - + +
588A CYS* 3.2 12.0 + - - -
590A PRO* 1.3 80.5 - - + +
592A TYR* 1.3 57.1 + - - +
594A ALA* 3.6 9.4 + - - +
595A TYR* 2.9 24.3 + - - +
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Residues in contact with TYR 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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156A PRO 2.9 25.6 - - - -
157A ILE* 3.5 16.6 - - - -
159A LYS* 3.4 26.4 + - + +
160A GLY* 3.9 15.5 - - - -
163A TYR* 5.1 17.7 - + + -
588A CYS 3.0 20.8 + - - +
589A ILE 3.9 2.9 - - - +
591A THR* 1.3 75.3 - - - +
593A ILE* 1.3 64.4 + - - +
594A ALA 3.2 0.2 - - - -
595A TYR* 2.9 32.0 + + + +
596A ARG* 2.9 50.9 + - + +
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Residues in contact with ILE 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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157A ILE* 3.1 44.8 - - + +
158A PHE* 3.7 30.3 - - + -
589A ILE* 3.1 18.4 + - + +
590A PRO* 3.0 13.2 + - + +
592A TYR* 1.3 76.8 - - - +
594A ALA* 1.3 57.6 + - - +
596A ARG* 3.5 1.7 + - - +
597A LEU* 2.9 33.7 + - + +
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Residues in contact with ALA 594 (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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590A PRO 2.8 15.6 + - - +
591A THR* 3.8 9.4 - - - +
593A ILE* 1.3 77.2 - - - +
595A TYR* 1.3 58.8 + - - +
597A LEU* 3.7 7.0 - - - +
598A ILE* 2.9 31.9 + - - +
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Residues in contact with TYR 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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591A THR 2.9 17.4 + - - +
592A TYR* 2.9 39.9 + + + +
594A ALA* 1.3 75.8 - - - +
596A ARG* 1.3 68.7 + - + +
598A ILE* 3.0 7.0 + - - +
599A ILE* 2.8 41.0 + - + +
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Residues in contact with ARG 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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152A ARG* 5.4 5.9 - - - +
156A PRO* 3.2 37.2 - - + +
157A ILE* 3.9 25.1 - - + -
159A LYS* 5.0 5.3 - - - +
592A TYR* 2.9 46.2 + - + +
595A TYR* 1.3 79.5 - - + +
597A LEU* 1.3 62.5 + - - +
599A ILE* 3.0 21.5 + - - -
600A THR* 3.0 25.9 + - - +
607A ARG* 5.0 1.5 - - - +
610A LYS 4.9 4.6 + - - -
611A SER* 4.6 10.5 - - - -
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Residues in contact with LEU 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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157A ILE* 5.1 2.2 - - + +
593A ILE* 2.9 23.3 + - + +
594A ALA* 3.8 8.3 - - - +
595A TYR 3.2 0.2 - - - -
596A ARG* 1.3 76.5 - - - +
598A ILE* 1.3 58.5 + - - +
600A THR 4.4 8.8 - - - +
607A ARG* 4.7 14.7 - - + +
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Residues in contact with ILE 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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594A ALA 2.9 17.7 + - - +
595A TYR* 3.0 5.6 + - - +
597A LEU* 1.3 78.9 - - - +
599A ILE* 1.3 59.2 + - - +
600A THR 5.0 1.5 - - - +
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Residues in contact with ILE 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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595A TYR* 2.8 29.8 + - + +
596A ARG* 3.0 15.2 + - - +
598A ILE* 1.3 80.1 - - - +
600A THR* 1.3 65.5 + - - +
601A PRO* 3.2 11.6 - - - +
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Residues in contact with THR 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 ARG* 3.0 19.9 + - - +
597A LEU 4.4 6.1 - - - +
598A ILE 5.0 0.9 - - - -
599A ILE* 1.3 75.7 - - - +
601A PRO* 1.3 72.3 - - - +
602A GLY 4.5 2.3 - - - +
607A ARG* 3.6 38.9 - - - +
610A LYS* 5.3 7.4 - - - -
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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