Contacts of the helix formed by residues 587 - 597 (chain A) in PDB entry 1RY2
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 587 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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520A GLU* 5.0 3.6 + - - -
572A LEU* 3.3 50.9 + - - +
574A ARG 6.4 0.2 - - - -
575A VAL* 5.1 2.0 - - - -
578A VAL* 3.7 17.4 - - - +
585A ARG 3.8 4.2 + - - -
586A LEU* 1.3 75.4 - - - +
588A THR* 1.3 65.0 + - - +
589A ALA 3.5 0.4 + - - -
590A GLU* 4.2 10.6 + - - +
591A ILE* 4.0 18.8 + - - +
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Residues in contact with THR 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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572A LEU 3.6 1.4 + - - -
573A GLY* 3.5 20.3 + - - +
577A ASP* 3.5 34.8 - - + +
578A VAL* 5.0 0.8 - - - +
579A VAL* 6.1 1.6 - - + -
586A LEU 4.8 1.6 - - - +
587A SER* 1.3 72.9 - - - +
589A ALA* 1.3 69.0 + - - +
591A ILE* 3.3 4.2 + - - +
592A GLU* 2.9 49.5 + - - +
606A VAL* 3.7 25.8 - - + +
678A ARG* 4.3 9.8 + - - -
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Residues in contact with ALA 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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445A PRO* 4.4 19.2 - - + +
571A ILE 3.6 13.0 - - - +
572A LEU* 3.1 34.1 + - + +
573A GLY 4.0 0.9 - - - +
587A SER 3.5 0.4 - - - -
588A THR* 1.3 82.0 + - - +
590A GLU* 1.3 62.7 + - - +
592A GLU* 4.3 3.4 - - - +
593A ALA* 3.1 27.2 + - - +
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Residues in contact with GLU 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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572A LEU* 5.8 6.7 - - + +
587A SER* 4.2 13.5 + - - +
588A THR 3.3 0.8 - - - -
589A ALA* 1.3 79.1 - - - +
591A ILE* 1.3 64.4 + - + +
593A ALA* 4.1 3.2 - - - +
594A ALA* 3.3 24.4 + - - +
653A ILE* 4.1 28.1 - - + +
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Residues in contact with ILE 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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579A VAL* 5.0 5.6 - - + -
586A LEU* 3.9 30.7 - - + -
587A SER 4.0 10.5 + - - +
588A THR* 3.3 7.8 + - - +
590A GLU* 1.3 76.6 - - + +
592A GLU* 1.3 60.3 + - - +
594A ALA* 3.6 5.7 + - - +
595A ILE* 3.0 33.7 + - + +
606A VAL* 3.8 24.7 - - + -
618A VAL* 5.0 3.4 - - + -
649A VAL* 4.7 10.0 - - + +
653A ILE* 4.5 13.7 - - + -
657A ALA* 4.0 37.9 - - + +
659A PRO* 5.0 6.1 - - + -
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Residues in contact with GLU 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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588A THR* 2.9 40.8 + - - +
589A ALA* 4.3 2.1 - - - +
591A ILE* 1.3 72.8 - - - +
593A ALA* 1.3 62.0 + - - +
594A ALA 3.2 0.2 - - - -
595A ILE* 3.0 9.0 + - - +
596A ILE* 2.9 35.8 + - + +
604A CYS* 3.5 16.9 - - - +
605A ALA* 2.9 12.2 - - - -
606A VAL* 2.6 44.6 + - + +
676A ILE* 6.1 0.2 - - - -
678A ARG* 3.8 18.0 + - - -
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Residues in contact with ALA 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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447A ALA* 3.9 23.9 - - + +
448A ALA 5.3 0.9 - - - +
589A ALA 3.1 20.3 + - - +
590A GLU* 4.1 4.7 - - - +
592A GLU* 1.3 76.6 - - - +
594A ALA* 1.3 57.9 + - - +
596A ILE* 3.0 14.6 - - - +
597A GLU* 3.0 34.9 + - - +
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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 GLU 3.3 16.7 + - - +
591A ILE 3.8 5.2 - - - +
593A ALA* 1.3 78.7 - - - +
595A ILE* 1.3 66.2 + - + +
597A GLU* 3.7 19.8 + - - +
598A ASP* 4.7 2.1 - - - +
648A THR* 5.3 7.0 + - - +
649A VAL* 6.1 1.8 - - + -
652A ASP* 5.9 1.6 - - + +
653A ILE* 3.7 27.1 - - + -
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Residues in contact with ILE 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 ILE* 3.0 26.0 - - + +
592A GLU 3.0 7.2 + - - +
594A ALA* 1.3 75.8 - - + +
596A ILE* 1.3 68.5 + - - +
597A GLU 2.8 2.7 + - - -
598A ASP* 3.0 18.9 + - - +
601A VAL* 3.0 19.2 - - + +
604A CYS* 3.4 31.9 - - + -
606A VAL* 5.3 0.9 - - + -
620A ALA* 5.7 1.6 - - + -
622A VAL* 4.6 12.6 - - + -
645A LEU* 3.9 26.0 - - + +
648A THR* 4.6 3.8 - - + -
649A VAL* 3.5 31.9 - - + -
659A PRO* 5.7 3.1 - - + -
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Residues in contact with ILE 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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418A ARG* 5.0 18.2 - - + +
447A ALA* 3.4 30.3 - - + +
449A GLU* 3.6 15.8 - - - +
450A VAL* 5.0 4.5 - - + -
592A GLU* 2.9 15.5 + - + +
593A ALA* 3.0 15.9 - - - +
595A ILE* 1.3 72.7 - - - +
597A GLU* 1.3 57.4 + - - +
598A ASP 2.6 21.2 + - - +
601A VAL* 3.3 19.1 - - - +
602A ALA* 4.5 3.7 - - - -
603A GLU* 3.6 13.7 - - - +
604A CYS* 3.2 34.3 - - + +
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Residues in contact with GLU 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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447A ALA* 5.0 0.9 - - - +
448A ALA* 4.1 12.6 + - - +
449A GLU* 3.3 53.9 + - + +
593A ALA* 3.0 21.3 + - - +
594A ALA* 3.7 14.2 - - - +
595A ILE 2.8 2.5 + - - -
596A ILE* 1.3 72.6 - - - +
598A ASP* 1.3 57.2 + - - +
599A PRO* 4.5 3.3 - - - +
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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