Contacts of the strand formed by residues 587 - 593 (chain A) in PDB entry 5E2Q
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 VAL 587 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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547A VAL* 3.6 37.9 - - + -
576A LEU* 4.0 8.1 - - + -
579A LEU* 4.1 20.7 + - + +
580A LEU* 3.2 35.0 - - + +
583A GLY* 4.7 1.1 + - - -
585A GLY* 5.0 2.6 - - - -
586A LEU* 1.3 91.7 + - + +
588A THR* 1.3 65.5 + - - +
589A ILE* 4.1 7.0 - - + -
603A VAL* 5.2 0.2 - - + -
604A ARG 3.5 5.4 - - - +
605A LEU* 3.7 21.8 - - + -
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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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580A LEU* 4.5 2.0 - - - -
585A GLY* 5.7 5.2 - - - +
586A LEU 5.7 0.2 - - - +
587A VAL* 1.3 76.4 - - - +
589A ILE* 1.3 72.9 + - - +
590A THR* 3.8 14.7 + - - +
602A ARG 3.8 0.9 - - - +
603A VAL* 3.8 1.6 - - - -
604A ARG* 3.2 53.3 + - + +
653A GLU* 5.6 0.4 - - - -
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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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547A VAL* 4.7 1.1 - - + +
551A LEU* 4.5 17.9 - - + -
576A LEU* 4.3 14.1 - - + -
580A LEU* 4.4 12.2 - - + +
587A VAL* 4.1 14.6 - - + -
588A THR* 1.3 84.4 + - - +
590A THR* 1.3 66.8 + - - +
591A PRO* 3.8 7.2 - - - +
601A ALA* 5.1 1.6 - - + -
602A ARG 3.6 6.5 - - - +
603A VAL* 3.8 20.2 - - + -
652A PRO* 4.9 9.7 - - - +
653A GLU* 4.2 30.6 + - + +
655A PHE* 4.7 5.6 - - + -
658A LEU* 3.6 31.0 - - + -
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Residues in contact with THR 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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588A THR* 3.8 15.1 + - - +
589A ILE* 1.3 78.5 + - - +
591A PRO* 1.3 76.1 - - + +
592A THR* 3.5 11.6 + - + +
601A ALA* 3.3 3.2 - - - -
602A ARG* 2.7 47.4 + - - -
604A ARG* 5.7 4.0 - - - +
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Residues in contact with PRO 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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589A ILE 3.8 8.3 - - - +
590A THR* 1.3 90.8 - - + +
592A THR* 1.3 63.5 + - - +
600A ASP 3.7 8.3 - - - +
601A ALA* 4.3 4.0 - - + -
652A PRO 5.1 7.4 - - - +
653A GLU 4.7 10.1 - - - +
654A SER* 6.0 2.2 - - - -
658A LEU* 4.2 19.1 - - + -
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Residues in contact with THR 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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590A THR* 3.5 22.2 + - + +
591A PRO* 1.3 79.9 - - - +
593A THR* 1.3 72.4 + - - +
599A PRO* 3.9 4.5 - - - +
600A ASP* 2.9 30.9 + - - +
601A ALA* 3.4 19.6 + - - -
602A ARG* 4.0 21.7 + - + +
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Residues in contact with THR 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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592A THR* 1.3 83.5 + - - +
594A GLY* 1.3 70.8 + - - +
597A GLY* 3.9 17.3 - - - +
598A ARG 3.9 15.0 - - - +
599A PRO* 5.1 1.6 - - - +
600A ASP* 4.2 0.7 - - - +
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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