Contacts of the helix formed by residues 590 - 597 (chain A) in PDB entry 1GPU
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 590 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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497A GLN* 3.5 16.7 - - - +
498A VAL* 2.8 35.1 + - - +
499A TRP* 3.6 24.2 - - + -
545A GLY* 3.0 9.6 + - - +
588A LEU* 3.2 2.1 + - - -
589A PRO* 1.3 81.3 - - - +
591A PHE* 1.3 69.0 + - - +
592A PHE* 3.2 7.6 + - - +
593A THR* 2.6 33.3 + - - +
594A PHE* 2.9 25.0 + - - +
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Residues in contact with PHE 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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491A ARG* 3.6 60.6 - - + +
498A VAL 4.5 1.4 + - - -
588A LEU* 4.1 14.1 - - + -
590A ASP* 1.3 75.1 + - - +
592A PHE* 1.3 58.0 + - - +
594A PHE* 3.2 3.1 + - - -
595A ASP* 2.8 36.8 + - - -
622A CYS* 3.8 22.2 - - + -
623A TRP* 3.7 40.2 - + - -
625A LYS* 4.0 15.7 - - + +
626A TYR* 3.4 41.1 + + - +
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Residues in contact with PHE 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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493A LEU 6.0 0.4 - - - -
495A ASN* 3.7 39.0 - - - -
496A ILE 3.5 29.6 - - - +
497A GLN* 3.7 17.3 - - + -
498A VAL* 6.1 0.2 - - + -
520A THR* 3.9 16.8 - - + -
590A ASP* 3.2 11.0 + - - +
591A PHE* 1.3 80.7 - - - +
593A THR* 1.3 68.9 + - - +
595A ASP* 3.3 7.6 + - + +
596A LYS* 3.2 56.1 + - + +
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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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497A GLN* 4.3 4.7 + - - -
499A TRP* 3.4 12.9 - - + -
513A ASN* 3.7 10.8 + - - +
543A SER 3.2 28.0 - - - +
544A LYS 3.5 1.6 - - - -
545A GLY* 3.5 19.3 - - - +
590A ASP* 2.6 23.7 + - - -
592A PHE* 1.3 84.3 - - - +
594A PHE* 1.3 62.6 + - - +
596A LYS* 3.1 13.1 + - + +
597A GLN* 2.9 28.2 + - - +
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Residues in contact with PHE 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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544A LYS 3.4 10.0 + - - -
545A GLY 3.8 7.0 - - - +
546A GLY* 3.5 31.4 - - - -
588A LEU* 3.9 10.3 - - + -
590A ASP 2.9 17.9 + - - +
591A PHE* 3.5 5.4 - - - +
593A THR* 1.3 77.5 - - - +
595A ASP* 1.3 63.6 + - - +
597A GLN* 3.0 18.7 + - - +
601A TYR* 4.1 6.5 - + - -
602A ARG* 3.3 58.6 - - + -
605A VAL* 4.1 18.6 - - + -
606A LEU* 4.0 15.0 - - + -
626A TYR* 3.6 36.1 - + - -
676A LEU* 4.4 1.6 - - + -
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Residues in contact with ASP 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 PHE* 2.8 24.5 + - - +
592A PHE* 3.3 6.7 + - + +
594A PHE* 1.3 72.5 - - - +
596A LYS* 1.3 62.4 + - + +
597A GLN 3.2 6.5 + - - +
602A ARG* 3.6 23.8 + - - +
625A LYS* 2.7 28.5 + - - -
626A TYR* 2.5 29.6 + - - -
676A LEU* 5.5 0.3 - - - +
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Residues in contact with LYS 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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592A PHE* 3.2 46.6 + - + +
593A THR* 3.1 12.1 + - - +
594A PHE 3.1 1.0 - - - -
595A ASP* 1.3 75.3 - - + +
597A GLN* 1.3 71.1 + - - +
598A PRO* 3.8 1.4 - - - +
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Residues in contact with GLN 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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543A SER 4.6 0.8 + - - -
544A LYS* 3.2 41.5 + - - +
593A THR* 2.9 27.5 + - - +
594A PHE* 3.0 17.1 + - - +
595A ASP 3.6 1.6 - - - +
596A LYS* 1.3 85.6 - - - +
598A PRO* 1.3 79.8 - - + +
599A LEU 3.5 0.3 + - - -
601A TYR* 3.6 28.9 - - + -
602A ARG* 3.0 19.4 + - + -
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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