Contacts of the helix formed by residues 590 - 597 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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497B GLN* 3.5 11.7 - - - +
498B VAL* 2.7 35.3 + - - +
499B TRP* 3.6 24.9 - - + -
545B GLY 3.1 8.8 + - - +
588B LEU* 3.1 1.3 + - - -
589B PRO* 1.3 80.8 - - - +
591B PHE* 1.3 67.8 + - - +
592B PHE* 3.4 11.5 + - - +
593B THR* 2.6 33.8 + - - +
594B PHE* 3.0 24.0 + - - +
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Residues in contact with PHE 591 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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491B ARG* 3.5 64.2 - - + +
498B VAL 4.5 1.2 + - - -
588B LEU* 3.9 16.4 - - + -
590B ASP* 1.3 74.4 + - - +
592B PHE* 1.3 56.5 + - - +
594B PHE* 3.2 0.7 + - - +
595B ASP* 2.8 37.2 + - - +
622B CYS* 3.8 21.8 - - + -
623B TRP* 3.6 38.4 - + - -
625B LYS* 4.0 15.7 - - + +
626B TYR* 3.3 41.0 + + - +
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Residues in contact with PHE 592 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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493B LEU 6.1 0.2 - - - -
495B ASN* 3.8 26.0 - - - -
496B ILE 3.5 28.7 - - - +
497B GLN* 3.7 18.2 - - + -
520B THR* 3.9 28.5 - - + -
590B ASP* 3.3 12.3 + - - +
591B PHE* 1.3 80.1 - - - +
593B THR* 1.3 69.5 + - - +
595B ASP* 3.2 8.1 + - + +
596B LYS* 3.2 54.8 + - + +
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Residues in contact with THR 593 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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497B GLN* 4.3 4.0 + - - +
499B TRP* 3.4 12.9 - - + -
513B ASN* 3.7 10.7 + - - +
543B SER 3.3 26.2 - - - +
544B LYS 3.5 1.8 - - - -
545B GLY* 3.5 19.7 - - - +
590B ASP* 2.6 24.8 + - - -
591B PHE 3.4 0.2 - - - -
592B PHE* 1.3 82.9 - - - +
594B PHE* 1.3 61.9 + - - +
596B LYS* 3.1 12.9 + - + +
597B GLN* 2.9 29.0 + - - +
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Residues in contact with PHE 594 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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544B LYS 3.4 9.3 + - - -
545B GLY 3.8 5.6 - - - -
546B GLY* 3.4 35.2 - - - -
588B LEU* 3.9 14.1 - - + -
590B ASP 3.0 18.4 + - - +
591B PHE 3.5 3.4 - - - +
593B THR* 1.3 77.3 - - - +
595B ASP* 1.3 62.1 + - - +
597B GLN* 3.0 17.3 + - - +
601B TYR* 4.1 7.2 - + - -
602B ARG* 3.2 59.5 - - + -
605B VAL* 4.1 16.8 - - + -
606B LEU* 4.0 15.0 - - + -
626B TYR* 3.6 35.0 - + - -
676B LEU* 4.5 1.6 - - + -
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Residues in contact with ASP 595 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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591B PHE 2.8 20.5 + - - +
592B PHE* 3.6 7.7 - - + +
594B PHE* 1.3 76.1 - - - +
596B LYS* 1.3 62.2 - - + +
597B GLN 3.3 7.8 + - - +
602B ARG* 3.7 20.8 + - - +
625B LYS* 2.7 29.1 + - - -
626B TYR* 2.5 30.4 + - - -
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Residues in contact with LYS 596 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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592B PHE* 3.2 47.6 + - + +
593B THR* 3.1 12.5 + - + +
594B PHE 3.0 0.6 - - - -
595B ASP* 1.3 76.6 - - + +
597B GLN* 1.3 71.6 + - - +
598B PRO* 3.8 1.7 - - - +
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Residues in contact with GLN 597 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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543B SER 4.7 0.8 + - - -
544B LYS* 3.2 43.5 + - - +
593B THR* 2.9 27.7 + - - +
594B PHE* 3.0 14.2 + - - +
595B ASP 3.6 1.9 - - - +
596B LYS* 1.3 86.7 - - - +
598B PRO* 1.3 77.7 - - + +
599B LEU 3.5 0.3 + - - -
601B TYR* 3.6 26.9 - - + -
602B ARG* 2.9 20.4 + - + -
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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