Contacts of the helix formed by residues 588 - 598 (chain N) in PDB entry 6PA7
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 GLU 588 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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586N VAL 4.4 7.4 - - - +
587N CYS* 1.3 75.7 - - - +
589N GLU* 1.3 62.4 - - + +
590N SER 3.5 0.7 - - - -
591N ILE* 3.8 6.9 - - - +
592N ALA* 2.9 30.0 + - - +
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Residues in contact with GLU 589 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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587N CYS* 3.6 3.7 - - + +
588N GLU* 1.3 78.8 - - + +
590N SER* 1.3 61.2 + - - +
592N ALA* 3.2 8.0 + - - +
593N VAL* 2.9 32.3 + - + +
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Residues in contact with SER 590 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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563N GLY* 3.6 22.4 - - - +
564N ILE* 3.4 41.9 + - - +
585N GLU* 5.1 6.3 - - - -
587N CYS* 4.7 4.7 + - - +
588N GLU 3.5 0.2 - - - -
589N GLU* 1.3 75.7 - - - +
591N ILE* 1.3 59.0 + - - +
593N VAL* 3.4 4.4 + - - +
594N GLY* 2.9 22.5 + - - -
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Residues in contact with ILE 591 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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563N GLY 4.5 9.4 - - - +
583N ALA* 5.1 3.8 - - + -
584N SER* 4.2 10.3 - - - +
585N GLU* 3.7 40.6 - - + +
587N CYS 3.3 23.1 + - - +
588N GLU* 3.5 6.8 + - - +
589N GLU 3.3 0.6 - - - -
590N SER* 1.3 74.9 - - - +
592N ALA* 1.3 59.1 + - - +
594N GLY* 3.7 0.8 - - - -
595N THR* 2.9 34.1 + - + +
604N TYR* 5.2 17.1 - - + -
605N VAL 5.6 2.0 - - - +
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Residues in contact with ALA 592 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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588N GLU 2.9 18.3 + - - +
589N GLU* 3.4 7.4 - - - +
591N ILE* 1.3 77.0 - - - +
593N VAL* 1.3 57.8 + - + +
595N THR* 3.3 9.3 - - + +
596N VAL* 3.0 39.3 + - + +
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Residues in contact with VAL 593 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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564N ILE* 4.1 31.0 - - + -
589N GLU* 2.9 22.1 + - + +
590N SER* 3.7 8.7 - - - +
591N ILE 3.3 0.2 - - - -
592N ALA* 1.3 75.9 - - + +
594N GLY* 1.3 57.7 + - - +
596N VAL* 4.2 3.1 - - - +
597N LYS* 2.9 42.3 + - + +
598N HIS* 6.2 0.4 - - + -
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Residues in contact with GLY 594 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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563N GLY 5.0 2.2 - - - -
564N ILE* 5.3 0.2 - - - +
565N ALA* 5.0 10.5 - - - -
590N SER 2.9 16.4 + - - -
591N ILE* 3.7 2.5 - - - -
592N ALA 3.3 0.2 - - - -
593N VAL* 1.3 78.8 - - - +
595N THR* 1.3 57.6 + - - +
598N HIS* 3.6 35.0 + - - +
602N ILE* 4.6 0.3 - - - +
604N TYR* 2.8 22.1 + - - -
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Residues in contact with THR 595 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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591N ILE* 2.9 25.2 + - + +
592N ALA* 3.3 16.8 - - + +
594N GLY* 1.3 75.1 - - - +
596N VAL* 1.3 65.6 + - + +
598N HIS 4.9 0.4 - - - -
599N GLU* 4.8 6.7 + - - -
600N GLY* 4.8 6.7 + - - +
604N TYR* 3.6 21.8 + - - -
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Residues in contact with VAL 596 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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592N ALA* 3.0 23.4 + - + +
593N VAL* 4.2 3.1 - - - +
595N THR* 1.3 85.6 - - + +
597N LYS* 1.3 66.5 + - - +
599N GLU* 4.1 13.9 + - - +
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Residues in contact with LYS 597 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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569N LEU* 5.3 15.5 - - + +
593N VAL* 2.9 27.0 + - + +
596N VAL* 1.3 82.3 - - - +
598N HIS* 1.3 79.5 + - + +
599N GLU* 3.3 15.6 + - - +
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Residues in contact with HIS 598 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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564N ILE* 5.2 6.1 - - + -
565N ALA* 3.4 41.9 + - + +
568N TYR* 3.6 30.9 - + + -
569N LEU* 3.5 27.6 - - + +
572N LYS* 5.7 3.7 + - + +
593N VAL* 6.2 0.2 - - + -
594N GLY* 3.6 23.8 + - - +
597N LYS* 1.3 95.3 - - + +
599N GLU* 1.3 62.1 + - - +
600N GLY 3.0 10.8 + - - -
601N ASN* 3.6 15.8 + - - +
602N ILE* 3.8 18.8 - - + -
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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