Contacts of the helix formed by residues 582 - 592 (chain W) in PDB entry 6NE3
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 ASN 582 (chain W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155I G 3.3 29.7 + - - +
341W GLN* 3.8 26.2 + - - +
342W ASN* 4.7 4.8 + - - -
580W ASP* 3.3 2.7 - - + +
581W TRP* 1.3 78.7 - - - +
583W PRO* 1.3 68.5 - - - +
584W GLN* 2.9 20.8 + - - +
585W VAL* 2.7 56.0 + - + +
586W ASP* 3.0 19.1 - - - +
624W LYS* 5.1 3.5 - - - +
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Residues in contact with PRO 583 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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581W TRP 3.7 7.2 - - - +
582W ASN* 1.3 90.9 - - - +
584W GLN* 1.3 68.0 + - + +
586W ASP* 3.2 15.6 - - + +
587W LEU* 2.9 30.5 + - + +
621W ALA* 3.4 37.9 - - + +
624W LYS* 3.9 24.2 - - + -
625W LEU* 4.1 21.9 - - + +
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Residues in contact with GLN 584 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338W THR* 3.4 21.7 + - + +
340W LEU* 2.4 31.1 + - - +
341W GLN* 3.0 42.8 + - - +
582W ASN* 2.9 12.8 + - - +
583W PRO* 1.3 85.2 - - + +
585W VAL* 1.3 61.6 + - + +
586W ASP 3.2 1.1 - - - -
587W LEU* 3.1 18.1 + - + +
588W GLN* 2.9 31.1 + - - +
624W LYS* 5.3 2.9 - - - +
625W LEU* 6.4 0.2 - - - -
628W ASP* 3.2 25.1 - - + +
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Residues in contact with VAL 585 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155I G 5.7 0.7 - - - +
341W GLN* 6.2 1.8 - - - +
559W THR* 4.4 12.5 - - + +
560W ARG* 5.9 10.5 - - + +
564W LEU* 5.8 8.3 - - + -
580W ASP* 5.0 12.1 - - + +
582W ASN* 2.7 41.3 + - + +
584W GLN* 1.3 70.6 - - + +
586W ASP* 1.3 68.3 + - - +
588W GLN* 3.5 12.2 - - + +
589W ALA* 3.0 28.9 + - - +
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Residues in contact with ASP 586 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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559W THR* 5.1 5.8 - - - +
576W LEU* 4.0 20.8 - - + +
578W ASP 4.8 0.7 - - - +
579W SER* 2.4 34.4 + - - +
580W ASP* 3.3 21.6 + - - +
582W ASN 3.0 18.3 - - - +
583W PRO* 3.2 15.8 - - + +
584W GLN 3.2 0.6 - - - -
585W VAL* 1.3 84.0 - - - +
587W LEU* 1.3 56.5 + - - +
589W ALA* 3.7 3.3 - - - -
590W MET* 2.8 30.8 + - + +
606W ARG* 6.0 1.8 - - - +
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Residues in contact with LEU 587 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338W THR* 5.3 6.1 - - + -
583W PRO* 2.9 22.3 + - + +
584W GLN* 3.1 22.6 + - + +
586W ASP* 1.3 75.5 - - + +
588W GLN* 1.3 62.8 + - - +
590W MET* 3.7 11.2 - - + -
591W ASP* 2.9 49.2 + - - +
625W LEU* 4.6 24.7 - - + -
628W ASP* 6.5 0.9 - - - -
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Residues in contact with GLN 588 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207W MET* 4.0 21.4 - - - +
309W GLU* 3.9 20.0 + - - +
311W HIS* 6.6 0.2 - - + -
337W GLY* 4.6 8.3 - - - -
338W THR* 3.4 26.4 - - + +
563W GLY 3.9 11.2 - - - +
564W LEU* 3.9 9.6 + - + +
584W GLN 2.9 17.7 + - - +
585W VAL* 3.2 15.9 + - + +
587W LEU* 1.3 78.6 - - - +
589W ALA* 1.3 58.2 + - - +
591W ASP* 3.3 2.4 + - - +
592W ARG* 3.0 64.1 + - - +
801W ADP 5.8 0.2 + - - -
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Residues in contact with ALA 589 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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505W PHE* 3.2 44.1 - - + -
559W THR* 3.8 23.1 - - + +
563W GLY* 4.0 7.5 + - - -
574W VAL* 3.7 4.1 - - - +
576W LEU* 5.6 5.2 - - + -
585W VAL 3.0 16.2 + - - +
586W ASP* 4.2 3.8 - - - +
588W GLN* 1.3 73.2 - - - +
590W MET* 1.3 64.9 + - - +
592W ARG* 3.8 12.6 - - - +
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Residues in contact with MET 590 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407W LYS* 3.5 20.6 + - - +
409W GLU* 4.6 6.7 - - + -
574W VAL* 3.9 23.8 - - - +
576W LEU* 4.1 22.6 - - + +
586W ASP* 2.8 20.4 + - + +
587W LEU* 3.3 17.7 - - + +
588W GLN 3.1 0.2 - - - -
589W ALA* 1.3 79.7 - - - +
591W ASP* 1.3 70.8 + - - +
592W ARG 3.3 1.8 + - - -
593W ALA* 3.9 6.2 + - - +
594W HIS 4.5 1.4 + - - -
604W VAL* 3.6 42.0 - - + -
606W ARG* 4.2 16.8 - - - +
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Residues in contact with ASP 591 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206W GLU* 4.1 16.3 - - - +
207W MET* 3.2 28.1 - - + +
407W LYS* 2.5 40.0 + - - +
587W LEU* 2.9 29.0 + - - +
588W GLN* 3.7 2.0 - - - +
590W MET* 1.3 79.7 - - - +
592W ARG* 1.3 64.3 + - - +
593W ALA 3.2 1.6 - - - -
594W HIS* 3.0 32.4 + - + +
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Residues in contact with ARG 592 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207W MET* 3.1 33.0 - - - +
503W LEU* 5.0 2.9 - - + -
505W PHE* 4.1 13.7 - - + -
563W GLY* 3.0 36.9 + - - +
564W LEU 3.3 12.2 + - - -
565W GLY* 3.2 7.3 - - - -
566W ILE* 2.4 58.9 + - + +
567W ASN* 4.7 0.9 - - - -
568W LEU* 3.6 18.3 + - + -
588W GLN* 3.0 50.1 + - - +
589W ALA* 3.8 12.8 - - - +
590W MET 3.3 0.6 - - - -
591W ASP* 1.3 77.2 - - - +
593W ALA* 1.3 61.4 + - - +
594W HIS 3.5 0.2 + - - -
595W ARG* 3.6 22.6 - - - +
801W ADP 4.8 1.8 + - - -
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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