Contacts of the helix formed by residues 588 - 600 (chain B) in PDB entry 3TVX
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 ILE 588 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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485B MET* 3.8 16.4 - - + -
488B HIS* 3.8 30.4 + - + -
489B MET* 5.0 7.2 - - + -
531B LEU* 3.7 27.4 - - + -
584B PHE* 3.0 41.0 + - + +
587B TYR* 1.3 89.5 - - + +
589B VAL* 1.3 66.1 + - - +
591B PRO* 3.4 4.4 - - - +
592B LEU* 3.3 23.0 + - - +
902B PNX 4.9 11.9 - - + -
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Residues in contact with VAL 589 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531B LEU* 3.5 29.8 - - + +
534B PRO* 4.0 11.9 - - + -
535B THR* 4.6 0.9 - - + -
584B PHE* 3.2 48.1 + - + +
585B ILE* 4.1 9.0 - - - -
588B ILE* 1.3 75.7 - - + +
590B HIS* 1.3 62.8 + - - +
592B LEU* 3.2 6.5 + - - +
593B TRP* 2.8 41.0 + - + +
611B LEU* 3.8 20.0 - - + -
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Residues in contact with HIS 590 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
585B ILE* 2.8 31.1 + - + +
586B ASP* 4.8 4.2 + - - +
589B VAL* 1.3 72.0 - - - +
591B PRO* 1.4 71.4 - - + +
592B LEU 3.0 0.2 + - - -
594B GLU* 2.8 67.1 + - + +
608B LEU* 3.9 8.1 - - + +
611B LEU* 3.6 27.5 - - + +
612B GLU* 3.3 36.3 + - + +
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Residues in contact with PRO 591 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492B LEU* 3.5 20.9 - - + +
496B LYS* 5.2 2.7 - - - -
585B ILE 3.4 11.7 - - - +
586B ASP 3.4 17.3 - - - +
587B TYR* 3.7 15.3 - - + +
588B ILE 3.4 12.8 - - - +
590B HIS* 1.4 96.0 - - + +
592B LEU* 1.3 57.2 + - - +
594B GLU* 4.0 8.1 - - + +
595B THR* 2.9 26.5 + - - -
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Residues in contact with LEU 592 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488B HIS* 4.1 9.4 - - + -
492B LEU* 3.8 20.6 - - + +
495B LEU* 4.2 4.4 - - + +
524B ASN* 4.1 16.4 - - - +
527B HIS* 3.6 35.7 - - + +
528B CYS* 3.8 31.2 - - - -
531B LEU* 3.8 23.1 - - + -
588B ILE 3.3 11.2 + - - +
589B VAL* 3.2 6.6 + - - +
590B HIS 3.1 0.6 - - - -
591B PRO* 1.3 77.7 - - - +
593B TRP* 1.3 66.1 + - + +
595B THR* 3.2 6.6 + - - -
596B TRP* 3.1 24.1 + - - +
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Residues in contact with TRP 593 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B TRP* 3.9 27.4 - + - -
387B LEU* 3.7 27.1 - - + -
528B CYS* 3.5 34.3 + - + +
531B LEU* 3.3 17.4 + - - +
532B SER* 4.2 2.2 - - - -
535B THR* 3.8 14.8 - - + +
589B VAL* 2.8 43.4 + - + +
592B LEU* 1.3 80.3 - - + +
594B GLU* 1.3 57.1 + - - +
595B THR 3.4 0.2 - - - -
596B TRP* 3.5 32.9 - + - +
597B ALA* 3.0 27.9 + - - +
604B ALA* 5.0 4.0 - - + -
607B ILE* 3.8 24.2 - - + -
608B LEU* 4.1 8.4 - - + +
611B LEU* 4.0 16.2 - - + -
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Residues in contact with GLU 594 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
590B HIS* 2.8 48.0 + - + +
591B PRO* 4.0 7.6 - - - +
593B TRP* 1.3 74.0 - - - +
595B THR* 1.3 61.1 + - - +
597B ALA* 3.3 5.2 + - - +
598B ASP* 3.0 42.4 + - - +
608B LEU* 4.1 17.4 - - + +
612B GLU* 5.3 0.9 - - - +
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Residues in contact with THR 595 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492B LEU* 3.4 9.5 - - + +
495B LEU* 3.7 39.2 - - + +
496B LYS* 3.7 31.1 - - + +
499B VAL* 3.4 15.5 - - + +
591B PRO 2.9 15.4 + - - -
592B LEU 3.2 8.1 + - - -
594B GLU* 1.3 75.1 - - - +
596B TRP* 1.3 65.0 - - - +
598B ASP* 3.4 8.0 + - - +
599B LEU* 3.1 18.0 + - - +
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Residues in contact with TRP 596 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387B LEU* 3.8 26.7 - - + +
390B THR* 5.3 1.5 - - + +
393B LEU* 3.9 18.4 - - + -
495B LEU* 3.9 14.9 - - + +
521B VAL* 3.8 31.0 - - + -
524B ASN* 4.5 4.3 - - + -
525B MET* 3.8 43.7 - - + -
528B CYS* 4.0 24.0 - - - -
592B LEU 3.1 12.5 + - - +
593B TRP* 3.5 31.9 - + + +
594B GLU 3.3 0.2 - - - -
595B THR* 1.3 74.3 - - - +
597B ALA* 1.3 65.2 + - - +
599B LEU* 3.0 27.7 + - + +
600B VAL* 3.1 38.4 + - + +
604B ALA* 4.4 5.7 - - + +
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Residues in contact with ALA 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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593B TRP 3.0 19.2 + - - +
594B GLU 3.3 6.5 + - - +
596B TRP* 1.3 75.1 - - - +
598B ASP* 1.3 63.5 + - - +
600B VAL* 3.3 2.3 + - - +
601B HIS* 3.1 29.2 + - - +
602B PRO* 5.2 0.3 - - - +
604B ALA* 3.8 26.8 + - + +
605B GLN* 5.3 2.9 - - - +
608B LEU* 3.8 26.0 - - + -
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Residues in contact with ASP 598 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499B VAL* 3.7 23.0 - - + +
502B LYS* 2.8 31.4 + - - +
594B GLU* 3.0 29.5 + - - +
595B THR* 3.6 11.8 - - - +
596B TRP 3.2 0.4 - - - -
597B ALA* 1.3 75.9 - - - +
599B LEU* 1.3 57.4 + - - +
600B VAL 3.4 0.2 + - - -
601B HIS* 3.6 12.3 + - - +
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Residues in contact with LEU 599 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393B LEU* 5.2 0.7 - - + -
495B LEU* 4.4 10.3 - - + -
498B MET* 3.9 32.8 - - + +
499B VAL* 3.9 17.9 - - + +
502B LYS* 4.3 10.3 + - + +
510B LEU* 3.2 45.2 - - + +
512B LEU* 5.8 1.1 - - + -
521B VAL* 4.2 18.8 - - + -
595B THR 3.1 13.5 + - - +
596B TRP* 3.0 39.4 + - + +
598B ASP* 1.3 77.7 - - - +
600B VAL* 1.3 69.2 + - + +
601B HIS 3.9 0.5 + - - -
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Residues in contact with VAL 600 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390B THR* 4.3 6.1 - - + +
392B ALA* 3.9 17.0 - - + -
393B LEU* 4.0 21.8 - - + -
510B LEU* 4.0 13.9 - - + -
596B TRP* 3.1 36.3 + - + +
597B ALA 3.5 1.1 - - - +
598B ASP 3.3 0.2 - - - -
599B LEU* 1.3 90.2 - - + +
601B HIS* 1.3 56.1 + - - +
603B ASP* 2.8 40.2 + - + +
604B ALA* 3.9 22.4 - - + +
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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