Contacts of the helix formed by residues 588 - 601 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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485A MET* 3.9 17.5 - - + -
488A HIS* 3.7 38.1 + - + -
489A MET* 4.7 9.0 - - + -
531A LEU* 3.9 23.8 - - + -
584A PHE* 2.8 33.2 + - + +
587A TYR* 1.3 96.5 - - + +
589A VAL* 1.3 64.1 + - - +
591A PRO* 3.5 3.6 - - - +
592A LEU* 3.2 24.8 + - - +
902A PNX 5.3 6.1 - - + -
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Residues in contact with VAL 589 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531A LEU* 3.6 17.7 - - + +
534A PRO* 4.3 10.5 - - + -
535A THR* 4.6 0.7 - - + -
584A PHE* 3.0 50.7 + - + +
585A ILE* 3.9 12.6 - - + -
588A ILE* 1.3 75.8 - - + +
590A HIS* 1.3 62.4 + - - +
592A LEU* 3.7 4.2 - - - +
593A TRP* 3.0 50.4 + - + +
611A LEU* 3.8 18.4 - - + -
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Residues in contact with HIS 590 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
585A ILE* 2.7 29.8 + - + +
586A ASP* 4.7 4.9 - - - +
589A VAL* 1.3 69.9 - - - +
591A PRO* 1.4 63.1 - - + +
594A GLU* 2.8 69.0 + - + +
608A LEU* 4.2 10.8 - - + +
611A LEU* 3.7 25.6 - - + +
612A GLU* 3.0 39.2 + - + -
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Residues in contact with PRO 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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492A LEU* 3.8 19.2 - - + +
585A ILE 3.6 0.2 - - - +
586A ASP 3.4 27.1 - - - +
587A TYR 3.5 14.6 - - - +
588A ILE 3.5 12.1 - - - +
590A HIS* 1.4 91.1 - - + +
592A LEU* 1.3 56.4 + - - +
594A GLU* 3.9 10.6 - - + +
595A THR* 2.8 32.1 + - - -
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Residues in contact with LEU 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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488A HIS* 4.2 7.6 - - + -
492A LEU* 3.8 19.7 - - + +
495A LEU* 4.5 2.5 - - + +
524A ASN* 4.6 10.1 - - - +
527A HIS* 3.6 39.7 - - + +
528A CYS* 3.7 34.8 - - - -
531A LEU* 4.1 22.2 - - + -
588A ILE 3.2 16.1 + - - +
589A VAL* 3.7 3.8 - - - +
590A HIS 3.2 0.6 - - - -
591A PRO* 1.3 79.8 - - - +
593A TRP* 1.3 66.3 + - + +
595A THR* 3.3 6.6 + - - -
596A TRP* 3.0 24.1 + - - +
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Residues in contact with TRP 593 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A TRP* 3.7 26.2 - + - -
387A LEU* 3.8 18.2 - - + -
528A CYS* 3.5 31.5 + - + +
531A LEU 3.0 19.2 + - - -
532A SER* 3.7 14.1 - - - -
535A THR* 3.5 16.7 - - + +
589A VAL* 3.0 38.8 + - + +
592A LEU* 1.3 81.5 - - + +
594A GLU* 1.3 60.4 + - - +
596A TRP* 3.6 32.1 - + - +
597A ALA* 2.9 30.8 + - - +
604A ALA* 5.1 3.6 - - + -
607A ILE* 3.8 26.2 - - + -
608A LEU* 3.9 8.7 - - + +
611A LEU* 4.1 12.8 - - + -
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Residues in contact with GLU 594 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
590A HIS* 2.8 50.5 + - + +
591A PRO* 3.9 9.7 - - - +
593A TRP* 1.3 71.3 - - - +
595A THR* 1.3 58.1 + - - +
597A ALA* 3.2 4.9 + - - +
598A ASP* 2.9 37.7 + - - +
608A LEU* 3.8 20.1 - - + +
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Residues in contact with THR 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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492A LEU* 3.6 12.7 - - + +
495A LEU* 3.8 13.9 - - + -
496A LYS* 3.7 48.1 - - + +
499A VAL* 3.5 15.8 - - + +
591A PRO 2.8 21.5 + - - -
592A LEU 3.3 5.7 + - - -
594A GLU* 1.3 75.6 + - - +
596A TRP* 1.3 65.3 + - - +
598A ASP* 3.4 8.1 + - - +
599A LEU 3.1 15.8 + - - -
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Residues in contact with TRP 596 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A LEU* 3.8 24.8 - - + +
390A THR* 5.1 1.9 - - + +
393A LEU* 4.1 18.6 - - + -
495A LEU* 4.3 12.9 - - + +
521A VAL* 3.8 25.1 - - + -
524A ASN* 4.5 4.3 - - + -
525A MET* 3.8 43.3 - - + -
528A CYS* 4.0 24.7 - - - -
592A LEU 3.0 13.6 + - - +
593A TRP* 3.6 29.8 - + - +
594A GLU 3.3 0.2 - - - -
595A THR* 1.3 75.6 - - - +
597A ALA* 1.3 58.8 + - - +
599A LEU* 3.0 41.4 + - + +
600A VAL* 3.0 39.3 + - + +
604A ALA* 4.4 4.9 - - + +
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Residues in contact with ALA 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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593A TRP 2.9 18.8 + - - +
594A GLU 3.4 4.9 - - - +
596A TRP* 1.3 74.4 - - - +
598A ASP* 1.3 60.7 + - - +
600A VAL* 3.6 0.6 - - - -
601A HIS* 2.8 39.2 + - + +
604A ALA* 3.8 30.9 - - + +
605A GLN* 5.2 1.1 - - - +
608A LEU* 4.0 21.5 - - + -
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Residues in contact with ASP 598 (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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496A LYS* 4.4 14.9 + - - -
499A VAL* 3.7 19.4 - - + +
500A GLU* 5.5 0.2 - - - +
502A LYS* 2.7 31.0 + - - -
594A GLU* 2.9 24.6 + - - +
595A THR* 3.5 13.4 - - - +
596A TRP 3.3 0.2 - - - -
597A ALA* 1.3 78.3 - - - +
599A LEU* 1.3 54.4 + - - +
601A HIS* 3.7 14.8 - - - +
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Residues in contact with LEU 599 (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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392A ALA* 4.9 0.2 - - - +
393A LEU* 5.6 0.2 - - + -
495A LEU* 4.0 14.6 - - + -
498A MET* 4.0 23.6 - - + -
499A VAL* 3.7 24.6 - - + +
502A LYS* 4.0 10.9 + - + +
510A LEU* 3.1 49.8 - - + +
512A LEU* 5.8 0.2 - - + -
521A VAL* 4.3 16.2 - - + -
595A THR 3.1 11.8 + - - +
596A TRP* 3.0 41.8 + - + +
598A ASP* 1.3 80.0 - - - +
600A VAL* 1.3 59.7 + - + +
601A HIS 3.4 0.7 + - - -
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Residues in contact with VAL 600 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A THR* 4.1 11.4 - - + +
392A ALA* 3.5 15.3 - - + +
393A LEU* 4.1 30.5 - - + -
510A LEU* 4.3 3.8 - - + -
596A TRP* 3.0 44.5 + - + +
597A ALA* 4.0 0.7 - - - -
599A LEU* 1.3 80.9 - - + +
601A HIS* 1.3 68.5 + - - +
603A ASP* 3.0 28.1 + - + -
604A ALA* 3.8 22.2 - - + +
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Residues in contact with HIS 601 (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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392A ALA* 4.9 3.8 - - - +
502A LYS* 4.7 6.2 + - - +
508A GLY* 4.9 5.9 - - - +
597A ALA* 2.8 22.3 + - + +
598A ASP* 3.7 17.3 - - - +
599A LEU 3.4 2.6 + - - -
600A VAL* 1.3 78.9 - - - +
602A PRO* 1.4 83.8 - - + +
603A ASP* 3.8 0.8 - - - +
605A GLN* 3.7 21.2 + - + -
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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