Contacts of the helix formed by residues 576 - 588 (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 SER 576 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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574B THR 3.8 3.2 + - - -
575B ALA* 1.3 71.1 - - - +
577B VAL* 1.3 59.2 + - - +
578B GLU* 3.7 10.9 + - - +
579B LYS* 3.3 48.9 + - - +
580B SER* 2.9 34.2 + - - -
622B ILE* 5.9 0.3 - - - -
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Residues in contact with VAL 577 (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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545B THR* 3.7 28.3 - - + +
546B ASP* 5.5 4.5 - - - +
549B MET* 3.7 39.9 - - + +
553B PHE* 4.3 13.7 - - + -
575B ALA 3.7 2.4 + - - +
576B SER* 1.3 70.9 + - - +
578B GLU* 1.3 76.3 + - - +
580B SER* 3.6 2.2 + - - -
581B GLN* 3.2 24.7 + - + +
618B TYR* 5.0 4.5 - - + -
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Residues in contact with GLU 578 (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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576B SER* 3.7 11.7 + - - +
577B VAL* 1.3 89.4 + - - +
579B LYS* 1.3 63.7 + - - +
581B GLN* 3.1 12.6 + - - +
582B VAL* 3.2 19.7 + - - +
617B TRP* 5.8 0.2 - - + -
618B TYR* 3.7 36.9 - - + +
621B ALA* 3.7 28.2 - - + +
622B ILE* 4.3 12.8 - - + +
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Residues in contact with LYS 579 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
576B SER* 3.3 30.0 + - - +
578B GLU* 1.3 76.9 - - + +
580B SER* 1.3 62.0 + - - +
582B VAL* 3.4 4.0 + - - +
583B GLY* 3.2 19.8 + - - -
622B ILE* 3.9 44.6 - - + +
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Residues in contact with SER 580 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549B MET* 4.8 9.1 - - - +
569B MET* 3.9 24.7 - - - +
575B ALA* 5.1 2.8 - - - +
576B SER 2.9 22.4 + - - -
577B VAL* 3.6 7.9 - - - -
578B GLU 3.3 0.2 - - - -
579B LYS* 1.3 77.2 - - - +
581B GLN* 1.3 57.1 + - - +
583B GLY* 3.5 1.1 + - - -
584B PHE* 2.8 30.0 + - - +
902B PNX 3.9 18.7 + - - -
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Residues in contact with GLN 581 (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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541B TYR* 2.6 32.7 + - - +
545B THR* 3.6 28.1 - - + +
548B ILE* 4.2 4.4 - - - +
549B MET* 5.0 3.4 - - - -
577B VAL 3.2 16.1 + - - +
578B GLU 3.1 6.0 + - - +
580B SER* 1.3 77.5 - - - +
582B VAL* 1.3 61.2 + - - +
584B PHE* 3.4 17.4 - - - +
585B ILE* 3.0 35.4 + - - +
618B TYR* 4.3 16.2 - - + -
902B PNX 3.4 46.0 + - - +
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Residues in contact with VAL 582 (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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578B GLU 3.2 14.6 + - - +
579B LYS* 3.9 7.0 - - - +
580B SER 3.3 0.2 - - - -
581B GLN* 1.3 74.5 - - - +
583B GLY* 1.3 60.6 + - - +
585B ILE* 3.3 6.4 + - - +
586B ASP* 2.8 49.3 + - - +
615B ARG* 3.6 29.6 - - - +
618B TYR* 3.6 25.1 - - + +
619B TYR* 3.7 24.5 - - + +
622B ILE* 4.4 8.3 - - + -
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Residues in contact with GLY 583 (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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579B LYS 3.2 10.4 + - - -
580B SER* 3.8 2.7 - - - -
582B VAL* 1.3 78.3 - - - +
584B PHE* 1.3 61.6 + - - +
586B ASP* 4.4 1.8 - - - -
587B TYR* 3.1 47.9 + - - +
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Residues in contact with PHE 584 (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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485B MET* 5.3 0.9 - - + -
531B LEU* 4.1 11.7 - - + -
534B PRO* 4.3 6.7 - - + -
580B SER 2.8 20.5 + - - +
581B GLN* 3.4 23.6 - - - +
583B GLY* 1.3 76.1 - - - +
585B ILE* 1.3 57.4 + - - +
588B ILE* 3.0 55.6 + - + +
589B VAL* 3.2 28.5 + - + -
902B PNX 3.3 94.0 - + + +
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Residues in contact with ILE 585 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534B PRO* 4.0 17.9 - - + -
541B TYR* 3.3 32.1 - - + +
581B GLN* 3.0 21.4 + - - +
582B VAL* 3.8 3.8 - - - +
584B PHE* 1.3 75.3 - - + +
586B ASP* 1.3 66.1 + - - +
587B TYR 3.1 1.4 + - - -
589B VAL* 4.1 7.0 - - + -
590B HIS* 2.8 40.1 + - + +
591B PRO* 3.4 0.9 - - - +
611B LEU* 3.7 23.1 - - + +
614B ASN 4.3 0.9 - - - +
615B ARG* 3.7 47.1 - - + +
618B TYR* 5.1 2.0 - - + -
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Residues in contact with ASP 586 (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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582B VAL* 2.8 30.8 + - - +
583B GLY* 3.4 1.6 + - - -
585B ILE* 1.3 73.6 - - - +
587B TYR* 1.3 90.1 + - + +
590B HIS* 4.8 4.2 + - - +
591B PRO* 3.4 15.3 - - - +
615B ARG* 2.8 47.2 + - - +
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Residues in contact with TYR 587 (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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488B HIS* 4.6 3.3 + - - -
489B MET* 4.7 9.2 - - - +
583B GLY* 3.1 32.4 + - - +
586B ASP* 1.3 101.4 + - + +
588B ILE* 1.3 72.9 + - + +
591B PRO* 3.7 13.4 - - - +
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Residues in contact with ILE 588 (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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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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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