Contacts of the helix formed by residues 604 - 612 (chain B) in PDB entry 1T9A
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 ASP 604 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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611A ALA* 2.9 19.8 + - - +
603B PRO* 1.3 70.4 - - - +
605B PHE* 1.3 55.9 + - - +
606B ILE* 3.0 1.7 + - - +
607B LYS* 2.8 53.7 + - + +
608B LEU* 2.8 31.3 + - - +
618B ARG* 3.0 28.2 + - - +
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Residues in contact with PHE 605 (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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550B ASP* 3.9 14.6 - - + -
553B PHE* 3.7 33.9 - + - -
554B ASN* 4.2 6.1 - - - -
574B ILE* 4.0 11.2 - - + -
576B ASN* 3.8 24.7 - - - -
602B ASN* 3.6 33.4 - - + -
603B PRO* 3.2 25.4 + - + -
604B ASP* 1.3 73.3 + - - +
606B ILE* 1.3 58.4 + - + +
608B LEU* 3.5 5.4 - - + +
609B ALA* 2.9 28.4 + - - +
618B ARG* 4.1 3.0 - - - +
640B LEU* 4.2 21.5 - - + +
642B GLU* 3.6 33.0 - - + +
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Residues in contact with ILE 606 (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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604B ASP* 3.0 8.3 + - - +
605B PHE* 1.3 76.1 - - + +
607B LYS* 1.3 71.1 + - + +
609B ALA* 3.2 7.6 + - - +
610B GLU* 3.0 44.0 + - - +
616B GLY* 3.9 8.6 - - - +
617B LEU 3.5 38.6 - - - +
618B ARG* 3.4 39.9 - - + +
640B LEU* 4.6 2.7 - - + -
642B GLU* 3.6 15.5 - - + +
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Residues in contact with LYS 607 (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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607A LYS* 4.6 4.3 - - - +
610A GLU* 5.2 8.0 + - + +
611A ALA* 3.7 24.5 - - + +
604B ASP* 2.8 37.1 + - + +
606B ILE* 1.3 77.9 - - + +
608B LEU* 1.3 57.3 + - - +
610B GLU* 3.4 12.7 + - - +
611B ALA* 2.9 29.3 + - - +
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Residues in contact with LEU 608 (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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608A LEU* 3.3 33.2 - - + -
611A ALA* 3.6 9.6 - - + +
612A MET* 4.2 9.9 - - + -
553B PHE* 3.9 18.6 - - + -
557B LEU* 3.7 29.4 - - + -
560B LEU* 4.1 12.1 - - + -
603B PRO* 4.4 11.4 - - + -
604B ASP 2.8 19.7 + - - +
605B PHE* 3.5 8.7 - - + +
607B LYS* 1.3 76.7 - - - +
609B ALA* 1.3 57.7 + - - +
611B ALA* 3.1 6.0 + - - +
612B MET* 2.9 40.3 + - + +
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Residues in contact with ALA 609 (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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560B LEU* 4.6 5.4 - - - +
605B PHE 2.9 17.9 + - - +
606B ILE 3.5 5.4 - - - +
608B LEU* 1.3 77.1 - - - +
610B GLU* 1.3 61.6 + - - +
612B MET* 3.1 7.7 + - - +
613B GLY 3.1 6.1 + - - -
614B LEU* 2.9 31.6 + - + +
615B LYS 4.1 13.0 - - - +
616B GLY* 4.1 6.1 - - - -
640B LEU* 4.0 27.1 - - + -
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Residues in contact with GLU 610 (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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607A LYS* 5.3 10.3 + - + +
606B ILE* 3.0 38.7 + - - +
607B LYS* 3.7 12.2 - - - +
609B ALA* 1.3 76.2 - - - +
611B ALA* 1.3 63.8 + - - +
613B GLY* 2.9 15.1 + - - -
614B LEU 3.4 13.2 - - - +
615B LYS* 5.4 1.1 - - - -
616B GLY 4.4 13.0 + - - +
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Residues in contact with ALA 611 (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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603A PRO* 3.4 3.3 - - - +
604A ASP* 3.0 33.0 + - - +
607A LYS* 3.8 17.6 - - + +
608A LEU* 3.7 37.5 - - + +
607B LYS 2.9 14.7 + - - +
608B LEU* 3.4 9.9 - - - +
610B GLU* 1.3 77.1 - - - +
612B MET* 1.3 60.3 + - + +
613B GLY* 3.3 1.6 + - - -
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Residues in contact with MET 612 (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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554A ASN* 5.7 0.2 - - - +
557A LEU* 3.9 34.8 - - + -
601A LEU* 6.1 0.5 - - - +
603A PRO* 3.6 22.1 - - + +
608A LEU* 4.1 17.5 - - + -
557B LEU 4.0 13.5 - - - +
558B THR* 4.1 5.6 - - - +
560B LEU* 3.5 31.6 - - + -
561B SER* 3.8 33.0 - - - +
564B VAL* 3.5 18.4 - - - +
608B LEU* 2.9 24.5 + - + +
609B ALA 3.1 5.1 + - - +
611B ALA* 1.3 75.6 - - + +
613B GLY* 1.3 58.0 + - - +
614B LEU* 3.7 3.6 - - + -
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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