Contacts of the helix formed by residues 611 - 621 (chain B) in PDB entry 3THY
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 611 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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346B ASN* 2.6 25.0 + - - +
347B VAL* 5.3 1.9 - - + +
349B GLU* 6.0 0.3 - - - -
350B ILE* 5.6 1.9 - - - +
561B SER* 3.2 22.8 + - - +
562B PHE* 4.2 3.2 - - - -
565B ARG* 2.8 41.0 + - - -
610B PRO* 1.3 68.2 - - - +
612B ILE* 1.3 63.2 + - - +
613B GLU 3.3 2.1 + - - -
614B ARG* 3.1 42.7 + - + +
615B GLY* 3.0 18.9 + - - -
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Residues in contact with ILE 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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562B PHE* 4.0 18.6 - - + -
609B LEU* 4.5 19.1 - - + -
610B PRO* 2.7 33.4 + - + +
611B ASP* 1.3 72.2 - - - +
613B GLU* 1.3 62.3 + - - +
615B GLY* 3.7 2.9 - - - +
616B LEU* 3.0 46.4 + - + +
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Residues in contact with GLU 613 (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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387B ALA 4.3 1.8 - - - -
388B THR* 4.4 6.8 - - - +
562B PHE* 4.3 8.3 - - - -
565B ARG* 4.1 10.1 - - - +
611B ASP* 3.1 8.3 + - - -
612B ILE* 1.3 80.5 - - - +
614B ARG* 1.3 60.2 + - - +
616B LEU* 3.7 5.8 + - - +
617B CYS* 3.5 25.7 + - - -
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Residues in contact with ARG 614 (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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286B ARG* 4.5 8.1 - - - +
330B LEU 4.7 5.3 + - - -
331B ILE* 4.1 15.4 - - + +
336B ASN* 4.2 17.6 + - - +
347B VAL* 3.4 28.1 + - + +
348B ASP* 2.5 31.1 + - - +
349B GLU* 4.5 6.3 - - - +
350B ILE* 4.1 20.7 - - - +
387B ALA* 3.3 38.7 - - - +
388B THR* 4.9 2.9 - - + +
565B ARG* 4.5 1.4 - - - +
611B ASP* 3.1 39.4 + - + +
613B GLU* 1.3 73.5 - - - +
615B GLY* 1.3 65.1 + - - +
617B CYS* 3.3 2.4 + - - +
618B SER* 3.1 23.5 + - - -
628B GLU* 5.5 0.4 - - - -
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Residues in contact with GLY 615 (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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611B ASP 3.0 13.1 + - - -
612B ILE* 3.7 4.5 - - - -
613B GLU 3.3 0.6 - - - -
614B ARG* 1.3 78.7 - - - +
616B LEU* 1.3 60.7 + - - +
618B SER* 3.3 6.4 + - - -
619B ILE* 3.2 30.6 + - - +
628B GLU* 4.7 12.3 - - - +
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Residues in contact with LEU 616 (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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612B ILE* 3.0 39.4 + - + +
613B GLU* 4.2 5.2 - - - +
615B GLY* 1.3 73.8 - - - +
617B CYS* 1.3 53.3 + - - +
619B ILE* 3.4 17.7 + - + +
620B TYR* 2.8 36.2 + - - +
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Residues in contact with CYS 617 (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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331B ILE* 4.9 2.0 - - + -
386B PRO 4.1 7.0 - - - +
387B ALA* 3.4 18.2 - - - +
388B THR* 3.1 42.2 - - - -
389B GLY* 3.5 8.3 - - - -
613B GLU 3.5 7.7 + - - -
614B ARG 3.3 2.9 + - - +
615B GLY 3.2 0.6 - - - -
616B LEU* 1.3 78.0 - - - +
618B SER* 1.3 67.2 + - - +
620B TYR* 3.7 7.6 - - - +
621B HIS* 3.0 38.1 + - + -
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Residues in contact with SER 618 (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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331B ILE* 3.9 17.1 - - - +
332B GLY* 3.9 18.0 + - - -
336B ASN* 4.8 1.9 + - - -
614B ARG* 3.1 12.3 + - - -
615B GLY 3.6 6.7 - - - -
617B CYS* 1.3 76.0 - - - +
619B ILE* 1.3 60.6 + - - +
621B HIS* 3.5 2.1 + - - +
622B LYS 3.2 2.9 + - - -
623B LYS* 2.9 27.9 + - - -
624B CYS* 3.6 16.9 + - - +
628B GLU* 2.9 29.1 + - - -
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Residues in contact with ILE 619 (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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615B GLY 3.2 19.0 + - - +
616B LEU* 3.5 19.3 - - + +
617B CYS 3.2 0.4 - - - -
618B SER* 1.3 74.5 - - - +
620B TYR* 1.3 60.1 + - - +
622B LYS* 2.5 32.1 + - - +
624B CYS* 3.5 27.5 - - + -
628B GLU* 5.3 2.5 - - + +
629B PHE* 3.6 50.7 - - + +
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Residues in contact with TYR 620 (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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508B LYS* 3.4 80.5 + - + +
509B MET* 4.5 7.6 - - + -
511B SER* 4.0 8.1 + - - -
512B LYS* 5.3 5.9 - - - +
616B LEU 2.8 21.2 + - - +
617B CYS* 3.3 9.2 + - - +
619B ILE* 1.3 74.6 - - - +
621B HIS* 1.3 73.4 + + - +
622B LYS* 3.3 5.2 + - - +
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Residues in contact with HIS 621 (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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331B ILE* 5.3 3.6 - - + -
386B PRO 4.5 10.3 + - - -
389B GLY* 6.0 0.4 - - - -
505B ASN 3.9 9.2 + - - +
506B LEU* 3.1 63.8 - - + +
508B LYS* 4.1 14.6 - - + +
509B MET* 4.0 26.7 - - + +
617B CYS* 3.0 37.0 + - + +
618B SER* 3.9 4.5 - - - +
620B TYR* 1.3 83.2 - + - +
622B LYS* 1.3 69.8 + - - +
623B LYS* 3.4 16.0 + - + +
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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