Contacts of the helix formed by residues 349 - 357 (chain D) in PDB entry 3THT
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 CYS 349 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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242D HIS* 3.0 11.7 - - + +
341D CYS* 3.5 19.7 - - - -
343D CYS* 4.0 0.4 - - - -
345D TYR 3.3 9.6 + - - +
346D PRO* 3.3 12.7 + - + -
348D VAL* 1.3 75.6 - - - +
350D ASP* 1.3 60.6 + - - +
351D SER 4.0 0.7 - - - -
352D GLN* 3.2 24.6 + - + +
353D ARG* 2.9 32.4 + - - +
401D ZN 2.3 36.1 - - - -
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Residues in contact with ASP 350 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241D THR* 3.7 14.8 - - + +
242D HIS* 3.4 5.6 - - - +
243D SER* 2.5 49.9 + - - -
348D VAL 3.8 4.2 + - - -
349D CYS* 1.3 69.2 - - - +
351D SER* 1.3 79.5 + - - +
352D GLN 3.0 1.6 + - - -
353D ARG* 4.1 11.8 - - - +
354D LYS* 3.0 39.3 + - + +
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Residues in contact with SER 351 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243D SER* 3.7 17.9 - - - -
340D PRO* 3.2 20.3 - - - +
341D CYS* 3.0 44.4 + - - -
349D CYS 3.4 0.6 - - - -
350D ASP* 1.3 83.1 + - - +
352D GLN* 1.3 61.2 + - - +
354D LYS* 4.1 17.4 - - - +
355D GLU* 4.3 8.0 - - - +
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Residues in contact with GLN 352 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341D CYS 3.7 16.2 - - - +
342D ASN* 4.2 8.6 - - + +
343D CYS* 3.7 28.8 + - - +
346D PRO* 4.0 31.8 - - + +
349D CYS* 3.2 20.3 + - + +
350D ASP 3.0 0.4 - - - -
351D SER* 1.3 79.0 - - - +
353D ARG* 1.3 58.1 + - - +
354D LYS 3.0 4.5 - - - -
355D GLU* 2.8 48.5 + - - +
356D ASN* 4.1 0.9 + - - +
359D PHE* 5.5 1.0 - - - -
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Residues in contact with ARG 353 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346D PRO 3.0 20.9 - - - +
347D LEU* 2.9 30.5 + - - +
348D VAL* 4.1 2.0 - - - +
349D CYS 2.9 21.0 + - - +
350D ASP* 3.3 9.2 + - - +
352D GLN* 1.3 74.9 - - - +
354D LYS* 1.3 62.5 + - - +
355D GLU 3.0 1.3 + - - -
356D ASN 3.7 0.9 + - - -
357D LEU* 3.3 19.9 + - - -
359D PHE* 3.3 67.3 + - + +
360D GLN* 5.2 2.9 - - - +
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Residues in contact with LYS 354 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243D SER* 4.8 5.8 + - - -
350D ASP* 3.0 35.8 + - + +
351D SER* 4.1 14.9 - - - +
352D GLN 2.9 0.2 + - - -
353D ARG* 1.3 77.0 - - - +
355D GLU* 1.3 65.2 + - + +
357D LEU* 4.1 7.9 + - - +
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Residues in contact with GLU 355 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351D SER 4.3 5.6 - - - +
352D GLN* 2.8 43.7 + - - +
353D ARG 3.0 0.2 - - - -
354D LYS* 1.3 79.7 - - + +
356D ASN* 1.3 67.2 + - + +
357D LEU* 3.3 3.6 + - - +
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Residues in contact with ASN 356 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352D GLN 4.1 0.6 + - - -
353D ARG 3.7 1.2 + - - -
355D GLU* 1.3 77.4 - - + +
357D LEU* 1.3 73.7 + - - +
358D TYR* 2.9 32.2 + - - +
359D PHE* 3.3 35.7 - - + -
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Residues in contact with LEU 357 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353D ARG 3.3 13.1 + - - -
354D LYS* 4.5 6.1 - - - +
355D GLU 3.3 8.2 - - - +
356D ASN* 1.3 83.9 - - - +
358D TYR* 1.3 61.8 + - + +
359D PHE* 3.0 6.5 - - - +
360D GLN* 3.0 36.1 - - + +
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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