Contacts of the helix formed by residues 31 - 40 (chain 5) in PDB entry 6AH0
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 THR 31 (chain 5).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295 LYS 4.7 0.9 - - - -
305 ILE* 1.3 72.2 - - - +
325 ALA* 1.3 51.4 + - - +
335 GLU 2.9 9.5 + - - +
345 GLU* 2.9 8.0 + - - +
355 MET* 2.7 32.1 + - - -
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Residues in contact with ALA 32 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4161 PRO 5.7 0.2 - - - -
4171 PRO* 4.4 20.7 - - - +
305 ILE 4.1 1.2 + - - -
315 THR* 1.3 71.3 - - - +
335 GLU* 1.3 57.6 + - - +
355 MET* 3.7 4.0 - - - +
365 TYR* 2.8 27.1 + - - +
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Residues in contact with GLU 33 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4171 PRO* 4.8 7.6 - - - +
315 THR* 2.9 2.2 - - - +
325 ALA* 1.3 76.0 - - - +
345 GLU* 1.3 66.1 + - - +
365 TYR* 4.1 0.2 - - - -
375 ASP* 2.9 21.1 + - - -
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Residues in contact with GLU 34 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315 THR* 2.9 9.8 + - - +
335 GLU* 1.3 74.6 - - - +
355 MET* 1.3 63.9 + - - +
375 ASP* 3.1 2.3 + - - -
385 ILE* 2.9 22.7 + - - -
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Residues in contact with MET 35 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315 THR 2.7 18.1 + - - -
325 ALA* 3.9 2.7 - - - +
345 GLU* 1.3 74.5 - - - +
365 TYR* 1.3 64.9 + - - +
395 PHE* 3.0 22.2 + - - -
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Residues in contact with TYR 36 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4211 TYR 6.5 0.9 - - - -
325 ALA* 2.8 19.7 + - - +
335 GLU 4.1 0.2 - - - -
355 MET* 1.3 69.7 - - - +
375 ASP* 1.3 67.4 + - - +
395 PHE 5.7 0.2 - - - -
405 GLY* 2.9 19.4 + - - -
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Residues in contact with ASP 37 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335 GLU 2.9 17.2 + - - -
345 GLU 3.6 2.0 - - - -
365 TYR* 1.3 76.2 - - - +
385 ILE* 1.3 57.2 + - - +
405 GLY* 2.8 25.6 + - - -
415 LYS 3.7 1.7 + - - -
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Residues in contact with ILE 38 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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345 GLU 2.9 16.8 + - - -
355 MET* 3.8 1.3 - - - +
375 ASP* 1.3 71.2 - - - +
395 PHE* 1.3 63.9 + - - +
405 GLY 2.8 1.6 + - - -
415 LYS* 3.1 10.0 + - - -
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Residues in contact with PHE 39 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355 MET 3.0 12.7 + - - -
365 TYR* 5.6 0.2 - - - +
385 ILE* 1.3 74.2 - - - +
405 GLY* 1.4 57.8 + - - +
415 LYS 2.8 7.2 + - - -
425 TYR* 3.5 9.0 + - - -
435 GLY 4.5 4.3 + - - +
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Residues in contact with GLY 40 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4251 ARG* 6.4 1.6 - - - -
4281 ALA* 5.2 7.1 - - - -
365 TYR 2.9 14.6 + - - -
375 ASP 2.8 16.2 + - - -
395 PHE* 1.4 75.4 - - - +
415 LYS* 1.3 65.4 + - - +
425 TYR 3.5 0.4 + - - -
435 GLY 3.7 17.7 + - - +
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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