Contacts of the helix formed by residues 226 - 235 (chain 1) 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 HIS 226 (chain 1).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2251 GLY* 1.3 69.8 - - - -
2271 THR* 1.3 53.2 + - - +
2291 SER* 2.5 30.0 + - - +
2301 LEU 3.1 6.6 + - - -
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Residues in contact with THR 227 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2251 GLY* 2.9 3.0 + - - +
2261 HIS* 1.3 74.4 - - - +
2281 PRO* 1.3 57.8 - - - +
2301 LEU* 2.8 19.8 + - - +
2311 ARG* 2.9 14.0 + - - -
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Residues in contact with PRO 228 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2251 GLY 2.8 15.3 - - - +
2271 THR* 1.3 75.0 - - - +
2291 SER* 1.3 60.2 + - - +
2311 ARG* 5.6 0.2 - - - -
2321 TRP* 3.0 25.5 + - - -
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Residues in contact with SER 229 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2251 GLY 4.2 0.6 + - - -
2261 HIS* 2.5 17.3 + - - +
2281 PRO* 1.3 73.6 - - - +
2301 LEU* 1.3 56.3 + - - +
2321 TRP* 5.2 0.2 - - - +
2331 ASP* 2.8 27.4 + - - +
2411 GLY* 6.0 4.5 - - - -
2451 PRO* 6.0 6.9 - - - +
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Residues in contact with LEU 230 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2261 HIS 3.1 6.3 + - - -
2271 THR* 2.8 11.6 + - - +
2291 SER* 1.3 74.6 - - - +
2311 ARG* 1.3 54.6 + - - +
2331 ASP* 2.6 26.0 + - - -
2341 GLU 3.1 5.0 + - - -
6071 ALA* 5.7 0.8 - - - -
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Residues in contact with ARG 231 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2271 THR 2.9 14.2 + - - -
2281 PRO 4.3 0.2 - - - -
2301 LEU* 1.3 68.6 - - - +
2321 TRP* 1.3 63.1 + - - +
2331 ASP 2.9 1.2 + - - -
2341 GLU* 3.0 12.5 + - - -
2351 THR* 3.1 9.0 + - - -
6071 ALA* 4.7 20.8 - - - +
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Residues in contact with TRP 232 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2281 PRO 3.0 16.6 + - - -
2291 SER* 4.7 0.7 - - - -
2311 ARG* 1.3 75.5 - - - +
2331 ASP* 1.3 61.3 + - - +
2351 THR* 4.3 2.0 - - - +
2361 PRO* 3.2 22.9 - - - +
2411 GLY* 5.5 4.2 - - - -
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Residues in contact with ASP 233 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2291 SER* 2.8 20.1 + - - +
2301 LEU 2.6 15.2 + - - -
2321 TRP* 1.3 71.4 - - - +
2341 GLU* 1.3 56.4 + - - +
2361 PRO 2.8 16.8 - - - +
2381 ARG* 3.2 23.8 + - - +
2411 GLY* 5.2 8.7 - - - -
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Residues in contact with GLU 234 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2301 LEU 3.1 5.9 + - - -
2311 ARG 3.0 7.2 + - - -
2331 ASP* 1.3 77.7 - - - +
2351 THR* 1.3 61.3 + - - +
2361 PRO 2.7 13.7 - - - +
6071 ALA* 5.0 9.9 - - - +
6111 SER* 5.0 6.1 - - - -
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Residues in contact with THR 235 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2311 ARG 3.1 12.4 + - - -
2321 TRP* 3.2 4.3 + - - +
2341 GLU* 1.3 77.8 - - - +
2361 PRO* 1.3 58.2 - - - +
3011 ARG* 5.1 4.7 - - - -
3021 ASP* 4.8 10.6 + - - -
6071 ALA 5.3 0.2 + - - -
6111 SER* 4.4 19.3 - - - +
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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