Contacts of the helix formed by residues 225 - 232 (chain A) in PDB entry 3H4B
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 SER 225 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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158A TYR* 3.8 26.6 + - - -
159A ASN* 4.3 8.8 + - - +
161A GLN* 2.5 34.2 + - - +
221A LEU* 3.8 4.9 - - - -
222A LEU 2.7 20.2 + - - -
223A PRO 2.8 0.4 + - - -
224A GLU* 1.3 71.1 - - - +
226A CYS* 1.3 62.1 + - - -
227A GLN 3.5 1.8 - - - -
228A HIS* 3.3 11.0 + - - +
229A LEU* 3.1 22.3 + - - +
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Residues in contact with CYS 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205A LEU* 4.3 16.3 - - + +
221A LEU* 4.5 13.7 - - + -
222A LEU 3.8 1.8 + - - -
223A PRO* 2.9 18.1 + - + +
224A GLU 3.5 0.8 - - - -
225A SER* 1.3 76.9 - - - +
227A GLN* 1.3 65.4 + - + +
229A LEU* 3.3 4.2 + - - +
230A ILE* 2.9 24.7 + - - +
286A PHE 3.6 23.8 - - - -
287A GLY* 3.9 15.5 - - - -
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Residues in contact with GLN 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224A GLU 5.0 2.0 + - - +
225A SER 3.5 0.2 - - - -
226A CYS* 1.3 81.9 - - + +
228A HIS* 1.3 58.2 + - - +
230A ILE* 3.0 8.1 + - - +
231A HIS* 2.6 53.5 + - + +
262A GLN* 3.2 26.0 + - - +
286A PHE* 3.0 33.8 + - - +
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Residues in contact with HIS 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A TYR* 2.9 33.5 + + + -
159A ASN* 3.5 39.2 + - + +
224A GLU 5.5 0.8 + - - +
225A SER* 3.3 16.3 + - - +
226A CYS 3.3 0.2 - - - -
227A GLN* 1.3 78.1 - - - +
229A LEU* 1.3 61.6 + - - +
231A HIS* 3.8 4.8 - - - +
232A SER* 3.1 25.6 + - - -
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Residues in contact with LEU 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A TYR* 3.4 32.9 + - + -
205A LEU* 4.2 11.9 - - + +
208A LEU* 3.5 47.6 - - + +
209A VAL* 4.2 9.2 - - + +
212A VAL* 4.9 3.4 - - + -
221A LEU* 4.2 22.7 - - + -
225A SER 3.1 13.1 + - - +
226A CYS* 3.6 7.0 - - - +
227A GLN 3.1 0.2 - - - -
228A HIS* 1.3 74.5 - - - +
230A ILE* 1.3 64.5 + - - +
232A SER* 2.6 27.2 + - - +
233A LEU* 4.0 6.6 + - + +
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Residues in contact with ILE 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204A LEU* 4.7 1.8 - - + -
205A LEU* 5.2 1.5 - - + +
208A LEU* 4.0 24.0 - - + -
226A CYS* 2.9 13.1 + - - +
227A GLN* 3.0 32.3 - - - +
229A LEU* 1.3 77.4 - - - +
231A HIS* 1.3 81.3 - - + +
232A SER 3.3 1.0 + - - -
233A LEU* 3.3 29.0 + - + +
239A ILE* 4.6 6.5 - - + -
258A VAL* 3.8 12.5 - - + +
262A GLN* 3.8 6.1 - - - +
284A LEU 3.9 17.3 - - - +
285A SER 3.2 20.6 - - - +
286A PHE 4.9 0.9 - - - -
287A GLY* 4.2 13.0 - - - +
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Residues in contact with HIS 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227A GLN* 2.6 46.9 + - + +
228A HIS* 3.8 4.3 - - - +
230A ILE* 1.3 75.7 - - + +
232A SER* 1.3 62.5 + - - +
233A LEU 3.1 10.9 + - - +
258A VAL* 4.7 5.7 - - + +
259A ARG* 3.3 60.5 + - + +
262A GLN* 3.2 33.8 + - - -
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Residues in contact with SER 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A TYR* 3.8 8.7 + - - -
228A HIS* 3.1 18.6 + - - -
229A LEU* 2.6 32.2 + - - +
230A ILE 3.2 0.2 - - - -
231A HIS* 1.3 77.2 - - - +
233A LEU* 1.3 65.1 + - - +
234A ASN* 3.7 13.2 + - - +
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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