Contacts of the helix formed by residues 225 - 235 (chain A) in PDB entry 6T2C
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 225 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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212A GLN* 4.4 9.4 + - - -
216A ASN* 2.9 17.6 + - - +
219A LEU* 3.3 11.1 - - - +
223A PHE* 4.8 0.2 - - - +
224A LYS* 1.3 80.2 + - + +
226A TYR* 1.3 72.4 + - - +
227A HIS* 3.3 23.7 + - - +
228A GLN* 3.2 22.3 + - + +
229A PHE* 3.1 18.0 + - - +
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Residues in contact with TYR 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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207A TYR* 3.9 26.9 + + - -
212A GLN* 4.8 3.6 - - - +
215A ALA* 4.0 16.4 - - + +
216A ASN* 2.9 15.1 + - - +
219A LEU* 3.9 21.5 - - + +
225A ASP* 1.3 78.1 + - - +
227A HIS* 1.3 83.5 + + - +
229A PHE* 3.3 2.5 + + - +
230A LYS* 2.9 59.0 + - + +
319B LEU* 4.7 2.9 - - + -
323B LEU* 4.0 24.5 - - + +
334B ARG 4.0 0.3 + - - -
335B ASP* 3.6 7.4 + - - -
338B ALA* 3.4 23.6 - - + +
342B ILE* 4.1 21.1 - - + -
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Residues in contact with HIS 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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207A TYR* 5.6 0.9 - + - -
212A GLN* 3.1 32.5 + - - -
225A ASP* 3.3 14.8 + - - +
226A TYR* 1.3 99.2 - + - +
228A GLN* 1.3 57.8 + - - +
230A LYS* 3.7 17.4 - - - +
231A ALA* 2.9 28.8 + - - +
335B ASP* 5.6 3.1 - - - -
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Residues in contact with GLN 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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222A SER 5.3 1.8 + - - -
223A PHE* 3.8 25.7 - - + +
224A LYS* 4.7 13.8 + - - +
225A ASP* 3.2 27.2 + - + +
226A TYR 3.2 0.4 - - - -
227A HIS* 1.3 80.3 - - - +
229A PHE* 1.3 57.0 + - - +
231A ALA* 3.3 6.4 + - + +
232A TYR* 2.9 26.7 + - + +
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Residues in contact with PHE 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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219A LEU* 3.7 27.6 - - + -
220A PRO* 3.6 33.9 - - + -
223A PHE* 3.9 31.6 - + + -
225A ASP 3.1 13.3 + - - +
226A TYR* 3.8 6.5 - + - +
228A GLN* 1.3 73.0 - - - +
230A LYS* 1.3 61.4 + - - +
232A TYR* 3.3 10.7 + + - +
233A VAL* 3.0 53.9 + - + +
85B THR* 4.8 4.9 - - + -
316B ARG 5.1 0.2 - - - -
319B LEU* 4.4 7.6 - - + -
320B ALA* 3.9 24.9 - - + -
323B LEU* 4.0 20.6 - - + -
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Residues in contact with LYS 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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226A TYR* 2.9 38.0 + - + +
227A HIS* 3.7 19.6 + - - +
228A GLN 3.3 0.2 - - - -
229A PHE* 1.3 77.4 - - - +
231A ALA* 1.3 56.1 + - - +
233A VAL* 4.0 1.6 - - - +
234A SER* 2.9 34.0 + - - -
323B LEU* 4.0 31.2 - - + -
331B GLU* 3.7 19.1 + - - +
334B ARG* 3.5 31.5 + - + +
335B ASP* 2.6 32.7 + - - -
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Residues in contact with ALA 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 HIS 2.9 18.5 + - - +
228A GLN* 3.7 7.2 - - - +
229A PHE 3.3 0.2 - - - -
230A LYS* 1.3 74.6 - - - +
232A TYR* 1.3 62.2 + - - +
234A SER* 4.6 3.3 - - - +
235A SER* 3.0 28.2 + - - -
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Residues in contact with TYR 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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223A PHE* 3.5 36.6 - + + -
228A GLN* 2.9 15.9 + - + +
229A PHE* 3.3 16.4 + + - +
231A ALA* 1.3 78.1 - - - +
233A VAL* 1.3 67.6 + - + +
235A SER* 3.7 3.5 + - - +
236A PHE* 3.6 44.7 + + - +
85B THR* 5.3 7.7 - - + +
86B ASP* 4.6 11.8 + - - +
89B LEU* 3.9 19.9 - - + +
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Residues in contact with VAL 233 (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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229A PHE* 3.0 51.2 + - + +
230A LYS 4.0 2.5 - - - +
231A ALA 3.4 0.2 - - - -
232A TYR* 1.3 79.7 - - + +
234A SER* 1.3 62.6 + - - +
235A SER 3.1 1.4 + - - -
236A PHE* 3.3 20.1 + - - +
89B LEU* 3.9 28.9 - - + -
320B ALA* 4.0 1.6 - - - +
323B LEU* 3.6 40.8 - - + +
324B ARG* 3.6 19.3 - - - +
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Residues in contact with SER 234 (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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230A LYS 2.9 19.3 + - - -
231A ALA* 4.0 4.5 + - - -
232A TYR 3.4 0.2 - - - -
233A VAL* 1.3 76.6 - - - +
235A SER* 1.3 56.8 + - - +
236A PHE 3.6 0.8 + - - -
324B ARG* 5.9 1.5 - - - -
327B ALA* 4.6 16.1 - - - +
328B GLY 5.2 3.1 + - - -
334B ARG* 3.4 31.9 + - - +
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Residues in contact with SER 235 (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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231A ALA 3.0 21.0 + - - -
232A TYR* 3.8 5.1 + - - +
233A VAL 3.2 0.6 - - - -
234A SER* 1.3 80.0 - - - +
236A PHE* 1.3 60.2 + - - +
237A LYS* 3.8 3.3 + - - +
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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