Contacts of the strand formed by residues 222 - 233 (chain C) in PDB entry 1T9G
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 222 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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166C TRP* 4.1 22.7 - - - -
167C ILE 3.2 15.9 - - - -
168C THR* 4.2 9.6 - - - +
211C LYS* 5.2 0.6 - - - +
212C GLU* 3.1 31.5 + - - +
214C ASN* 3.8 20.1 + - - +
217C GLN 5.5 1.3 - - - +
220C SER* 3.7 20.3 + - - +
221C ASP* 1.3 77.5 - - - +
223C ARG* 1.3 64.2 + - - +
399C FAD 4.1 21.9 - - + +
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Residues in contact with ARG 223 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165C MET* 4.4 0.7 - - - -
166C TRP 4.2 3.8 - - - -
167C ILE* 3.1 37.9 + - - +
171C GLY* 3.6 11.8 - - - +
172C LYS* 3.7 15.7 - - - +
208C ILE* 3.5 18.5 - - + +
209C GLY 2.9 19.9 + - - +
210C ARG* 3.1 21.5 - - - +
211C LYS* 3.8 25.2 - - - +
212C GLU* 4.6 4.3 - - - -
221C ASP* 2.9 37.7 + - - +
222C THR* 1.3 78.5 + - - +
224C GLY* 1.3 69.0 + - - +
225C ILE* 3.8 3.5 - - + +
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Residues in contact with GLY 224 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163C GLN* 5.6 3.6 - - - -
164C LYS 3.1 16.2 - - - -
165C MET* 3.7 22.4 - - - +
209C GLY* 2.7 28.3 + - - -
210C ARG 4.7 1.8 + - - -
212C GLU* 4.4 4.0 + - - -
223C ARG* 1.3 72.0 - - - +
225C ILE* 1.3 67.3 + - - +
226C VAL* 5.8 0.4 - - - -
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Residues in contact with ILE 225 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134C CYS* 4.0 11.4 - - - -
163C GLN* 3.8 1.2 - - - +
164C LYS* 3.0 33.4 + - + +
167C ILE* 4.7 5.2 - - + -
170C GLY* 4.3 17.5 - - - +
176C TYR* 3.4 38.8 - - + +
206C ILE* 4.3 8.5 - - + -
207C GLN 3.4 10.1 - - - +
208C ILE* 3.9 10.5 - - - -
223C ARG* 3.8 12.6 - - + +
224C GLY* 1.3 79.1 - - - +
226C VAL* 1.3 62.7 + - - +
227C PHE* 3.6 30.0 - - + -
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Residues in contact with VAL 226 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162C GLY 3.6 8.1 - - - +
163C GLN* 4.6 21.1 - - + +
205C GLY 3.5 0.7 - - - +
206C ILE* 3.4 4.3 - - - +
207C GLN* 2.8 58.2 + - + +
224C GLY 5.8 0.2 - - - -
225C ILE* 1.3 76.9 - - - +
227C PHE* 1.3 72.3 + - - +
228C GLU* 3.9 24.9 - - + +
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Residues in contact with PHE 227 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134C CYS* 4.5 1.1 - - - -
149C THR* 5.2 1.1 - - + -
160C ILE* 3.7 28.3 - - + +
161C ASN* 3.1 6.4 + - - -
162C GLY* 2.8 44.2 + - - +
164C LYS* 3.7 17.3 - - + -
176C TYR* 4.3 7.4 - + - -
178C LEU* 3.4 31.4 - - + -
199C VAL* 4.1 11.9 - - + -
205C GLY 3.8 3.6 - - - -
206C ILE* 3.7 33.9 - - + -
225C ILE* 3.6 35.7 - - + -
226C VAL* 1.3 78.4 - - - +
228C GLU* 1.4 58.0 - - - +
230C VAL* 3.8 14.1 - - + -
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Residues in contact with GLU 228 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161C ASN* 3.5 5.6 - - - +
205C GLY* 3.0 37.0 + - - +
207C GLN* 3.1 26.5 + - - +
226C VAL* 3.9 15.5 - - + +
227C PHE* 1.4 70.3 - - - +
229C ASP* 1.3 68.8 + - + +
230C VAL 3.3 0.4 - - - -
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Residues in contact with ASP 229 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159C ILE* 3.4 21.4 - - + +
160C ILE 3.2 0.6 + - - -
161C ASN* 2.6 33.8 + - - +
205C GLY* 4.8 2.2 + - - -
228C GLU* 1.3 73.7 - - - +
230C VAL* 1.3 64.5 + - - +
231C LYS* 3.4 10.6 + - - +
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Residues in contact with VAL 230 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158C TYR 3.0 2.4 - - - +
159C ILE* 3.0 9.5 - - - -
160C ILE* 2.8 43.5 + - + +
199C VAL* 4.3 13.5 - - + -
203C THR* 3.8 14.8 - - + -
205C GLY* 3.3 41.1 - - - +
206C ILE* 3.5 14.6 - - + -
227C PHE* 3.8 16.4 - - + -
229C ASP* 1.3 76.5 - - - +
231C LYS* 1.3 61.3 + - - +
232C VAL* 3.8 20.8 + - + -
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Residues in contact with LYS 231 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157C GLU* 2.9 38.8 - - - +
158C TYR 3.5 3.4 - - - -
159C ILE* 4.2 13.5 - - + -
203C THR* 3.5 27.1 + - + +
204C PRO* 6.5 1.1 - - + -
205C GLY 5.4 0.2 - - - +
229C ASP 3.4 11.2 + - - +
230C VAL* 1.3 73.6 - - - +
232C VAL* 1.3 62.1 + - - +
233C PRO* 4.2 3.8 - - - +
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Residues in contact with VAL 232 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157C GLU* 4.3 3.1 + - - -
158C TYR* 2.5 50.4 + - + +
160C ILE* 3.8 14.4 - - + -
197C PHE* 3.9 22.7 - - + -
198C ILE 3.7 22.2 - - - +
199C VAL* 3.7 24.5 - - + -
230C VAL* 3.8 16.4 - - + -
231C LYS* 1.3 78.8 - - - +
233C PRO* 1.3 70.8 - - + +
236C ASN* 4.1 6.7 - - + -
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Residues in contact with PRO 233 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156C ASP 3.7 9.9 - - - +
157C GLU* 4.3 10.7 - - + +
158C TYR* 4.8 1.3 - - - -
231C LYS 4.2 4.5 - - - +
232C VAL* 1.3 91.0 - - + +
234C LYS* 1.3 53.2 + - - +
235C GLU* 2.7 35.5 + - - +
236C ASN* 2.7 39.5 + - - +
237C VAL* 4.3 0.3 + - - +
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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