Contacts of the helix formed by residues 150 - 162 (chain C) in PDB entry 1Y9A
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 150 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37C CYS* 3.6 0.2 - - - -
59C HIS* 3.0 4.2 + - - -
60C GLU* 3.6 21.7 - - + +
85C ALA* 4.2 3.8 - - + -
146C VAL 4.5 0.4 + - - -
147C MET 4.4 0.4 - - - -
148C LEU 3.1 0.6 + - - -
149C SER* 1.3 81.3 - - - +
151C MET* 1.3 72.0 + - - +
152C VAL 3.5 1.8 - - - -
153C THR* 3.6 6.1 - - - -
154C THR* 2.8 46.6 + - - -
295C THR* 4.6 0.7 - - - +
2000C ZN 2.0 36.8 - - - -
2001C CAC 2.6 31.4 + - - +
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Residues in contact with MET 151 (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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37C CYS* 4.1 11.0 - - - -
60C GLU* 3.4 19.2 + - - +
147C MET* 3.2 18.6 + - - +
150C ASP* 1.3 94.7 - - - +
152C VAL* 1.3 58.6 + - - +
154C THR* 4.3 0.3 - - - -
155C GLY* 3.0 23.6 + - - -
177C PRO* 3.7 26.7 - - + +
178C VAL* 3.7 27.9 - - + -
181C MET* 3.4 13.3 - - + +
319C LEU* 4.2 17.3 - - + -
346C LYS* 3.6 36.8 - - + +
2001C CAC 5.4 0.2 - - - +
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Residues in contact with VAL 152 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147C MET* 2.9 24.5 + - + +
148C LEU* 4.1 13.7 - - + -
151C MET* 1.3 72.9 - - - +
153C THR* 1.3 61.6 + - - +
156C PHE* 2.8 53.2 + - + +
181C MET* 3.7 19.1 - - + -
305C LEU* 4.1 17.0 - - + -
314C LEU* 3.8 19.1 - - + -
316C THR* 3.6 30.7 - - + -
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Residues in contact with THR 153 (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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148C LEU 3.4 18.3 + - - +
149C SER 3.4 17.7 - - - +
150C ASP* 3.5 8.3 - - - +
152C VAL* 1.3 79.5 - - - +
154C THR* 1.3 58.4 + - - +
157C HIS* 2.9 25.6 + - - +
295C THR* 2.5 28.4 + - + +
296C PRO 3.3 6.9 + - - +
301C ARG* 2.8 34.0 + - - +
302C MET* 4.1 7.9 - - + -
305C LEU* 3.6 21.1 - - - -
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Residues in contact with THR 154 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150C ASP* 2.8 35.3 + - - -
151C MET 4.3 0.7 - - - -
153C THR* 1.3 74.1 - - - +
155C GLY* 1.3 65.3 + - - +
157C HIS* 3.1 2.6 + - - -
158C GLY 3.0 18.4 + - - -
178C VAL* 3.9 16.8 - - + -
265C VAL* 3.5 34.3 - - + +
293C GLY 5.7 0.4 - - - +
295C THR* 3.3 24.8 - - - +
2001C CAC 3.2 15.6 + - - +
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Residues in contact with GLY 155 (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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151C MET 3.0 15.0 + - - -
154C THR* 1.3 75.7 - - - +
156C PHE* 1.3 61.4 - - - +
158C GLY 3.2 7.4 + - - -
159C ALA 3.4 4.2 + - - -
178C VAL* 3.5 20.9 - - - +
181C MET 3.8 2.0 - - - -
182C SER* 2.9 42.7 + - - -
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Residues in contact with PHE 156 (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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152C VAL* 2.8 36.3 + - + +
153C THR* 3.9 2.7 - - - +
155C GLY* 1.3 76.6 - - - +
157C HIS* 1.3 56.9 + - - +
159C ALA* 3.0 5.4 + - - +
160C GLU* 2.9 32.6 + - + +
181C MET* 3.2 27.4 - - + -
184C ALA* 4.0 7.0 - - + -
185C GLY* 3.5 25.1 - - - -
188C HIS* 4.3 15.9 - - + -
189C LEU* 5.0 0.3 - - - +
301C ARG* 4.2 9.0 - - - +
305C LEU* 3.8 18.6 - - + -
308C LEU* 3.6 27.8 - - + -
314C LEU* 4.0 18.2 - - + -
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Residues in contact with HIS 157 (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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153C THR 2.9 19.6 + - - +
154C THR* 3.1 8.5 + - - +
156C PHE* 1.3 77.4 - - - +
158C GLY* 1.3 55.8 + - - +
160C GLU* 2.8 28.7 + - + +
161C LEU* 2.7 67.1 + - + +
265C VAL* 3.9 3.1 - - + -
293C GLY* 3.9 10.4 - - - -
294C LEU 3.6 25.4 + - - -
295C THR* 4.5 0.7 - - - -
296C PRO* 3.6 19.7 - - + +
301C ARG* 3.7 3.0 - - - +
2003C EDO 3.3 31.7 + - - -
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Residues in contact with GLY 158 (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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154C THR 3.0 11.5 + - - -
155C GLY 3.2 5.7 + - - -
157C HIS* 1.3 74.7 - - - +
159C ALA* 1.3 56.4 + - - +
161C LEU* 3.4 4.6 + - - +
162C ALA* 3.0 29.1 + - - +
240C VAL* 3.7 22.2 - - - +
263C GLY* 3.9 7.1 - - - -
265C VAL* 3.3 18.7 - - - +
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Residues in contact with ALA 159 (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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155C GLY 3.4 4.5 + - - +
156C PHE 3.0 9.2 + - - +
158C GLY* 1.3 73.2 - - - +
160C GLU* 1.3 63.9 + - - +
162C ALA 3.4 1.0 + - - -
163C ASN 3.4 14.9 + - - -
164C ILE* 3.6 25.0 + - + +
182C SER 4.0 8.1 - - - +
185C GLY* 3.6 9.4 - - - -
186C ALA* 3.5 28.5 - - - +
189C LEU* 3.6 15.0 - - + +
240C VAL* 3.9 4.1 - - + +
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Residues in contact with GLU 160 (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 PHE* 2.9 16.1 + - + +
157C HIS* 2.8 38.2 + - + +
159C ALA* 1.3 76.6 - - - +
161C LEU* 1.3 57.2 + - - +
163C ASN* 3.0 20.6 + - - +
164C ILE 5.6 0.2 - - - +
189C LEU* 4.2 16.8 - - + -
296C PRO* 4.7 0.3 - - - +
301C ARG* 2.9 38.1 + - - -
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Residues in contact with LEU 161 (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 HIS* 2.7 55.9 + - + +
158C GLY 3.8 0.4 - - - +
160C GLU* 1.3 71.7 - - - +
162C ALA* 1.3 59.8 + - - +
163C ASN* 3.3 2.4 + - - +
261C ASP* 4.0 0.3 - - - +
263C GLY* 3.7 14.8 - - - -
264C ASN 3.5 13.9 - - - +
265C VAL* 4.2 3.4 - - + -
291C HIS* 3.0 43.4 + - + +
292C GLY* 4.3 3.8 - - - +
293C GLY* 3.5 30.1 - - - +
2003C EDO 4.1 9.4 - - - +
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Residues in contact with ALA 162 (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 GLY 3.0 17.5 + - - +
159C ALA 3.7 5.6 - - - +
160C GLU 3.2 0.4 - - - -
161C LEU* 1.3 72.5 - - - +
163C ASN* 1.3 69.3 + - - +
164C ILE* 3.2 9.9 + - + -
238C LYS* 3.0 25.6 - - + +
239C VAL 3.5 24.9 - - - +
240C VAL* 3.8 12.1 - - + -
261C ASP* 3.3 8.7 - - - +
263C GLY* 3.8 7.5 - - - +
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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