Contacts of the helix formed by residues 153 - 168 (chain C) in PDB entry 1SIW
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 GLY 153 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83C ILE* 3.4 19.4 - - - +
84C GLU* 4.6 4.0 - - - -
87C GLN* 3.2 24.9 - - - -
150C HIS 2.9 4.6 + - - -
151C MET 3.1 4.6 + - - -
152C ASP* 1.3 79.2 - - - +
154C SER* 1.3 63.7 + - - +
155C GLU 3.4 2.2 - - - -
156C MET 4.0 0.7 - - - -
157C MET* 3.1 25.1 + - - +
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Residues in contact with SER 154 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150C HIS* 3.1 34.6 + - - +
152C ASP* 3.2 21.6 + - - -
153C GLY* 1.3 79.4 - - - +
155C GLU* 1.3 72.9 + - - +
157C MET* 3.4 12.1 + - - +
158C LYS* 3.5 21.1 + - - +
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Residues in contact with GLU 155 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C GLN* 5.1 3.1 - - - +
146C PHE* 4.9 4.6 - - - +
147C SER* 5.0 6.5 - - - +
150C HIS* 3.6 42.8 + - + +
153C GLY 3.4 0.4 - - - -
154C SER* 1.3 79.9 + - - +
156C MET* 1.3 66.8 + - - +
158C LYS* 2.8 43.3 + - - +
159C LEU* 2.8 22.6 - - + +
179C GLY 4.4 1.9 - - - +
180C VAL* 4.0 6.3 - - - -
181C ALA* 3.3 27.4 + - - +
184C PHE* 3.6 24.8 - - + -
807C HEM 5.7 0.2 - - - +
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Residues in contact with MET 156 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C GLY* 5.3 13.0 - - - +
70C MET* 6.1 2.0 - - + -
83C ILE* 3.4 27.8 - - + +
86C LYS* 4.2 9.6 - - + +
87C GLN* 3.5 48.4 + - - +
90C ALA* 4.1 13.7 - - + -
153C GLY 3.7 1.9 + - - +
154C SER 3.5 0.2 - - - -
155C GLU* 1.3 79.3 - - - +
157C MET* 1.3 57.1 + - - +
159C LEU* 3.3 3.2 + - - +
160C VAL* 2.8 47.8 + - + +
807C HEM 3.1 44.1 + - + +
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Residues in contact with MET 157 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C ILE* 3.9 37.9 - - + +
153C GLY 3.1 19.7 + - - +
154C SER* 3.5 8.7 - - - +
155C GLU 3.1 0.2 + - - -
156C MET* 1.3 77.0 - - - +
158C LYS* 1.3 57.7 + - + +
160C VAL* 3.9 8.1 - - - +
161C GLY* 3.0 24.4 + - - -
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Residues in contact with LYS 158 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154C SER* 3.5 15.3 - - - +
155C GLU* 2.8 33.6 + - - +
157C MET* 1.3 74.5 - - + +
159C LEU* 1.3 64.0 + - + +
161C GLY* 2.9 17.0 + - - -
162C TRP* 2.9 12.0 + - - +
176C HIS* 3.1 34.4 - - - +
177C LEU* 4.3 5.2 - - + -
178C ASP 3.2 25.3 + - - +
179C GLY* 3.5 15.4 + - - -
180C VAL* 4.3 10.1 - - + -
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Residues in contact with LEU 159 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C MET* 5.3 1.9 - - - +
155C GLU* 2.8 34.1 + - + +
156C MET* 3.8 6.1 - - - +
158C LYS* 1.3 79.4 - - + +
160C VAL* 1.3 59.2 + - + +
162C TRP* 3.2 5.8 + - + +
163C ALA* 2.9 29.7 + - - +
177C LEU* 3.6 23.3 - - + -
180C VAL* 3.6 21.1 - - + -
184C PHE* 4.1 24.9 - - + -
188C LEU* 3.8 21.8 - - + -
807C HEM 3.5 36.8 - - + +
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Residues in contact with VAL 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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69C GLY 3.7 22.0 - - - +
70C MET* 3.9 19.7 - - + +
72C THR 4.9 2.0 - - - +
83C ILE* 5.2 3.1 - - + -
156C MET* 2.8 38.3 + - + +
157C MET* 4.0 10.8 - - - +
159C LEU* 1.3 77.7 - - + +
161C GLY* 1.3 63.7 + - - +
163C ALA* 4.4 4.9 - - - -
164C GLN* 3.1 47.7 + - - +
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Residues in contact with GLY 161 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157C MET 3.0 13.4 + - - -
158C LYS 2.9 8.6 + - - -
160C VAL* 1.3 78.7 - - - +
162C TRP* 1.3 56.1 + - - +
164C GLN* 3.7 4.5 + - - +
165C SER* 2.6 32.6 + - - -
176C HIS* 3.4 23.4 + - - -
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Residues in contact with TRP 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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9C PHE* 3.1 42.9 + + - +
13C PRO* 4.6 1.6 - - + -
70C MET* 6.2 0.4 - - - -
158C LYS 2.9 5.2 + - - +
159C LEU 3.4 11.0 - - - +
161C GLY* 1.3 75.3 - - - +
163C ALA* 1.3 85.7 + - + +
165C SER* 2.8 14.4 + - - -
166C VAL* 2.9 30.0 + - + +
173C ALA* 3.2 41.5 - - + +
174C SER 4.1 0.4 - - - -
176C HIS* 3.6 3.0 - - + +
177C LEU* 3.6 30.1 - - + -
188C LEU* 3.6 36.6 - - + -
192C MET* 3.8 37.5 - - + -
807C HEM 4.0 11.9 - - + -
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Residues in contact with ALA 163 (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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70C MET* 4.0 33.2 - - + +
71C LEU* 4.9 4.9 - - + -
159C LEU 2.9 16.1 + - - +
160C VAL 3.9 4.0 - - - +
161C GLY 3.5 0.2 - - - -
162C TRP* 1.3 92.4 - - + +
164C GLN* 1.3 62.4 + - - +
166C VAL* 3.1 7.6 + - - +
167C VAL* 3.1 28.5 + - + +
807C HEM 5.9 0.7 - - + -
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Residues in contact with GLN 164 (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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70C MET 3.2 21.9 + - - +
71C LEU* 3.7 8.6 + - + +
72C THR 2.7 33.7 + - - -
160C VAL* 3.1 29.4 + - - +
161C GLY* 4.2 3.9 - - - +
163C ALA* 1.3 74.5 - - - +
165C SER* 1.3 52.4 + - - +
167C VAL* 3.8 10.5 - - + -
168C THR* 2.6 41.8 + - + +
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Residues in contact with SER 165 (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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14C TYR* 3.7 0.5 + - - -
161C GLY 2.6 20.1 + - - -
162C TRP 2.8 9.2 + - - -
164C GLN* 1.3 74.3 - - - +
166C VAL* 1.3 65.7 + - - +
168C THR* 3.4 4.8 + - - -
169C PHE 3.2 2.6 + - - -
170C HIS* 2.9 43.8 + - - +
171C GLY 5.6 0.4 - - - -
173C ALA* 3.5 22.7 - - - -
176C HIS* 2.8 21.2 + - - -
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Residues in contact with VAL 166 (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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9C PHE 4.4 4.5 - - - +
13C PRO* 4.2 24.2 - - + +
14C TYR* 2.6 42.8 + - + +
162C TRP* 2.9 49.6 + - + +
163C ALA* 3.1 8.7 + - - +
165C SER* 1.3 76.5 - - - +
167C VAL* 1.3 65.0 + - + +
169C PHE* 3.1 9.7 + - - -
173C ALA* 4.0 10.3 - - + -
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Residues in contact with VAL 167 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C LEU* 4.3 26.5 - - + -
163C ALA* 3.1 15.9 + - + +
164C GLN* 3.7 15.5 - - + +
166C VAL* 1.3 81.8 - - + +
168C THR* 1.3 65.2 + - + +
169C PHE* 3.4 17.6 - - - -
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Residues in contact with THR 168 (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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164C GLN* 2.6 27.4 + - + +
165C SER* 3.4 6.1 + - - -
166C VAL 3.2 0.6 - - - -
167C VAL* 1.3 86.0 - - + +
169C PHE* 1.3 72.3 + - - +
170C HIS* 3.1 32.6 + - - -
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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