Contacts of the helix formed by residues 163 - 178 (chain C) in PDB entry 1SMK
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 PRO 163 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130C ARG* 3.6 31.0 - - + +
131C ASP* 4.2 13.7 - - + +
134C PHE* 4.0 28.5 - - + +
137C ASN* 4.9 0.2 - - + -
138C ALA 5.8 0.2 - - - +
161C SER 3.8 1.3 - - - -
162C ASN* 1.3 84.5 - - + +
164C VAL* 1.3 53.3 + - - +
165C ASN* 3.1 6.1 - - + +
166C SER* 2.7 43.7 + - - +
167C THR* 2.8 21.3 + - + -
220C HIS 6.1 0.2 - - - +
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Residues in contact with VAL 164 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159C LEU 4.4 2.0 - - - +
160C ILE 3.2 29.4 - - - +
161C SER 3.4 3.1 + - - +
162C ASN* 3.6 10.6 + - - +
163C PRO* 1.3 71.2 - - - +
165C ASN* 1.3 62.9 + - - +
166C SER 2.9 1.6 + - - -
167C THR* 3.4 9.6 - - - +
168C VAL* 3.2 41.6 + - + +
188C GLY* 3.8 18.2 - - - -
189C VAL 4.5 9.9 - - - +
190C THR* 5.1 0.4 - - + -
220C HIS* 4.4 25.4 + - + -
297C PHE* 3.8 12.6 - - + -
1313C CIT 5.2 0.2 - - - +
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Residues in contact with ASN 165 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163C PRO* 3.0 5.7 + - + -
164C VAL* 1.3 77.1 - - - +
166C SER* 1.3 56.9 + - - +
169C PRO* 3.4 17.8 - - - +
219C GLY* 3.2 6.4 - - - -
220C HIS* 2.7 27.4 + - - +
221C ALA* 3.8 14.1 - - + +
224C THR* 3.0 31.3 + - - +
297C PHE* 4.0 11.2 - - - -
342C GLU* 5.7 1.8 + - - +
343C LEU* 3.3 18.2 - - + +
346C SER* 3.6 31.9 + - - +
347C ILE* 3.9 6.9 - - - +
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Residues in contact with SER 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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131C ASP* 4.6 2.4 + - - -
134C PHE* 3.7 29.2 - - - -
163C PRO* 2.7 15.7 + - - +
165C ASN* 1.3 78.6 - - - +
167C THR* 1.3 63.1 + - - -
168C VAL 3.3 1.8 - - - -
169C PRO* 3.1 5.7 - - - +
170C ILE* 3.1 25.8 + - - +
346C SER* 2.5 33.6 + - - -
349C LYS* 4.1 8.7 - - - +
350C GLY* 3.5 5.4 - - - -
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Residues in contact with THR 167 (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 PHE* 5.7 0.7 - - + -
137C ASN 5.0 0.7 - - - +
138C ALA* 5.0 5.6 - - - -
141C VAL* 3.9 28.1 - - + +
159C LEU* 3.5 18.5 - - - +
161C SER 2.8 27.2 + - - +
162C ASN 3.9 4.9 - - - +
163C PRO* 2.8 34.2 + - + +
164C VAL* 3.4 8.1 - - - -
166C SER* 1.3 71.5 - - - +
168C VAL* 1.3 61.8 + - - +
170C ILE* 3.2 16.5 + - + +
171C ALA* 2.8 24.1 + - - +
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Residues in contact with VAL 168 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159C LEU* 3.9 17.0 - - + -
164C VAL* 3.2 17.7 + - + +
167C THR* 1.3 79.4 + - - +
169C PRO* 1.3 73.8 - - + +
171C ALA* 3.0 5.3 + - - +
172C ALA* 2.8 20.3 + - - +
186C LEU* 3.6 16.8 - - + +
187C LEU 4.5 0.7 - - - -
188C GLY* 3.4 35.4 - - - +
297C PHE* 3.7 15.5 - - + +
298C VAL* 5.2 0.9 - - - -
307C PHE* 3.7 27.8 - - + -
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Residues in contact with PRO 169 (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 VAL 3.8 0.4 - - - +
165C ASN 3.4 19.7 - - - +
166C SER 3.1 16.4 - - - +
168C VAL* 1.3 97.4 - - + +
170C ILE* 1.3 55.7 + - - +
172C ALA* 3.3 1.7 + - - +
173C GLU* 2.9 36.2 + - - +
297C PHE* 4.2 1.8 - - + -
307C PHE* 3.6 38.1 - - + -
347C ILE* 3.9 26.5 - - + +
350C GLY 4.6 1.3 - - - -
351C VAL* 4.0 9.8 - - + +
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Residues in contact with ILE 170 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134C PHE* 3.9 15.0 - - + -
138C ALA* 3.7 38.4 - - + +
141C VAL* 4.4 12.3 - - + -
142C LYS* 4.6 2.5 - - - -
166C SER 3.1 17.1 + - - +
167C THR* 3.3 17.5 - - + +
168C VAL 3.1 0.2 - - - -
169C PRO* 1.3 74.9 - - - +
171C ALA* 1.3 65.6 + - - +
173C GLU* 3.2 3.8 + - - +
174C VAL* 2.9 27.1 + - + +
350C GLY* 3.3 22.9 - - - +
353C PHE* 3.9 11.0 - - + -
354C ILE* 3.8 22.4 - - + +
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Residues in contact with ALA 171 (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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145C CYS* 3.5 30.7 - - - -
157C VAL* 6.1 0.2 - - + -
159C LEU* 3.8 12.6 - - + -
167C THR 2.8 14.8 + - - +
168C VAL 3.3 8.3 - - - +
170C ILE* 1.3 76.5 - - - +
172C ALA* 1.3 63.3 + - - +
174C VAL* 3.1 5.1 + - - +
175C PHE* 3.0 30.3 + - + -
186C LEU* 3.9 16.6 - - + -
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Residues in contact with ALA 172 (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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168C VAL 2.8 9.4 + - - +
169C PRO 3.5 5.4 - - - +
171C ALA* 1.3 76.7 - - - +
173C GLU* 1.3 62.0 + - - +
175C PHE* 3.2 3.8 + - - +
176C LYS* 2.9 35.4 + - - +
181C TYR* 3.8 26.4 - - + -
186C LEU* 3.6 9.8 - - + +
307C PHE* 3.5 31.4 - - + -
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Residues in contact with GLU 173 (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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169C PRO 2.9 21.3 + - - +
170C ILE 3.7 1.3 - - - +
172C ALA* 1.3 77.6 - - - +
174C VAL* 1.3 63.7 + - - +
176C LYS* 3.2 39.0 + - - +
177C LYS* 3.0 25.1 + - - +
307C PHE* 5.8 2.1 - - - -
351C VAL* 3.8 36.8 - - + +
354C ILE* 3.6 25.2 - - + +
355C ARG* 3.0 33.2 + - - +
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Residues in contact with VAL 174 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142C LYS* 4.1 21.8 - - + +
145C CYS* 3.8 13.9 - - + +
146C GLU* 3.8 40.2 - - + +
149C ALA* 5.0 1.8 - - + -
170C ILE 2.9 20.9 + - - +
171C ALA 3.1 7.6 + - - +
173C GLU* 1.3 77.3 - - - +
175C PHE* 1.3 64.1 + - + +
177C LYS* 3.4 5.3 + - - +
178C ALA* 3.1 21.3 + - + +
354C ILE* 3.8 26.9 - - + -
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Residues in contact with PHE 175 (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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145C CYS* 3.4 44.4 - - + -
148C ILE* 4.1 23.8 - - + -
149C ALA* 3.9 16.4 - - + -
157C VAL* 4.4 13.2 - - + -
171C ALA* 3.0 27.7 + - + -
172C ALA* 3.7 4.7 - - - +
174C VAL* 1.3 74.1 - - + +
176C LYS* 1.3 61.2 + - - +
178C ALA* 3.0 3.7 + - - -
179C GLY 2.9 24.1 + - - -
180C THR* 3.0 20.9 + - - +
181C TYR* 3.7 33.2 - + + -
182C ASP 5.5 1.6 - - - -
185C ARG 5.9 0.4 - - - -
186C LEU* 4.4 18.6 - - + -
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Residues in contact with LYS 176 (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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172C ALA* 2.9 19.4 + - - +
173C GLU* 3.2 39.0 + - - +
175C PHE* 1.3 77.1 - - - +
177C LYS* 1.3 57.9 + - - +
179C GLY* 3.0 19.2 + - - -
181C TYR* 3.5 43.1 - - + -
307C PHE* 6.1 2.5 - - - -
355C ARG* 5.1 9.1 - - - +
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Residues in contact with LYS 177 (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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173C GLU 3.0 16.7 + - - +
174C VAL* 3.7 7.0 - - - +
176C LYS* 1.3 77.3 - - - +
178C ALA* 1.3 58.0 + - - +
179C GLY 3.3 0.6 + - - -
354C ILE* 5.0 20.4 + - + +
356C SER 6.0 0.4 + - - -
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Residues in contact with ALA 178 (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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146C GLU* 6.3 0.2 - - - -
149C ALA* 3.7 26.9 - - + -
174C VAL* 3.1 15.8 + - + +
175C PHE 3.0 5.9 + - - +
177C LYS* 1.3 77.1 - - - +
179C GLY* 1.3 64.1 + - - +
180C THR* 3.4 10.9 + - + +
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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