Contacts of the helix formed by residues 163 - 178 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133F LEU* 5.9 2.9 - - + -
134F PHE* 3.9 28.0 - - + -
137F ASN* 5.5 0.7 - - + -
161F SER 3.5 1.1 - - - -
162F ASN* 1.3 96.3 - - - +
164F VAL* 1.3 67.1 + - - +
165F ASN* 3.1 6.7 - - + +
166F SER* 2.9 33.1 + - - +
167F THR* 2.9 15.6 + - + +
221F ALA* 5.8 8.5 - - + -
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Residues in contact with VAL 164 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159F LEU 4.0 10.5 - - - +
160F ILE* 3.6 27.8 - - - +
161F SER 3.3 5.3 + - - +
162F ASN* 3.7 1.8 - - - +
163F PRO* 1.3 70.5 - - - +
165F ASN* 1.3 63.6 + - - +
166F SER 3.0 1.2 + - - -
167F THR* 3.3 8.1 - - - +
168F VAL* 3.1 24.1 + - + +
188F GLY* 4.0 18.4 - - - -
189F VAL 4.4 5.4 - - - +
190F THR* 4.5 1.1 - - + -
220F HIS* 3.9 37.7 - - + +
297F PHE* 3.7 26.8 - - + -
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Residues in contact with ASN 165 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163F PRO* 3.0 6.1 + - + -
164F VAL* 1.3 76.3 - - - +
166F SER* 1.3 58.4 + - - +
169F PRO* 3.3 18.1 - - - +
219F GLY* 3.2 7.7 - - - -
220F HIS* 2.7 27.6 + - - +
221F ALA* 3.7 14.4 - - + +
224F THR* 3.2 29.9 + - - +
297F PHE* 3.7 19.1 - - - -
343F LEU* 3.6 16.5 - - + +
346F SER* 3.7 29.3 + - - +
347F ILE* 4.0 2.6 + - - +
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Residues in contact with SER 166 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134F PHE* 3.8 27.6 - - - -
163F PRO* 2.9 13.4 + - - +
165F ASN* 1.3 76.6 - - - +
167F THR* 1.3 66.3 + - - +
168F VAL 3.3 2.0 - - - -
169F PRO* 3.2 4.8 - - - +
170F ILE* 3.1 27.0 + - - +
346F SER* 2.6 32.9 + - - -
349F LYS* 4.4 5.5 - - - +
350F GLY* 3.7 12.0 + - - -
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Residues in contact with THR 167 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134F PHE* 5.5 0.9 - - + -
137F ASN 5.4 0.4 - - - +
138F ALA* 5.4 4.7 - - - +
141F VAL* 3.9 21.6 - - + +
159F LEU* 3.1 25.9 - - - +
161F SER 2.7 27.8 + - - +
162F ASN 3.7 5.8 - - - +
163F PRO* 2.9 26.7 + - + +
164F VAL* 3.3 9.0 - - - -
166F SER* 1.3 75.9 - - - +
168F VAL* 1.3 66.0 + - - +
170F ILE* 3.4 15.6 + - + +
171F ALA* 3.0 17.0 + - - +
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Residues in contact with VAL 168 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159F LEU* 3.7 17.5 - - + -
164F VAL* 3.1 14.2 + - + +
167F THR* 1.3 78.1 + - - +
169F PRO* 1.3 77.3 - - + +
171F ALA* 3.0 5.6 + - - +
172F ALA 2.9 18.2 + - - -
186F LEU* 3.7 16.2 - - + +
187F LEU 4.6 0.9 - - - -
188F GLY* 3.5 33.9 - - - +
297F PHE* 3.8 19.1 - - + +
298F VAL* 5.4 0.9 - - - -
307F PHE* 3.8 26.9 - - + -
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Residues in contact with PRO 169 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165F ASN 3.3 23.8 - - - +
166F SER 3.2 11.4 - - - +
168F VAL* 1.3 95.7 - - + +
170F ILE* 1.3 56.1 + - - +
172F ALA* 3.0 3.5 + - - +
173F GLU* 2.8 34.5 + - - +
297F PHE* 4.3 1.3 - - + -
307F PHE* 3.5 38.4 - - + -
347F ILE* 4.0 17.7 - - + +
351F VAL* 3.9 20.6 - - + +
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Residues in contact with ILE 170 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134F PHE* 4.3 6.3 - - + -
138F ALA* 3.7 41.3 - - + +
141F VAL* 4.5 8.5 - - + -
142F LYS* 4.7 2.0 - - - -
166F SER 3.1 19.2 + - - +
167F THR* 3.5 16.4 - - + +
168F VAL 3.1 0.2 - - - -
169F PRO* 1.3 76.9 - - - +
171F ALA* 1.3 58.7 + - - +
173F GLU* 3.2 4.2 + - - +
174F VAL* 2.9 32.2 + - + +
350F GLY* 3.2 25.8 + - - +
353F PHE* 3.7 13.0 - - + -
354F ILE* 3.4 28.7 - - + -
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Residues in contact with ALA 171 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141F VAL* 4.7 0.2 - - + -
145F CYS* 3.4 31.4 - - - -
157F VAL* 5.9 0.2 - - + -
159F LEU* 3.9 12.3 - - + -
167F THR 3.0 12.6 + - - +
168F VAL 3.0 9.5 + - - +
170F ILE* 1.3 75.8 - - - +
172F ALA* 1.3 52.8 + - - +
174F VAL* 3.1 4.7 + - - +
175F PHE* 2.8 50.5 + - + -
186F LEU* 4.1 9.0 - - + -
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Residues in contact with ALA 172 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168F VAL 2.9 9.1 + - - +
169F PRO 3.0 8.9 + - - +
171F ALA* 1.3 76.0 - - - +
173F GLU* 1.3 59.9 + - - +
175F PHE* 3.1 3.1 + - - +
176F LYS* 2.8 36.4 + - + +
181F TYR* 3.7 29.1 - - + -
186F LEU* 3.8 5.3 - - + +
307F PHE* 3.4 31.0 - - + -
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Residues in contact with GLU 173 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169F PRO 2.8 16.8 + - - +
170F ILE* 3.4 7.4 - - - +
172F ALA* 1.3 77.5 - - - +
174F VAL* 1.3 58.1 + - - +
176F LYS* 3.1 24.4 + - - +
177F LYS* 2.9 30.1 + - - +
307F PHE* 5.9 1.2 - - - -
351F VAL* 3.5 50.7 - - + +
354F ILE* 3.5 21.0 - - + +
355F ARG* 2.8 36.0 + - - -
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Residues in contact with VAL 174 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142F LYS* 4.2 20.0 - - + +
145F CYS* 3.5 27.1 - - + +
146F GLU* 3.7 27.6 - - + +
149F ALA* 5.4 0.2 - - + -
170F ILE 2.9 19.2 + - - +
171F ALA* 3.4 7.9 - - - +
173F GLU* 1.3 77.4 - - - +
175F PHE* 1.3 62.0 + - + +
177F LYS* 3.6 11.7 + - + +
178F ALA* 3.2 21.4 + - + +
354F ILE* 3.6 28.3 - - + -
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Residues in contact with PHE 175 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145F CYS* 3.5 39.0 - - + -
148F ILE* 4.0 18.2 - - + -
149F ALA* 3.9 15.0 - - + -
153F PRO* 6.1 1.1 - - + -
157F VAL* 4.2 13.9 - - + -
171F ALA* 2.8 37.6 + - + +
172F ALA* 3.1 2.9 + - - +
174F VAL* 1.3 72.5 - - - +
176F LYS* 1.3 59.9 + - - +
178F ALA 3.3 1.2 + - - -
179F GLY 2.9 7.1 + - - -
180F THR* 2.8 44.0 + - - +
181F TYR* 3.6 36.6 - + + +
182F ASP 5.7 0.4 - - - -
186F LEU* 4.3 19.1 - - + -
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Residues in contact with LYS 176 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172F ALA* 2.8 18.2 + - - +
173F GLU* 3.3 33.9 + - - +
175F PHE* 1.3 75.9 - - - +
177F LYS* 1.3 55.5 + - - +
179F GLY* 2.6 26.9 + - - -
181F TYR* 3.7 34.1 - - + +
355F ARG* 4.4 16.0 - - - +
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Residues in contact with LYS 177 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142F LYS* 4.7 14.1 - - - +
146F GLU* 4.4 14.6 + - - +
173F GLU 2.9 15.4 + - - +
174F VAL* 3.8 10.5 - - + +
176F LYS* 1.3 76.8 - - - +
178F ALA* 1.3 58.7 + - + +
179F GLY 3.6 0.2 + - - -
354F ILE* 5.1 14.5 - - + +
355F ARG* 6.0 5.6 - - - +
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Residues in contact with ALA 178 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146F GLU* 6.0 0.7 - - - -
149F ALA* 3.6 28.3 - - + -
174F VAL* 3.2 18.3 + - + +
175F PHE 3.9 2.9 - - - +
176F LYS 3.1 1.2 - - - -
177F LYS* 1.3 76.5 - - + +
179F GLY* 1.3 63.9 + - - +
180F THR* 3.2 10.7 + - + +
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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