Contacts of the helix formed by residues 163 - 178 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130E ARG* 6.5 0.7 - - - -
133E LEU* 4.6 11.0 - - + -
134E PHE* 3.8 34.1 - - + -
137E ASN* 5.0 0.9 - - + -
162E ASN* 1.3 93.4 - - - +
164E VAL* 1.3 56.4 + - - +
165E ASN* 4.6 6.5 - - + +
166E SER* 3.0 14.3 + - - +
167E THR* 2.7 41.7 + - + -
220E HIS 5.9 1.3 - - - +
349E LYS* 6.2 0.4 - - + +
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Residues in contact with VAL 164 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159E LEU 4.6 1.6 - - - +
160E ILE* 4.0 19.3 - - + +
161E SER 3.4 11.9 + - - +
162E ASN* 4.5 3.7 - - - +
163E PRO* 1.3 71.6 - - - +
165E ASN* 1.3 63.0 + - - +
166E SER 3.1 1.0 + - - -
167E THR* 3.0 7.0 - - - -
168E VAL* 3.2 40.7 + - + +
188E GLY* 4.0 15.3 - - - -
189E VAL 4.5 6.3 - - - +
190E THR* 4.9 0.2 - - + -
220E HIS* 3.2 46.5 + - + +
297E PHE* 3.5 13.9 - - + -
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Residues in contact with ASN 165 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163E PRO* 3.3 4.5 - - + +
164E VAL* 1.3 76.9 - - - +
166E SER* 1.3 58.5 + - - +
169E PRO* 3.1 20.1 - - - +
219E GLY* 3.1 12.0 - - - -
220E HIS* 2.7 29.0 + - - +
221E ALA* 3.3 32.5 - - - +
224E THR* 3.4 9.9 + - - +
297E PHE* 3.8 12.2 - - - -
342E GLU* 5.1 0.6 + - - -
343E LEU* 4.0 11.7 - - + +
346E SER* 3.7 25.1 + - - -
347E ILE* 3.7 14.2 - - - +
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Residues in contact with SER 166 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134E PHE* 3.5 28.6 - - - -
163E PRO* 3.0 14.8 + - - +
165E ASN* 1.3 78.5 - - - +
167E THR* 1.3 58.7 + - - +
169E PRO* 3.1 9.0 - - - +
170E ILE* 2.8 33.5 + - - +
346E SER* 2.9 30.2 + - - -
349E LYS* 4.3 6.1 - - - +
350E GLY* 3.8 5.8 + - - -
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Residues in contact with THR 167 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134E PHE* 5.7 0.7 - - + -
137E ASN 5.2 0.2 - - - +
138E ALA* 5.2 3.8 - - - -
141E VAL* 3.6 27.8 - - + +
159E LEU* 3.4 19.0 - - - +
161E SER 2.7 30.2 + - - +
162E ASN 4.0 3.8 - - - +
163E PRO* 2.7 37.0 + - + +
164E VAL* 3.0 10.6 - - - -
166E SER* 1.3 69.3 - - - +
168E VAL* 1.3 53.3 + - - +
170E ILE* 3.0 15.8 + - + +
171E ALA* 2.7 32.1 + - - +
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Residues in contact with VAL 168 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159E LEU* 3.3 18.8 - - + +
164E VAL* 3.2 17.2 + - + +
167E THR* 1.3 76.2 + - - +
169E PRO* 1.3 72.9 - - + +
171E ALA* 3.0 5.5 + - - +
172E ALA* 2.9 21.1 + - - +
186E LEU* 3.9 16.0 - - + +
187E LEU 4.8 0.2 - - - -
188E GLY* 3.6 24.2 - - - +
297E PHE* 3.6 30.3 - - + +
298E VAL* 5.0 2.0 - - - -
307E PHE* 4.0 21.3 - - + -
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Residues in contact with PRO 169 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165E ASN 3.1 27.4 - - - +
166E SER 3.1 12.3 - - - +
168E VAL* 1.3 96.7 - - + +
170E ILE* 1.3 60.5 + - - +
172E ALA* 3.4 3.3 - - - +
173E GLU* 3.2 27.8 + - - +
297E PHE* 4.0 1.8 - - + -
307E PHE* 3.6 39.2 - - + -
347E ILE* 3.9 28.0 - - + +
350E GLY 4.8 1.8 - - - -
351E VAL* 4.2 6.0 - - + +
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Residues in contact with ILE 170 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134E PHE* 3.8 20.9 - - + -
138E ALA* 3.5 40.6 - - + +
141E VAL* 4.7 8.7 - - + -
142E LYS 4.9 1.6 - - - +
166E SER 2.8 27.3 + - - +
167E THR* 3.2 12.8 - - + +
169E PRO* 1.3 74.6 - - - +
171E ALA* 1.3 66.7 + - - +
173E GLU 3.3 1.6 + - - -
174E VAL* 3.1 25.2 + - + +
350E GLY* 3.4 20.0 - - - +
353E PHE* 3.9 7.6 - - + -
354E ILE* 3.5 28.9 - - + +
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Residues in contact with ALA 171 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141E VAL* 4.6 0.7 - - + -
145E CYS* 3.6 30.1 - - - -
157E VAL* 6.2 0.4 - - + -
159E LEU* 4.2 11.4 - - + -
167E THR 2.7 15.4 + - - +
168E VAL 3.0 8.9 + - - +
170E ILE* 1.3 74.4 - - - +
172E ALA* 1.3 61.8 + - - +
174E VAL* 3.1 5.7 + - - +
175E PHE* 3.0 30.8 + - + -
186E LEU* 3.7 18.2 - - + -
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Residues in contact with ALA 172 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168E VAL 2.9 8.8 + - - +
169E PRO 3.4 7.9 - - - +
170E ILE 3.2 0.2 - - - -
171E ALA* 1.3 77.0 - - - +
173E GLU* 1.3 63.2 + - - +
175E PHE* 3.2 4.2 + - - +
176E LYS* 2.9 34.2 + - - +
181E TYR* 3.5 27.0 - - + -
186E LEU* 3.9 3.3 - - + +
307E PHE* 3.3 34.3 - - + -
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Residues in contact with GLU 173 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169E PRO 3.2 13.6 + - - +
170E ILE 3.7 3.4 - - - +
171E ALA 3.3 0.2 - - - -
172E ALA* 1.3 78.9 - - - +
174E VAL* 1.3 64.8 + - - +
176E LYS* 2.6 52.6 + - - +
177E LYS* 3.1 13.9 + - - +
307E PHE* 5.7 1.0 - - - -
351E VAL* 4.1 22.9 - - + +
354E ILE* 3.4 25.9 - - + +
355E ARG* 2.9 51.1 + - + +
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Residues in contact with VAL 174 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142E LYS* 4.4 13.5 - - + -
145E CYS* 3.7 22.0 - - + +
146E GLU* 3.6 33.7 - - + +
149E ALA* 5.7 0.4 - - + -
170E ILE* 3.1 19.3 + - + +
171E ALA* 3.1 7.7 + - - +
173E GLU* 1.3 76.3 - - - +
175E PHE* 1.3 60.9 + - + +
177E LYS* 3.7 7.7 + - - +
178E ALA* 3.4 19.2 + - - +
354E ILE* 3.4 29.4 - - + +
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Residues in contact with PHE 175 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145E CYS* 3.5 42.4 - - + -
148E ILE* 4.0 21.1 - - + -
149E ALA* 3.7 23.6 - - + -
157E VAL* 4.5 7.4 - - + -
171E ALA* 3.0 24.8 + - + -
172E ALA 3.6 2.0 - - - +
173E GLU 3.1 0.2 - - - -
174E VAL* 1.3 75.9 - - - +
176E LYS* 1.3 60.5 + - - +
178E ALA* 3.1 2.1 + - - -
179E GLY 2.9 8.7 + - - -
180E THR* 2.8 33.3 + - - +
181E TYR* 3.4 37.5 - + + +
182E ASP 5.4 1.3 - - - -
186E LEU* 3.9 28.9 - - + -
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Residues in contact with LYS 176 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172E ALA* 2.9 26.8 + - - +
173E GLU* 2.6 43.2 + - - +
175E PHE* 1.3 77.9 - - - +
177E LYS* 1.3 61.6 + - - +
179E GLY* 3.0 13.1 + - - -
181E TYR* 3.5 43.1 - - + -
307E PHE* 5.1 7.5 - - - -
355E ARG* 5.2 8.1 - - - +
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Residues in contact with LYS 177 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146E GLU* 5.6 3.6 + - - -
173E GLU 3.1 13.9 + - - +
174E VAL* 4.0 6.7 - - - +
176E LYS* 1.3 72.4 - - - +
178E ALA* 1.3 59.8 + - - +
179E GLY* 3.0 8.2 + - - -
354E ILE* 6.1 4.5 - - + -
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Residues in contact with ALA 178 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146E GLU* 6.4 0.4 - - - -
149E ALA* 3.7 26.5 - - + -
174E VAL* 3.4 12.7 + - + +
175E PHE 3.1 8.8 + - - +
177E LYS* 1.3 77.7 - - - +
179E GLY* 1.3 64.8 + - - +
180E THR* 3.3 9.3 - - + +
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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