Contacts of the helix formed by residues 163 - 179 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B ARG* 5.3 6.1 - - - +
133B LEU* 4.7 12.1 - - + -
134B PHE* 4.3 20.9 - - + -
137B ASN* 5.1 0.2 - - + -
161B SER 3.6 2.0 - - - -
162B ASN* 1.3 97.0 - - - +
164B VAL* 1.3 55.7 + - - +
165B ASN* 3.1 8.3 - - + +
166B SER* 2.7 44.4 + - - +
167B THR* 2.9 17.4 + - + -
221B ALA* 5.9 6.7 - - + -
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Residues in contact with VAL 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B LEU 4.1 7.6 - - - +
160B ILE 3.6 26.7 - - - +
161B SER 3.3 4.0 + - - +
162B ASN* 3.8 1.7 - - - +
163B PRO* 1.3 70.9 - - - +
165B ASN* 1.3 63.9 + - - +
166B SER 3.0 1.6 + - - -
167B THR* 3.3 9.4 - - - +
168B VAL* 3.3 23.9 + - + +
188B GLY* 3.8 21.5 - - - -
189B VAL 4.3 5.6 - - - +
190B THR* 4.8 0.9 - - + -
220B HIS* 3.6 38.4 + - + +
297B PHE* 3.6 27.3 - - + -
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Residues in contact with ASN 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163B PRO* 3.0 6.8 + - + +
164B VAL* 1.3 78.3 - - - +
166B SER* 1.3 59.3 + - - +
169B PRO* 3.5 17.1 - - - +
219B GLY* 3.3 6.9 - - - -
220B HIS* 2.8 26.6 + - - +
221B ALA* 3.8 12.5 - - + +
224B THR* 3.1 32.3 - - - +
297B PHE* 3.7 16.2 - - - -
342B GLU* 5.3 1.6 + - - -
343B LEU* 3.8 13.0 - - + +
346B SER* 3.7 24.0 + - - -
347B ILE* 3.8 14.9 + - - +
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Residues in contact with SER 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B PHE* 3.7 28.9 - - - -
163B PRO* 2.7 23.0 + - - +
165B ASN* 1.3 73.3 - - - +
167B THR* 1.3 60.2 + - - -
169B PRO* 2.8 21.1 - - - +
170B ILE* 2.9 18.7 + - - +
346B SER* 3.0 29.9 + - - -
349B LYS* 4.3 5.0 - - - +
350B GLY* 3.9 5.9 + - - -
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Residues in contact with THR 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134B PHE* 6.0 0.9 - - + -
137B ASN* 5.1 3.8 - - + -
138B ALA* 5.2 2.7 - - + +
141B VAL* 3.9 25.6 - - + +
159B LEU* 3.4 21.7 - - - +
161B SER 2.8 29.8 + - - +
162B ASN 4.0 4.9 - - - +
163B PRO* 2.9 19.7 + - + +
164B VAL* 3.3 10.4 - - - -
166B SER* 1.3 75.0 - - - +
168B VAL* 1.3 56.6 + - - +
170B ILE* 3.1 16.1 + - + +
171B ALA* 2.8 25.5 + - - +
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Residues in contact with VAL 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B LEU* 3.6 18.6 - - + -
164B VAL* 3.3 16.7 + - + +
167B THR* 1.3 81.1 + - - +
169B PRO* 1.3 74.3 - - + +
171B ALA* 3.0 4.9 + - - +
172B ALA* 2.9 19.8 + - - +
186B LEU* 3.5 20.3 - - + +
187B LEU 4.5 1.6 - - - -
188B GLY* 3.6 34.5 - - - +
297B PHE* 3.9 17.5 - - + +
298B VAL* 5.4 1.3 - - - -
307B PHE* 4.1 19.3 - - + -
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Residues in contact with PRO 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B VAL 3.8 0.9 - - - +
165B ASN 3.5 18.8 - - - +
166B SER 2.8 22.9 - - - +
168B VAL* 1.3 90.0 - - + +
170B ILE* 1.3 56.6 + - - +
172B ALA* 3.5 2.3 - - - +
173B GLU* 2.9 34.0 + - - +
297B PHE* 4.3 1.8 - - + -
307B PHE* 3.3 40.8 - - + -
347B ILE* 3.8 25.8 - - + +
350B GLY 4.9 0.2 - - - -
351B VAL* 3.9 9.9 - - + +
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Residues in contact with ILE 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B PHE* 4.3 6.1 - - + -
138B ALA* 3.6 38.6 - - + +
141B VAL* 4.3 12.8 - - + -
142B LYS 4.7 1.8 - - - +
166B SER 2.9 20.8 + - - +
167B THR* 3.2 16.4 - - + +
168B VAL 3.1 0.2 - - - -
169B PRO* 1.3 77.2 - - - +
171B ALA* 1.3 59.0 + - - +
173B GLU* 3.0 4.3 + - - +
174B VAL* 2.9 37.6 + - + +
350B GLY* 3.3 26.9 - - - +
353B PHE* 3.9 12.3 - - + -
354B ILE* 3.7 25.4 - - + -
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Residues in contact with ALA 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B VAL* 4.5 0.2 - - + -
145B CYS* 3.4 32.3 - - - -
157B VAL* 6.1 0.2 - - + -
159B LEU* 4.1 11.0 - - + -
167B THR 2.8 12.4 + - - +
168B VAL 3.4 8.1 - - - +
170B ILE* 1.3 77.0 - - - +
172B ALA* 1.3 56.5 + - - +
174B VAL* 3.2 4.9 + - - +
175B PHE* 2.9 42.7 + - + -
186B LEU* 4.0 13.7 - - + -
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Residues in contact with ALA 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168B VAL 2.9 8.6 + - - +
169B PRO 3.5 8.5 - - - +
171B ALA* 1.3 77.8 - - - +
173B GLU* 1.3 57.4 + - + +
175B PHE* 3.3 2.1 + - - +
176B LYS* 2.9 39.7 + - - +
181B TYR* 3.8 30.0 - - + -
186B LEU* 3.8 4.6 - - + +
307B PHE* 3.5 28.9 - - + -
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Residues in contact with GLU 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B PRO 2.9 16.5 + - - +
170B ILE 3.4 7.9 - - - +
172B ALA* 1.3 78.0 - - - +
174B VAL* 1.3 62.4 + - - +
176B LYS* 3.1 35.6 + - - +
177B LYS* 3.3 22.9 + - - +
307B PHE* 6.2 0.3 - - - -
351B VAL* 3.7 43.6 - - + +
354B ILE* 3.5 25.4 - - + +
355B ARG* 3.1 30.1 + - - -
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Residues in contact with VAL 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B LYS* 3.9 16.8 - - + -
145B CYS* 3.7 24.0 - - + +
146B GLU* 3.7 29.6 - - + +
149B ALA* 5.4 0.4 - - + -
170B ILE* 2.9 24.1 + - + +
171B ALA* 3.2 8.7 + - - +
173B GLU* 1.3 78.7 - - - +
175B PHE* 1.3 60.7 + - + +
177B LYS* 3.7 4.5 + - - +
178B ALA* 3.3 20.3 + - + +
354B ILE* 3.6 27.4 - - + -
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Residues in contact with PHE 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145B CYS* 3.1 47.6 - - + -
148B ILE* 4.3 15.3 - - + -
149B ALA* 3.6 23.3 - - + -
157B VAL* 4.7 11.7 - - + -
171B ALA* 2.9 31.4 + - + +
172B ALA* 3.9 2.0 - - - +
174B VAL* 1.3 77.2 - - - +
176B LYS* 1.3 56.1 + - - +
178B ALA* 3.2 2.4 + - - -
179B GLY 2.7 28.2 + - - -
180B THR* 2.9 24.3 + - - +
181B TYR* 3.7 28.3 - + + -
182B ASP 5.8 0.2 - - - -
186B LEU* 4.4 18.8 - - + -
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Residues in contact with LYS 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172B ALA* 2.9 26.2 + - - +
173B GLU* 3.1 38.0 + - - +
174B VAL 3.4 0.2 - - - -
175B PHE* 1.3 77.0 - - - +
177B LYS* 1.3 58.0 - - - +
179B GLY* 2.9 20.4 + - - +
181B TYR* 3.7 39.0 - - + -
307B PHE* 6.2 1.7 - - - -
355B ARG* 4.6 14.3 - - - +
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Residues in contact with LYS 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142B LYS* 6.0 2.6 - - - +
173B GLU 3.3 13.8 + - - +
174B VAL* 4.0 5.4 - - - +
175B PHE 3.3 0.4 - - - -
176B LYS* 1.3 80.1 - - - +
178B ALA* 1.3 60.9 + - - +
179B GLY* 3.5 0.5 + - - -
354B ILE* 5.5 9.6 - - + -
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Residues in contact with ALA 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B GLU* 6.3 0.4 - - - -
149B ALA* 3.7 27.6 - - + -
174B VAL* 3.3 15.9 + - + +
175B PHE 3.2 5.1 + - - +
176B LYS 3.1 0.6 - - - -
177B LYS* 1.3 79.3 - - - +
179B GLY* 1.3 63.2 + - - +
180B THR* 3.7 9.0 + - + +
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Residues in contact with GLY 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175B PHE 2.7 7.5 + - - -
176B LYS* 2.9 14.9 + - - -
177B LYS 3.2 0.6 - - - -
178B ALA* 1.3 80.5 - - - +
180B THR* 1.3 58.5 + - - +
181B TYR 3.7 1.6 - - - -
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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
------------------------------------------------------------
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