Contacts of the helix formed by residues 169 - 180 (chain B) in PDB entry 1P1C
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 ASN 169 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135B THR 5.4 2.9 - - - -
137B PRO* 4.8 1.6 - - - +
143B TRP 3.2 21.3 + - - +
144B HIS 4.1 2.4 - - - -
146B HIS* 3.4 18.6 + - + +
147B GLN* 2.9 41.4 + - - +
168B CYS* 1.3 74.0 - - - +
170B LEU* 1.3 63.5 + - - +
171B THR* 3.8 6.8 + - - -
172B SER* 2.9 36.3 + - - -
173B TRP* 3.0 39.5 + - - +
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Residues in contact with LEU 170 (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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220A ARG* 4.0 25.0 - - - +
45B GLU* 5.7 3.8 - - + -
48B TYR* 3.5 31.2 - - + -
49B MET* 4.1 5.8 - - + -
168B CYS* 3.3 31.0 - - + -
169B ASN* 1.3 76.8 - - - +
171B THR* 1.3 58.3 + - - +
173B TRP* 4.3 13.0 - - + -
174B GLY* 2.9 28.1 + - - -
221B TYR* 3.7 29.6 - - + +
222B TYR* 3.7 15.6 - - + +
227B MET* 3.9 20.4 - - + -
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Residues in contact with THR 171 (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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171A THR* 6.5 0.9 - - + -
220A ARG* 2.3 46.3 + - - +
221A TYR* 5.0 2.7 - - + -
136B TYR* 5.7 1.2 - - - +
137B PRO* 4.9 13.7 - - + +
143B TRP* 3.7 38.0 + - + +
169B ASN* 3.3 6.3 - - - -
170B LEU* 1.3 80.2 - - - +
172B SER* 1.3 59.9 + - - +
174B GLY* 4.3 0.9 - - - -
175B GLU* 3.6 18.2 + - - +
221B TYR* 4.3 16.9 - - + +
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Residues in contact with SER 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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143B TRP* 3.8 9.9 - - - -
144B HIS* 2.7 37.3 + - - +
169B ASN* 2.9 34.0 + - - -
171B THR* 1.3 78.3 - - - +
173B TRP* 1.3 69.6 + - - +
175B GLU* 3.3 4.6 + - - +
176B LEU* 3.0 32.7 + - - +
192B GLN* 5.2 1.0 + - - -
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Residues in contact with TRP 173 (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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48B TYR* 3.7 17.5 - - - -
147B GLN* 4.3 0.4 - - - +
167B TYR* 3.8 20.4 - + - -
168B CYS* 3.8 17.3 - - - -
169B ASN* 3.0 30.8 + - + +
170B LEU* 4.2 13.5 - - + +
172B SER* 1.3 83.4 + - - +
174B GLY* 1.3 66.7 + - - +
175B GLU 2.9 1.8 - - - -
176B LEU* 3.8 5.8 - - + +
177B MET* 2.9 30.9 + - + +
184B ILE* 5.6 0.2 - - + -
187B MET* 3.7 27.8 - - + -
188B PHE* 4.2 2.5 - + - -
192B GLN* 3.1 43.3 + - + +
222B TYR* 4.0 14.8 - - + +
228B ILE* 3.4 33.0 - - + -
230B PRO* 4.2 7.6 - - + -
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Residues in contact with GLY 174 (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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170B LEU 2.9 11.8 + - - -
173B TRP* 1.3 77.8 - - - +
175B GLU* 1.3 58.4 + - - +
177B MET* 3.9 3.5 + - - +
178B LYS* 3.0 29.7 + - - +
221B TYR 3.1 23.5 - - - +
222B TYR* 3.2 23.5 - - - -
223B ALA 4.7 2.8 + - - -
224B PHE* 5.6 0.4 + - - -
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Residues in contact with GLU 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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140A GLU* 6.0 2.1 - - - +
143A TRP* 3.4 49.2 + - + -
175A GLU* 4.8 2.4 - - - +
143B TRP* 3.6 23.9 + - - -
144B HIS* 3.0 27.1 + - - -
171B THR 3.6 11.3 + - - +
172B SER 3.3 8.9 + - - +
173B TRP 2.9 0.6 - - - -
174B GLY* 1.3 76.2 - - - +
176B LEU* 1.3 64.5 + - - +
177B MET 3.2 1.3 - - - -
178B LYS* 3.2 2.6 + - - +
179B SER* 2.8 38.8 + - - +
221B TYR 3.9 0.8 + - - +
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Residues in contact with LEU 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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144B HIS* 3.5 24.9 - - + +
172B SER* 3.0 31.1 + - - +
173B TRP* 3.2 6.5 + - + +
175B GLU* 1.3 78.9 - - - +
177B MET* 1.3 53.3 + - - +
179B SER* 4.6 1.3 - - - -
180B LYS* 2.9 30.1 + - + +
181B TYR* 2.6 44.7 + - + -
187B MET* 3.9 25.1 - - + -
191B THR* 3.9 24.2 - - + +
192B GLN* 4.9 1.3 - - - +
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Residues in contact with MET 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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173B TRP* 2.9 22.2 + - - +
174B GLY 4.3 3.8 - - - +
176B LEU* 1.3 76.6 - - + +
178B LYS* 1.3 63.0 + - + +
181B TYR* 2.8 55.1 - - + +
182B THR* 5.1 0.3 - - - +
183B ASP 4.3 0.9 - - - -
184B ILE* 3.8 37.5 - - + -
187B MET* 3.1 32.8 - - + -
222B TYR* 4.6 1.6 - - - +
224B PHE* 3.7 47.3 - - + -
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Residues in contact with LYS 178 (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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136A TYR* 4.5 10.0 - - - +
137A PRO* 3.1 35.4 + - - +
138A LEU* 3.5 35.6 - - + +
139A SER* 5.4 0.2 - - - -
143A TRP* 4.1 17.8 - - + -
171A THR* 5.1 0.2 - - - +
174B GLY 3.0 21.0 + - - +
175B GLU 3.2 5.4 + - - +
177B MET* 1.3 82.2 - - - +
179B SER* 1.3 63.1 + - - +
181B TYR 5.1 0.9 + - - +
219B CYS 5.2 2.0 + - - -
220B ARG 3.8 22.2 + - - -
221B TYR 4.4 7.8 + - - +
222B TYR 5.6 0.2 - - - -
223B ALA* 4.2 28.9 - - + +
224B PHE 5.8 0.7 - - - +
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Residues in contact with SER 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A LEU 3.3 7.4 + - - -
139A SER* 3.5 5.2 - - - +
140A GLU* 2.7 57.3 + - - +
143A TRP* 4.3 5.6 - - - -
175B GLU* 2.8 27.8 + - - +
176B LEU* 4.6 1.3 - - - -
178B LYS* 1.3 77.0 - - - +
180B LYS* 1.3 64.0 + - - +
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Residues in contact with LYS 180 (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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140A GLU* 2.9 30.3 - - - +
176B LEU* 2.9 28.0 + - + +
179B SER* 1.3 77.5 - - - +
181B TYR* 1.3 87.7 + - + +
182B THR* 5.8 0.6 - - - +
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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