Contacts of the helix formed by residues 155 - 169 (chain B) in PDB entry 4PKO
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 ASP 155 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149B THR* 3.1 17.6 + - - +
152B ALA* 3.7 15.7 - - + +
153B ASN 3.3 1.3 - - - +
154B SER* 1.3 77.4 - - - +
156B GLU* 1.3 60.9 + - - +
157B THR* 3.0 24.3 + - - -
158B VAL* 3.2 31.0 + - + +
159B GLY 3.5 12.1 + - - -
185B ASP* 5.1 0.7 - - - +
392B LYS* 3.6 19.8 + - - -
395B ARG* 4.3 8.5 + - - +
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Residues in contact with GLU 156 (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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149B THR* 3.6 19.2 + - + +
154B SER 3.7 6.0 + - - +
155B ASP* 1.3 72.0 + - - +
157B THR* 1.3 67.0 + - - +
159B GLY* 3.3 0.9 + - - -
160B LYS* 3.0 26.1 + - - +
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Residues in contact with THR 157 (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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155B ASP* 3.0 10.6 + - - -
156B GLU* 1.3 79.0 - - - +
158B VAL* 1.3 57.0 + - - +
160B LYS* 3.8 4.0 - - - +
161B LEU* 2.8 39.0 + - + +
184B GLN* 5.8 3.6 - - - +
185B ASP* 3.5 30.1 - - + +
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Residues in contact with VAL 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B ALA* 3.9 19.7 - - + -
155B ASP* 3.2 35.6 + - + +
156B GLU 3.3 0.2 - - - -
157B THR* 1.3 75.4 - - - +
159B GLY* 1.3 58.3 + - - +
161B LEU* 3.4 6.8 + - - +
162B ILE* 2.9 54.5 + - + +
185B ASP* 4.7 11.0 - - - +
392B LYS* 4.7 4.9 - - - -
395B ARG* 5.6 1.8 - - + +
396B VAL* 4.2 28.9 - - + -
399B ALA* 4.0 5.2 - - + -
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Residues in contact with GLY 159 (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 ILE 4.8 0.2 - - - +
145B ALA* 3.4 16.6 - - - -
148B GLY* 4.1 5.4 - - - -
149B THR* 3.3 27.7 - - - +
155B ASP 3.5 4.9 + - - -
156B GLU 3.3 3.2 + - - -
157B THR 3.3 0.6 - - - -
158B VAL* 1.3 78.9 - - - +
160B LYS* 1.3 56.8 + - - +
162B ILE* 3.3 3.5 + - - +
163B ALA* 2.8 30.5 + - - +
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Residues in contact with LYS 160 (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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141B SER* 4.6 22.4 + - - -
142B LYS* 5.6 2.0 - - - +
145B ALA* 4.2 12.6 - - + +
149B THR* 4.5 0.2 + - - -
156B GLU 3.0 17.1 + - - +
157B THR* 4.1 4.3 - - - +
159B GLY* 1.3 74.9 - - - +
161B LEU* 1.3 57.0 + - - +
163B ALA* 3.6 5.2 - - + +
164B GLU* 2.8 58.5 + - - +
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Residues in contact with LEU 161 (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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157B THR* 2.8 24.9 + - + +
158B VAL* 3.8 5.6 - - - +
160B LYS* 1.3 78.6 - - - +
162B ILE* 1.3 56.2 + - - +
164B GLU* 3.4 15.4 + - - +
165B ALA* 3.0 26.7 + - - +
185B ASP* 3.5 40.2 - - + +
186B GLU 4.3 2.9 - - - +
187B LEU* 3.8 32.6 - - + +
379B ILE* 4.2 26.0 - - + +
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Residues in contact with ILE 162 (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 ILE* 5.2 0.2 - - + -
148B GLY* 4.9 1.6 - - - -
158B VAL* 2.9 34.5 + - + +
159B GLY* 3.7 4.5 - - - +
161B LEU* 1.3 73.6 - - + +
163B ALA* 1.3 66.6 + - - +
165B ALA* 3.2 7.4 + - + +
166B MET* 3.0 31.5 + - + +
379B ILE* 4.2 16.4 - - + -
396B VAL* 4.2 6.1 - - + +
399B ALA* 3.6 42.0 - - + +
400B LEU* 3.8 18.2 - - + +
403B THR* 3.5 33.7 - - + +
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Residues in contact with ALA 163 (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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141B SER* 3.7 19.7 + - - +
144B ILE* 4.5 14.3 - - + +
145B ALA* 3.5 28.0 - - + +
159B GLY 2.8 17.8 + - - +
160B LYS* 3.6 10.5 - - + +
162B ILE* 1.3 79.0 - - - +
164B GLU* 1.3 61.0 + - - +
166B MET* 3.6 2.8 + - - +
167B ASP* 3.2 24.4 + - - +
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Residues in contact with GLU 164 (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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160B LYS* 2.8 51.0 + - - +
161B LEU* 3.5 17.2 - - - +
162B ILE 3.2 0.2 - - - -
163B ALA* 1.3 74.1 - - - +
165B ALA* 1.3 64.8 + - - +
167B ASP* 3.4 4.8 + - - +
168B LYS* 3.1 27.9 + - + +
187B LEU* 3.8 18.5 - - + +
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Residues in contact with ALA 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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161B LEU 3.0 14.3 + - - +
162B ILE* 3.2 11.6 + - + +
164B GLU* 1.3 77.5 - - - +
166B MET* 1.3 63.3 + - + +
168B LYS* 4.0 2.3 - - - +
169B VAL* 3.3 30.5 + - - +
175B ILE* 4.0 24.5 - - + -
187B LEU* 3.9 24.6 - - + +
189B VAL* 5.5 0.9 - - - -
377B ALA* 4.6 2.9 - - + -
379B ILE* 4.4 6.7 - - + -
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Residues in contact with MET 166 (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 ILE* 3.5 30.7 - - + -
162B ILE* 3.0 23.9 + - + +
163B ALA* 4.0 4.7 - - - +
165B ALA* 1.3 77.9 - - + +
167B ASP* 1.3 60.6 + - - +
170B GLY* 3.7 20.3 + - - +
171B LYS* 3.2 40.7 + - + +
175B ILE* 5.7 7.9 - - + -
400B LEU* 6.0 2.0 - - + -
403B THR* 4.0 22.9 - - - +
404B ARG* 5.0 8.5 - - + +
407B VAL* 3.5 28.7 - - + -
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Residues in contact with ASP 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B SER* 3.9 19.7 + - - +
163B ALA 3.2 15.8 + - - +
164B GLU* 3.8 5.6 - - - +
165B ALA 3.2 0.4 - - - -
166B MET* 1.3 79.2 - - - +
168B LYS* 1.3 64.2 + - - +
170B GLY* 4.3 3.3 + - - -
171B LYS* 4.7 4.0 + - - +
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Residues in contact with LYS 168 (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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164B GLU* 3.1 17.6 + - + +
165B ALA 4.1 2.0 - - - +
167B ASP* 1.3 79.7 - - - +
169B VAL* 1.3 62.2 + - - +
170B GLY 3.4 0.7 + - - -
187B LEU* 5.6 3.3 - - + +
189B VAL* 3.7 41.7 - - + +
191B GLU* 3.3 20.6 - - - +
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Residues in contact with VAL 169 (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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165B ALA 3.3 12.1 + - - +
166B MET* 5.7 0.2 - - - -
168B LYS* 1.3 77.8 - - + +
170B GLY* 1.3 64.1 + - - +
172B GLU* 4.9 0.5 + - - +
173B GLY* 3.3 30.4 + - - -
175B ILE* 4.8 2.9 - - + -
189B VAL* 3.8 17.7 - - + -
190B VAL 4.2 1.1 - - - +
191B GLU* 4.3 6.5 - - - +
374B GLY* 4.5 4.7 - - - -
375B GLY* 3.0 47.0 + - - +
376B VAL 3.6 15.7 - - - +
377B ALA* 4.1 16.8 - - + +
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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