Contacts of the helix formed by residues 168 - 183 (chain B) in PDB entry 4P22
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 168 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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166B ASN 4.0 5.4 - - - +
167B THR* 1.3 91.4 - - + +
169B LEU* 1.3 68.3 + - - +
170B GLU* 4.5 6.3 - - + +
171B ASP* 3.2 29.2 + - - +
172B GLN* 3.0 16.8 + - - +
337B HIS* 4.7 4.5 - - + +
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Residues in contact with LEU 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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167B THR 3.6 1.0 + - - -
168B PRO* 1.3 72.2 - - - +
170B GLU* 1.3 58.9 + - - +
172B GLN* 2.9 39.5 + - - +
173B LEU* 2.9 28.7 + - + +
306B LEU* 5.5 1.1 - - + -
310B LEU* 4.3 31.9 - - + -
334B GLN* 4.7 14.1 - - + +
337B HIS* 3.7 46.8 + - + -
338B GLN* 6.1 2.5 - - + -
423B TRP* 6.3 1.1 - - + -
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Residues in contact with GLU 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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168B PRO* 3.3 4.1 - - + +
169B LEU* 1.3 78.4 - - - +
171B ASP* 1.3 72.1 + - - +
173B LEU* 3.7 10.2 + - - +
174B ARG* 3.2 35.7 + - - +
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Residues in contact with ASP 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B THR* 3.6 14.8 - - + -
168B PRO* 3.2 34.1 + - + +
169B LEU 3.1 0.4 - - - -
170B GLU* 1.3 88.0 - - - +
172B GLN* 1.3 64.8 + - - +
174B ARG* 2.6 34.4 + - - +
175B VAL* 3.1 31.7 + - + +
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Residues in contact with GLN 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B LEU* 4.1 19.1 + - + +
165B THR 6.1 0.2 - - - -
167B THR* 2.8 37.8 + - + +
168B PRO 3.0 12.9 + - - +
169B LEU* 2.9 26.8 + - + +
171B ASP* 1.3 76.8 - - - +
173B LEU* 1.3 57.3 + - - +
175B VAL* 3.8 1.6 - - - +
176B GLY* 2.9 23.4 + - - -
186B LEU* 4.9 0.2 - - - +
188B VAL* 3.4 29.4 - - + +
190B ASP* 5.8 4.8 - - - -
197B GLN* 5.0 4.3 + - - +
306B LEU* 3.4 25.1 - - + +
337B HIS* 4.1 14.5 + - - -
423B TRP* 5.9 2.3 - - - -
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Residues in contact with LEU 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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169B LEU* 2.9 30.9 + - + +
170B GLU* 4.1 7.6 - - - +
172B GLN* 1.3 75.5 - - - +
174B ARG* 1.3 64.9 + - - +
176B GLY* 3.9 0.6 - - - -
177B GLU* 3.0 24.9 + - - +
306B LEU* 3.6 28.5 - - + -
307B VAL* 4.1 29.9 - - + +
310B LEU* 3.9 29.4 - - + -
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Residues in contact with ARG 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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151B LEU* 3.5 27.9 + - - +
156B LEU* 5.8 0.4 - - - +
170B GLU* 3.2 26.1 + - - +
171B ASP* 2.6 38.5 + - - +
172B GLN 3.4 0.2 - - - -
173B LEU* 1.3 78.0 - - - +
175B VAL* 1.3 76.4 + - - +
177B GLU* 3.5 15.5 + - - +
178B PHE* 3.3 20.3 + - - +
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Residues in contact with VAL 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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151B LEU* 4.1 25.8 - - + -
156B LEU* 4.4 18.4 - - + -
162B VAL* 4.6 0.9 - - + -
164B LEU* 3.8 27.8 - - + -
167B THR* 5.9 0.4 - - + -
171B ASP* 3.1 23.9 + - + +
172B GLN 3.9 2.2 - - - +
174B ARG* 1.3 97.2 - - - +
176B GLY* 1.3 56.2 + - - +
178B PHE* 3.3 7.0 + - - +
179B CYS* 3.0 40.1 + - - -
186B LEU* 4.5 4.3 - - + -
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Residues in contact with GLY 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 GLN 2.9 17.9 + - - -
173B LEU 3.9 0.9 - - - -
175B VAL* 1.3 73.8 - - - +
177B GLU* 1.3 64.8 + - - +
178B PHE 3.2 1.1 - - - -
179B CYS* 4.2 1.9 - - - +
180B HIS* 3.1 26.0 + - - +
186B LEU* 3.8 24.3 - - - +
201B ASP* 4.7 2.6 - - - +
305B SER* 4.5 2.4 - - - -
306B LEU* 4.7 9.1 + - - -
307B VAL* 5.1 3.8 - - - -
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Residues in contact with GLU 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 LEU 3.0 16.4 + - - +
174B ARG* 3.6 16.6 - - - +
176B GLY* 1.3 75.5 - - - +
178B PHE* 1.3 62.6 + - - +
180B HIS* 3.9 3.6 - - - +
181B ASN* 3.1 43.0 + - - +
305B SER* 5.4 1.8 - - - -
307B VAL* 4.4 16.7 - - + +
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Residues in contact with PHE 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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153B GLU* 3.5 53.6 - - + +
156B LEU* 3.5 40.6 - - + -
157B SER* 4.2 4.5 - - - -
174B ARG 3.3 10.1 + - - +
175B VAL* 3.3 10.2 + - - +
176B GLY 3.2 0.4 - - - -
177B GLU* 1.3 78.6 - - - +
179B CYS* 1.3 69.9 - - - +
181B ASN* 3.2 8.8 + - + +
182B ARG* 3.1 73.3 + - + +
184B ILE* 4.1 9.9 - - + -
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Residues in contact with CYS 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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156B LEU* 4.9 2.5 - - - -
162B VAL* 4.1 21.1 - - - -
175B VAL* 3.0 26.2 + - - +
176B GLY* 3.7 5.6 + - - +
177B GLU 3.5 0.2 - - - -
178B PHE* 1.3 82.9 - - - +
180B HIS* 1.3 57.4 + - - +
182B ARG 3.3 0.6 + - - +
183B GLY* 2.9 9.2 + - - -
184B ILE* 2.8 71.7 + - + +
186B LEU* 4.3 17.5 - - + -
201B ASP* 6.0 0.2 - - - +
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Residues in contact with HIS 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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176B GLY 3.1 19.8 + - - +
177B GLU* 3.9 4.3 - - - +
179B CYS* 1.3 78.4 - - - +
181B ASN* 1.3 67.4 + - - +
183B GLY* 3.4 10.5 + - - -
184B ILE 4.8 1.6 - - - -
201B ASP* 2.5 37.0 + - - +
203B GLY* 4.3 9.0 - - - -
204B GLU* 3.3 30.1 + - + +
303B PHE 3.0 26.6 + - - -
304B LYS* 5.0 0.2 - - - -
305B SER* 3.4 26.6 + - - -
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Residues in contact with ASN 181 (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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177B GLU* 3.1 35.9 + - - +
178B PHE* 3.2 7.1 + - + +
180B HIS* 1.3 83.8 - - - +
182B ARG* 1.3 70.8 + - + +
183B GLY 3.7 0.2 + - - -
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Residues in contact with ARG 182 (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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153B GLU* 4.8 7.9 + - - +
157B SER* 4.8 13.0 - - - -
178B PHE* 3.1 61.9 + - + +
179B CYS 4.1 0.2 - - - +
181B ASN* 1.3 86.1 - - + +
183B GLY* 1.3 60.9 + - - +
184B ILE* 3.5 21.5 + - + +
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Residues in contact with GLY 183 (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 GLN* 4.6 1.4 - - - +
179B CYS 2.9 5.4 + - - -
180B HIS* 3.4 11.4 + - - -
181B ASN 3.4 0.6 + - - -
182B ARG* 1.3 79.1 - - - +
184B ILE* 1.3 62.0 + - - +
185B LYS* 3.7 5.2 + - - +
203B GLY* 5.9 4.0 - - - -
205B GLU* 3.8 25.2 - - - +
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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