Contacts of the helix formed by residues 168 - 182 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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166A ASN 3.8 6.5 - - - +
167A THR* 1.3 89.8 - - + +
169A LEU* 1.3 67.4 + - - +
170A GLU* 4.5 10.1 - - + +
171A ASP* 3.1 29.4 + - - +
172A GLN* 3.0 17.5 + - - +
337A HIS* 4.8 5.2 - - + -
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Residues in contact with LEU 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A THR 3.7 1.0 + - - -
168A PRO* 1.3 72.2 - - - +
170A GLU* 1.3 64.2 + - - +
172A GLN* 3.1 25.6 + - + +
173A LEU* 2.9 49.9 + - + +
306A LEU* 5.6 2.5 - - + -
310A LEU* 5.3 12.8 - - + -
334A GLN* 3.3 33.9 - - - +
337A HIS* 3.7 46.1 - - + +
423A TRP* 6.5 0.9 - - + -
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Residues in contact with GLU 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A PRO* 4.5 7.9 - - + +
169A LEU* 1.3 78.1 - - - +
171A ASP* 1.3 76.4 + - - +
173A LEU* 3.1 16.9 + - + +
174A ARG* 2.9 29.3 + - - +
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Residues in contact with ASP 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A THR* 3.6 20.2 - - + -
168A PRO* 3.1 30.2 + - - +
170A GLU* 1.3 85.8 - - - +
172A GLN* 1.3 60.7 + - - +
174A ARG* 2.4 37.4 + - - +
175A VAL* 2.8 37.7 + - + +
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Residues in contact with GLN 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A LEU* 3.8 17.2 - - + +
167A THR* 2.6 35.9 + - + +
168A PRO 3.0 13.0 + - - +
169A LEU* 3.2 20.2 - - + +
171A ASP* 1.3 77.1 - - - +
173A LEU* 1.3 56.5 + - - +
175A VAL* 4.1 0.2 - - - +
176A GLY* 2.8 25.6 + - - -
188A VAL* 3.3 30.4 - - - +
190A ASP* 5.5 3.6 + - - +
197A GLN* 5.1 3.9 + - - +
306A LEU* 3.3 29.2 - - + +
337A HIS* 3.7 22.2 + - - -
423A TRP* 5.8 1.9 - - - -
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Residues in contact with LEU 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169A LEU* 2.9 44.9 + - + +
170A GLU* 3.5 15.0 - - + +
172A GLN* 1.3 74.4 - - - +
174A ARG* 1.3 57.7 + - - +
177A GLU* 2.9 32.6 + - - +
306A LEU* 4.3 15.5 - - + -
307A VAL* 3.6 33.5 - - + +
310A LEU* 4.9 11.9 - - + -
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Residues in contact with ARG 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A LEU* 3.6 25.9 + - - +
170A GLU 2.9 15.2 + - - +
171A ASP* 2.4 40.5 + - - +
173A LEU* 1.3 74.6 - - - +
175A VAL* 1.3 79.9 + - - +
176A GLY 3.3 0.2 + - - -
177A GLU* 3.3 12.3 + - + +
178A PHE* 3.2 21.3 + - - +
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Residues in contact with VAL 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A LEU* 4.3 19.3 - - + -
156A LEU* 4.3 21.1 - - + -
162A VAL* 4.5 6.5 - - + -
164A LEU* 3.8 30.5 - - + -
167A THR* 6.0 0.9 - - + -
171A ASP* 2.8 25.0 + - + +
174A ARG* 1.3 93.1 - - - +
176A GLY* 1.3 58.8 + - - +
178A PHE* 3.4 6.3 + - - +
179A CYS* 2.9 43.5 + - - +
186A LEU* 4.7 1.8 - - + -
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Residues in contact with GLY 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A GLN 2.8 20.1 + - - -
173A LEU 3.8 0.4 - - - -
175A VAL* 1.3 76.0 - - - +
177A GLU* 1.3 63.8 + - - +
179A CYS* 4.0 0.9 - - - +
180A HIS* 3.1 24.9 + - - +
186A LEU* 3.7 24.5 - - - -
201A ASP* 4.4 3.1 - - - +
305A SER* 4.7 1.7 - - - -
306A LEU* 4.6 11.7 + - - -
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Residues in contact with GLU 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173A LEU 2.9 16.4 + - - +
174A ARG* 3.4 17.9 - - - +
176A GLY* 1.3 72.7 - - - +
178A PHE* 1.3 70.9 + - - +
180A HIS* 3.7 5.0 - - - +
181A ASN* 3.0 42.4 + - - +
305A SER* 5.0 5.8 - - - +
307A VAL* 4.1 16.7 - - + +
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Residues in contact with PHE 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A GLU* 3.1 62.8 - - + -
156A LEU* 3.8 27.6 - - + -
157A SER* 4.0 5.6 - - - -
174A ARG 3.2 8.6 + - - +
175A VAL* 3.5 9.9 - - - +
177A GLU* 1.3 85.2 - - + +
179A CYS* 1.3 68.4 + - - +
181A ASN* 2.9 11.2 + - + +
182A ARG* 2.9 65.6 + - + -
184A ILE* 4.2 10.1 - - + -
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Residues in contact with CYS 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156A LEU* 5.0 3.4 - - - -
162A VAL* 3.8 27.8 - - - -
175A VAL* 2.9 33.8 + - - +
176A GLY 4.0 3.8 - - - +
177A GLU 3.4 0.2 - - - -
178A PHE* 1.3 79.5 - - - +
180A HIS* 1.3 62.7 + - - +
182A ARG 3.5 0.2 + - - -
183A GLY 3.0 4.5 + - - -
184A ILE* 2.7 63.8 + - - +
186A LEU* 4.2 15.3 - - + -
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Residues in contact with HIS 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176A GLY 3.1 17.7 + - - +
177A GLU 3.7 4.3 - - - +
179A CYS* 1.3 78.8 - - - +
181A ASN* 1.3 70.1 + - - +
183A GLY* 3.7 7.9 + - - -
184A ILE 4.6 1.3 - - - -
201A ASP* 2.8 34.3 + - - +
203A GLY* 4.1 7.4 - - - -
204A GLU* 3.2 38.5 + - + +
303A PHE 3.0 27.6 - - - -
305A SER* 3.5 28.8 + - - -
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Residues in contact with ASN 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A GLU* 3.0 34.4 + - - +
178A PHE* 2.9 13.5 + - + +
180A HIS* 1.3 87.6 - - - +
182A ARG* 1.3 64.6 + - + +
183A GLY 3.2 2.5 + - - -
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Residues in contact with ARG 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A GLU* 4.6 8.5 + - - -
154A ASP* 3.1 27.8 + - - -
157A SER* 2.9 31.6 + - - +
178A PHE* 2.9 50.3 + - + +
181A ASN* 1.3 79.5 - - + +
183A GLY* 1.3 60.6 + - - +
184A ILE* 3.3 13.2 + - + +
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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