Contacts of the helix formed by residues 173 - 187 (chain A) in PDB entry 2PCU
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 GLU 173 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129A THR* 2.8 24.0 + - + -
131A SER* 2.7 34.4 + - - -
141A ALA* 3.6 22.4 - - + +
143A PRO* 4.9 2.5 - - + -
146A ASN* 3.0 24.0 + - + +
168A PRO* 4.5 4.7 - - - +
171A ASN 3.7 2.9 - - - +
172A SER* 1.3 99.8 + - - +
174A VAL* 1.3 69.2 + - - +
175A GLU* 3.7 11.8 - - - +
176A VAL* 3.0 17.2 + - + +
177A LYS 3.0 18.4 + - - -
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Residues in contact with VAL 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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40A HIS* 3.4 44.4 - - + +
41A SER 3.5 3.6 - - - +
42A PHE* 3.4 32.3 - - + +
172A SER 3.4 6.0 + - - +
173A GLU* 1.3 72.1 - - - +
175A GLU* 1.3 62.4 + - - +
177A LYS* 4.1 15.5 - - + -
178A SER* 2.8 41.2 + - - +
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Residues in contact with GLU 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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40A HIS 4.4 3.1 - - - -
41A SER* 3.4 20.1 - - - -
42A PHE* 3.0 30.4 + - - +
47A MET* 3.9 20.8 - - + +
68A ILE* 6.5 0.2 - - + -
111A ALA 3.6 20.4 - - - +
112A ASN* 4.8 5.0 - - + +
113A PRO* 4.3 4.3 - - + -
114A ASP* 3.7 8.7 - - - +
129A THR* 3.7 22.3 - - + +
143A PRO* 5.8 2.0 - - + -
173A GLU* 3.7 13.1 - - + +
174A VAL* 1.3 87.2 + - - +
176A VAL* 1.3 62.7 + - + +
178A SER* 3.7 3.7 + - - -
179A VAL* 3.6 23.0 + - - +
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Residues in contact with VAL 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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68A ILE* 4.6 2.7 - - + -
143A PRO* 3.6 40.4 - - + +
146A ASN* 3.8 17.9 - - - +
147A TRP* 3.7 41.7 - - + +
171A ASN* 3.6 19.5 - - - +
173A GLU* 3.0 11.3 + - + +
175A GLU* 1.3 74.4 - - + +
177A LYS* 1.3 66.4 + - - +
178A SER 3.1 1.6 - - - -
179A VAL* 3.1 5.6 + - - +
180A VAL* 2.9 21.3 + - - +
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Residues in contact with LYS 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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171A ASN* 3.7 33.3 + - + +
173A GLU 3.0 7.8 + - - +
174A VAL* 3.8 17.7 - - + +
176A VAL* 1.3 76.9 - - - +
178A SER* 1.3 57.9 + - - +
180A VAL* 3.7 6.2 - - + +
181A ASP* 2.7 68.6 + - - +
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Residues in contact with SER 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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38A ILE* 3.6 29.9 + - - +
39A GLY* 3.5 20.3 - - - -
40A HIS 3.8 7.0 + - - -
47A MET* 5.0 2.5 - - - -
174A VAL* 2.8 29.1 + - - +
175A GLU* 3.7 8.5 - - - -
176A VAL 3.1 0.4 - - - -
177A LYS* 1.3 77.6 - - - +
179A VAL* 1.3 56.8 + - - +
181A ASP* 3.6 5.1 + - - +
182A PHE* 3.1 28.2 + - - +
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Residues in contact with VAL 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A ILE* 3.8 14.6 - - + -
47A MET* 4.7 0.2 - - + -
63A TRP* 3.7 24.7 - - + +
65A ASN* 4.6 2.9 - - - +
108A LEU* 3.7 29.6 - - + -
111A ALA* 5.8 0.9 - - + -
147A TRP* 3.8 23.3 - - + -
175A GLU 3.6 14.6 + - - +
176A VAL* 3.1 7.5 + - - +
178A SER* 1.3 72.1 - - - +
180A VAL* 1.3 61.8 + - - +
182A PHE* 3.2 2.5 + - - +
183A ILE* 2.9 45.0 + - + +
192A PHE* 4.5 0.2 - - + -
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Residues in contact with VAL 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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147A TRP* 3.5 27.8 - - + -
171A ASN* 3.6 31.4 - - - +
176A VAL 2.9 20.1 + - - +
177A LYS* 3.7 5.2 - - + +
179A VAL* 1.3 75.8 - - - +
181A ASP* 1.3 64.3 + - - +
183A ILE* 3.9 0.9 - - - +
184A GLN* 2.9 53.2 + - - +
257A TRP* 3.7 31.4 - - + +
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Residues in contact with ASP 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 LYS* 2.7 62.7 + - - +
178A SER* 3.9 5.2 - - - +
180A VAL* 1.3 81.1 - - - +
182A PHE* 1.3 57.8 + - - +
184A GLN* 3.8 10.4 + - - +
185A LYS* 2.9 32.1 + - - +
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Residues in contact with PHE 182 (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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36A VAL* 4.4 14.4 - - + -
37A LYS 5.8 0.2 - - - -
38A ILE* 3.8 33.2 - - + +
63A TRP* 3.6 19.1 - + + -
106A PHE* 3.5 45.8 - + - -
178A SER 3.1 18.3 + - - +
179A VAL* 3.2 5.6 + - - +
181A ASP* 1.3 75.5 - - - +
183A ILE* 1.3 61.4 + - + +
185A LYS* 3.3 4.3 + - - +
186A HIS* 2.9 55.9 + + + +
189A PHE* 4.5 1.3 - + - -
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Residues in contact with ILE 183 (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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63A TRP* 3.8 28.7 - - + -
179A VAL* 2.9 30.2 + - + +
180A VAL 3.9 2.7 - - - +
182A PHE* 1.3 74.2 - - - +
184A GLN* 1.3 60.2 + - + +
187A GLY* 3.0 29.3 + - - -
189A PHE* 3.7 27.9 - - + -
192A PHE* 3.7 35.2 - - + -
257A TRP* 3.9 23.1 - - + -
263A ILE* 4.0 15.0 - - + -
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Residues in contact with GLN 184 (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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180A VAL* 2.9 37.5 + - - +
181A ASP* 3.9 10.1 + - - +
183A ILE* 1.3 79.8 - - + +
185A LYS* 1.3 61.8 + - - +
187A GLY* 3.9 6.4 + - - -
257A TRP* 3.8 23.7 + - + -
261A ASN* 4.2 11.3 - - + +
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Residues in contact with LYS 185 (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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181A ASP 2.9 18.3 + - - +
182A PHE* 3.9 4.3 - - + +
184A GLN* 1.3 76.6 - - - +
186A HIS* 1.3 67.7 + - - +
187A GLY* 4.6 0.2 - - - -
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Residues in contact with HIS 186 (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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51A LYS* 4.4 13.9 - - - -
58A ARG* 5.2 12.2 + - - +
59A ARG 4.6 9.0 + - - -
61A ALA* 4.5 7.0 - - + +
104A ASP* 4.7 4.4 + - - -
106A PHE* 3.7 27.2 - + - -
182A PHE* 2.9 38.5 + + + +
185A LYS* 1.3 80.4 - - - +
187A GLY* 1.3 82.8 + - - +
189A PHE* 3.7 20.0 - + + -
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Residues in contact with GLY 187 (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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58A ARG* 4.4 8.5 - - - -
59A ARG 4.8 0.9 - - - +
61A ALA* 4.9 0.5 - - - +
183A ILE 3.0 15.7 + - - -
184A GLN 4.4 5.6 - - - -
185A LYS 3.4 1.6 - - - -
186A HIS* 1.3 96.8 - - - +
188A ASN* 1.3 72.1 - - - +
189A PHE* 3.3 8.4 + - - -
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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