Contacts of the helix formed by residues 172 - 188 (chain C) in PDB entry 2NP5
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 172 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168C PRO 3.4 5.8 - - - +
169C ALA* 3.8 11.0 - - - +
170C LEU 3.4 6.3 - - - -
171C TYR* 1.3 94.2 - - - +
173C PRO* 1.3 77.6 - - + +
174C GLU* 3.2 11.7 - - + +
175C TYR* 3.0 31.9 + - + +
176C LEU* 3.0 7.4 + - - +
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Residues in contact with PRO 173 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94C PRO 4.4 5.4 - - - +
95C LEU* 3.6 47.3 - - + +
171C TYR 3.7 1.3 - - - +
172C PRO* 1.3 81.8 - - + +
174C GLU* 1.3 75.7 + - + +
176C LEU* 3.2 4.9 + - + +
177C GLU* 3.0 33.1 + - - +
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Residues in contact with GLU 174 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172C PRO* 3.8 11.0 - - + +
173C PRO* 1.3 93.2 - - + +
175C TYR* 1.3 57.5 + - - +
177C GLU* 3.5 14.4 + - - +
178C HIS* 3.1 27.7 + - - +
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Residues in contact with TYR 175 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A ARG* 3.0 33.7 + - - -
147A GLU* 3.7 6.7 + - + +
148A THR* 3.6 30.9 + - + -
151A ALA* 3.3 25.0 - - + +
160C LEU* 5.7 0.2 - - + -
170C LEU 3.8 15.7 - - - -
171C TYR* 4.2 14.6 - + - -
172C PRO* 3.0 28.0 + - + +
174C GLU* 1.3 76.9 - - - +
176C LEU* 1.3 62.5 + - - +
178C HIS* 3.3 10.6 + + + +
179C ALA* 2.8 34.2 + - + +
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Residues in contact with LEU 176 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93C LEU* 4.2 14.5 - - + +
94C PRO* 3.9 37.7 - - + +
95C LEU* 3.6 19.7 - - + -
160C LEU* 4.2 25.6 - - + +
164C ALA* 4.0 8.3 - - + -
171C TYR* 3.4 51.8 - - + +
172C PRO 3.0 8.2 + - - +
173C PRO* 3.6 7.6 - - + +
175C TYR* 1.3 75.2 - - + +
177C GLU* 1.3 57.7 + - - +
179C ALA* 3.3 4.7 + - - +
180C LEU* 2.9 30.1 + - - +
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Residues in contact with GLU 177 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C PHE* 3.4 38.7 - - + -
93C LEU* 5.6 0.2 - - - -
95C LEU* 3.9 25.0 - - + +
173C PRO* 3.0 23.8 + - - +
174C GLU* 3.8 15.5 - - - +
175C TYR 3.2 0.2 - - - -
176C LEU* 1.3 72.2 - - - +
178C HIS* 1.3 66.3 + - - +
180C LEU* 3.3 2.5 + - - -
181C ASP* 3.0 23.8 + - - +
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Residues in contact with HIS 178 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A GLU* 2.9 37.0 + - - -
148A THR* 3.3 24.4 + - + -
174C GLU 3.1 14.8 + - - +
175C TYR* 3.6 15.7 - + + +
177C GLU* 1.3 76.3 - - - +
179C ALA* 1.3 61.9 + - - +
181C ASP* 3.2 14.5 + - + +
182C ILE* 3.0 39.5 + - + +
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Residues in contact with ALA 179 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A THR* 3.5 22.7 - - + +
151A ALA* 5.7 0.9 - - + -
152A LEU* 3.5 26.5 - - + +
160C LEU* 4.1 13.9 - - + -
175C TYR* 2.8 31.1 + - + +
176C LEU* 3.3 6.9 + - - +
178C HIS* 1.3 71.7 - - - +
180C LEU* 1.3 58.6 + - - +
182C ILE 3.2 1.2 + - - -
183C GLN 2.9 25.1 + - - -
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Residues in contact with LEU 180 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C PHE* 3.7 31.9 - - + +
89C MSE 3.7 18.8 - - + -
90C SER* 3.8 28.7 - - - +
93C LEU* 3.9 17.9 - - + -
153C LEU* 4.2 5.6 - - + -
157C VAL* 3.8 18.6 - - + -
160C LEU* 4.7 4.8 - - + +
176C LEU 2.9 17.1 + - - +
177C GLU* 3.6 4.9 - - - +
179C ALA* 1.3 77.4 - - - +
181C ASP* 1.3 56.6 + - - +
183C GLN* 3.3 4.9 + - + +
184C ILE* 2.9 42.2 + - + +
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Residues in contact with ASP 181 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C PHE* 3.2 24.8 - - - +
177C GLU* 3.0 17.4 + - - +
178C HIS* 3.3 19.4 + - - +
180C LEU* 1.3 75.1 - - - +
182C ILE* 1.3 59.8 + - + +
184C ILE* 3.2 5.7 + - - +
185C GLY* 2.8 32.9 + - - -
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Residues in contact with ILE 182 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145A GLU* 3.8 25.8 - - + +
148A THR* 3.9 9.2 - - + -
149A ARG* 4.1 21.1 - - + +
152A LEU* 3.7 16.6 - - + -
178C HIS* 3.0 42.8 + - + +
179C ALA 3.2 7.4 + - - +
181C ASP* 1.3 82.4 - - + +
183C GLN* 1.3 61.7 + - - +
185C GLY* 3.3 2.1 + - - +
186C MSE 3.0 32.1 + - + +
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Residues in contact with GLN 183 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A LEU* 3.6 23.5 - - + +
183A GLN* 3.0 41.0 + - - -
186A MSE 4.0 5.7 - - - +
152C LEU* 5.3 0.6 - - - +
153C LEU* 3.9 16.1 - - + +
156C THR* 3.7 19.0 + - + +
157C VAL* 6.0 0.7 - - + -
179C ALA 2.9 15.9 + - - +
180C LEU* 3.7 7.2 - - + +
182C ILE* 1.3 76.5 - - - +
184C ILE* 1.3 63.9 + - - +
186C MSE 3.2 14.5 + - - +
187C ILE* 2.9 53.3 + - + +
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Residues in contact with ILE 184 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82C ALA* 4.1 17.0 - - + +
85C LEU* 3.7 17.9 - - + +
86C PHE* 3.4 45.3 - - + +
153C LEU* 4.2 13.9 - - + -
180C LEU* 2.9 42.0 + - + +
181C ASP* 3.7 4.9 - - - +
183C GLN* 1.3 71.4 - - - +
185C GLY* 1.3 64.6 + - - +
187C ILE* 3.1 8.4 + - + +
188C LEU* 3.0 45.2 + - + +
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Residues in contact with GLY 185 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181C ASP 2.8 19.9 + - - -
182C ILE* 3.7 2.5 - - - -
184C ILE* 1.3 75.5 - - - +
186C MSE 1.3 60.5 + - - +
188C LEU* 3.4 7.6 + - - +
189C GLN* 3.4 26.1 + - - +
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Residues in contact with MSE 186 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A ARG* 3.9 25.1 - - + +
152A LEU* 3.8 27.1 - - + -
183A GLN* 5.0 0.2 - - - +
186A MSE 3.6 56.1 - - + +
187A ILE* 3.9 20.6 - - + -
149C ARG* 4.0 2.3 + - - -
182C ILE* 3.0 26.4 + - + +
183C GLN* 3.5 19.3 - - - +
184C ILE 3.2 0.2 - - - -
185C GLY* 1.3 73.9 - - - +
187C ILE* 1.3 65.3 + - - +
189C GLN* 3.2 24.5 + - + +
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Residues in contact with ILE 187 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186A MSE 3.9 16.2 - - + -
85C LEU* 5.5 1.6 - - + -
138C LEU* 3.8 39.3 - - + -
143C THR* 3.2 9.2 - - - +
149C ARG* 2.9 35.1 + - + +
153C LEU* 3.4 48.9 - - + +
183C GLN* 2.9 40.0 + - - +
184C ILE* 3.1 6.5 + - - +
186C MSE 1.3 75.1 - - - +
188C LEU* 1.3 59.6 + - + +
189C GLN 3.2 0.2 - - - -
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Residues in contact with LEU 188 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81C PRO* 4.9 2.0 - - + -
82C ALA* 3.9 26.2 - - + +
85C LEU* 4.1 7.2 - - + -
138C LEU* 3.8 21.1 - - + -
141C ILE* 3.6 30.5 - - + -
143C THR* 4.4 1.8 - - - +
184C ILE* 3.0 39.3 + - + +
185C GLY* 3.9 7.4 - - - +
186C MSE 3.2 0.4 - - - -
187C ILE* 1.3 75.8 - - + +
189C GLN* 1.3 66.4 + - - +
190C GLY 3.1 0.5 + - - -
191C ALA* 2.9 23.7 + - + +
193C VAL 4.4 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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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