Contacts of the helix formed by residues 172 - 188 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168D PRO 3.6 3.7 - - - +
169D ALA* 3.7 11.7 - - - +
170D LEU 3.5 8.5 - - - +
171D TYR* 1.3 90.7 - - - +
173D PRO* 1.4 77.8 - - + +
174D GLU* 3.2 16.6 - - - +
175D TYR* 2.9 28.6 + - + +
176D LEU* 2.9 11.0 + - - +
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Residues in contact with PRO 173 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94D PRO 4.7 4.3 - - - +
95D LEU* 3.6 43.1 - - + +
171D TYR 3.9 1.1 - - - +
172D PRO* 1.4 82.9 - - + +
174D GLU* 1.3 72.1 + - + +
176D LEU* 3.3 3.7 + - + +
177D GLU* 2.9 39.4 + - - +
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Residues in contact with GLU 174 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172D PRO* 3.6 14.8 - - + +
173D PRO* 1.3 97.5 - - + +
175D TYR* 1.3 57.1 + - - +
177D GLU* 3.9 11.7 - - - +
178D HIS* 3.0 28.6 + - - +
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Residues in contact with TYR 175 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131B ARG* 3.0 23.4 + - - -
147B GLU* 3.8 14.3 + - + +
148B THR* 3.8 22.1 - - + -
151B ALA* 3.0 32.9 - - + +
160D LEU* 5.4 0.9 - - + -
170D LEU 3.9 13.2 - - - -
171D TYR* 4.0 21.8 - + - -
172D PRO* 2.9 28.5 + - + +
174D GLU* 1.3 80.0 - - - +
176D LEU* 1.3 58.7 + - - +
178D HIS* 3.2 10.6 + + + +
179D ALA* 2.9 35.8 + - + +
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Residues in contact with LEU 176 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93D LEU* 4.1 16.0 - - + +
94D PRO* 3.9 27.8 - - + +
95D LEU* 3.5 23.6 - - + -
160D LEU* 4.1 41.1 - - + +
164D ALA* 4.2 4.9 - - + -
171D TYR* 3.5 37.2 - - + +
172D PRO 2.9 11.4 + - - +
173D PRO* 3.5 8.3 - - + +
175D TYR* 1.3 77.3 - - + +
177D GLU* 1.3 56.4 + - - +
179D ALA* 3.4 5.4 + - - +
180D LEU* 2.9 30.0 + - - +
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Residues in contact with GLU 177 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86D PHE* 3.7 27.3 - - + -
93D LEU* 5.4 0.7 - - - -
95D LEU* 3.5 32.3 - - + +
99D ARG* 5.5 1.7 + - - -
173D PRO* 2.9 24.3 + - - +
174D GLU* 3.9 11.8 - - - +
176D LEU* 1.3 75.6 - - - +
178D HIS* 1.3 63.2 + - - +
180D LEU* 3.3 2.0 + - - -
181D ASP* 3.0 31.0 + - - +
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Residues in contact with HIS 178 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B GLU* 2.9 36.2 + - - -
148B THR* 3.3 24.0 - - + -
174D GLU 3.0 18.6 + - - +
175D TYR* 3.6 12.3 - + - +
177D GLU* 1.3 77.1 - - - +
179D ALA* 1.3 56.3 - - - +
181D ASP* 3.2 14.7 + - + +
182D ILE* 2.9 42.6 + - + +
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Residues in contact with ALA 179 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148B THR* 3.7 19.7 - - + +
151B ALA* 5.8 1.1 - - + -
152B LEU* 3.5 28.4 - - + +
160D LEU* 4.1 17.3 - - + -
175D TYR* 2.9 26.7 + - + +
176D LEU* 3.6 5.8 - - - +
178D HIS* 1.3 74.1 - - - +
180D LEU* 1.3 60.9 + - - +
182D ILE 3.2 1.0 + - - -
183D GLN 2.9 25.1 + - - -
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Residues in contact with LEU 180 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86D PHE* 3.6 29.8 - - + +
89D MSE 3.9 8.3 - - + -
90D SER* 3.8 32.1 - - - +
93D LEU* 4.0 14.8 - - + -
153D LEU* 3.9 10.3 - - + -
157D VAL* 3.8 25.8 - - + -
160D LEU* 4.6 5.8 - - + +
176D LEU 2.9 17.6 + - - +
177D GLU 3.7 4.5 - - - +
179D ALA* 1.3 75.6 - - - +
181D ASP* 1.3 58.4 + - - +
183D GLN* 3.2 5.3 + - + +
184D ILE* 2.9 45.0 + - + +
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Residues in contact with ASP 181 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86D PHE* 3.1 28.3 - - - -
177D GLU* 3.0 17.7 + - - +
178D HIS* 3.2 20.0 + - - +
180D LEU* 1.3 76.2 - - - +
182D ILE* 1.3 63.9 + - + +
184D ILE* 3.5 5.8 + - - +
185D GLY* 3.0 20.6 + - - -
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Residues in contact with ILE 182 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145B GLU* 3.7 32.1 - - + +
148B THR* 4.0 9.0 - - + -
149B ARG* 4.1 25.8 - - + +
152B LEU* 3.5 19.3 - - + -
178D HIS* 2.9 41.4 + - + +
179D ALA 3.7 3.8 - - - +
181D ASP* 1.3 80.0 - - + +
183D GLN* 1.4 61.3 + - - +
185D GLY* 3.3 3.6 + - - -
186D MSE 3.1 25.0 + - + +
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Residues in contact with GLN 183 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152B LEU* 3.6 13.7 - - + +
183B GLN* 3.0 42.2 + - - +
186B MSE 4.3 2.4 - - - +
152D LEU 4.1 5.3 + - - -
153D LEU* 3.8 21.1 - - + -
156D THR* 3.4 24.2 + - + +
157D VAL* 6.2 0.2 - - + -
179D ALA 2.9 16.5 + - - +
180D LEU* 3.7 7.6 - - + +
182D ILE* 1.4 76.7 - - - +
184D ILE* 1.3 57.7 + - - +
186D MSE 3.2 21.1 + - - +
187D ILE* 2.9 51.4 + - + +
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Residues in contact with ILE 184 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82D ALA* 4.1 18.4 - - + +
85D LEU* 3.9 15.5 - - + +
86D PHE* 3.5 44.0 - - + +
153D LEU* 4.1 13.0 - - + -
180D LEU* 2.9 43.4 + - + +
181D ASP* 3.8 5.2 - - - +
183D GLN* 1.3 71.5 - - - +
185D GLY* 1.3 64.3 + - - +
187D ILE* 3.1 8.2 + - - +
188D LEU* 3.0 45.3 + - + +
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Residues in contact with GLY 185 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181D ASP 3.0 14.4 + - - -
182D ILE* 3.3 4.7 + - - -
184D ILE* 1.3 75.9 - - - +
186D MSE 1.3 61.9 + - - +
188D LEU* 3.4 7.4 + - - +
189D GLN* 3.2 26.4 + - - +
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Residues in contact with MSE 186 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149B ARG* 3.8 27.1 - - + +
152B LEU* 3.7 17.7 - - + -
183B GLN* 4.2 2.0 - - - +
186B MSE 3.6 49.0 - - + +
187B ILE* 3.5 32.5 - - + -
189B GLN* 6.4 0.2 - - + -
149D ARG* 3.7 2.3 + - - -
182D ILE* 3.1 13.7 + - + +
183D GLN* 3.2 33.2 + - - +
185D GLY* 1.3 74.2 - - - +
187D ILE* 1.3 63.7 + - - +
189D GLN* 3.2 23.8 + - - +
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Residues in contact with ILE 187 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186B MSE 3.9 14.1 - - + -
85D LEU* 5.1 2.0 - - + -
138D LEU* 3.6 37.2 - - + -
143D THR* 3.3 14.4 - - - +
149D ARG* 2.7 60.1 + - + +
153D LEU* 4.1 18.6 - - + +
183D GLN* 2.9 46.0 + - + +
184D ILE* 3.1 11.0 + - - +
186D MSE 1.3 75.5 - - - +
188D LEU* 1.3 57.6 + - + +
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Residues in contact with LEU 188 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81D PRO* 5.0 2.0 - - + -
82D ALA* 3.6 37.5 - - + +
85D LEU* 4.0 9.4 - - + -
138D LEU* 3.7 22.2 - - + -
141D ILE* 3.6 30.3 - - + -
143D THR* 4.6 0.7 - - - +
184D ILE* 3.0 28.7 + - + +
185D GLY* 3.8 7.9 - - - +
186D MSE 3.2 0.2 - - - -
187D ILE* 1.3 75.3 - - + +
189D GLN* 1.3 60.0 + - - +
190D GLY 3.2 0.5 + - - -
191D ALA* 3.0 29.6 + - + +
192D ASP* 4.9 4.6 - - - +
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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