Contacts of the helix formed by residues 176 - 191 (chain P) in PDB entry 6NRB
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 176 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49P PRO 4.7 2.7 - - - +
50P ASN* 4.5 4.5 - - - +
165P ARG* 4.1 11.4 - - + -
168P ILE* 3.1 14.0 - - - +
169P MET* 3.1 46.8 - - + +
172P GLN* 3.0 39.9 - - - +
173P TYR 3.8 1.0 - - - -
174P GLY 2.8 22.0 + - - +
175P ASN* 1.3 70.3 - - - +
177P VAL* 1.3 58.9 + - + +
178P PHE* 3.2 1.6 - - - +
179P LEU 3.3 1.9 + - - -
180P ALA* 2.5 37.6 + - - +
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Residues in contact with VAL 177 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165P ARG* 3.3 45.8 - - - +
176P GLU* 1.3 77.8 - - + +
178P PHE* 1.3 58.0 + - + +
181P LYS* 2.5 59.3 + - + +
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Residues in contact with PHE 178 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175P ASN* 4.0 27.8 - - + +
176P GLU 3.2 0.8 - - - +
177P VAL* 1.3 85.8 - - + +
179P LEU* 1.3 62.8 + - + +
181P LYS* 3.3 8.1 + - + +
182P LEU* 2.8 64.5 + - + +
212P ILE 4.2 5.4 - - - -
213P SER* 3.0 50.7 - - - -
215P SER 3.7 3.6 - - - -
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Residues in contact with LEU 179 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168P ILE* 4.3 1.1 - - + -
172P GLN* 3.1 30.1 - - - +
175P ASN* 3.3 19.7 + - + +
176P GLU 3.3 2.8 + - - +
178P PHE* 1.3 79.8 - - + +
180P ALA* 1.3 57.5 + - - +
182P LEU* 3.8 23.8 - - + +
183P ILE* 2.7 38.9 + - - +
212P ILE 5.5 0.7 - - - +
215P SER* 5.0 7.6 - - - -
377P LEU* 5.0 2.2 - - + -
388P ILE* 3.5 32.5 - - + -
391P ALA* 3.7 17.7 - - + -
392P VAL* 4.2 18.2 - - + +
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Residues in contact with ALA 180 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161P SER* 3.4 20.4 - - - +
164P LEU* 5.1 0.4 - - - -
165P ARG* 3.4 25.4 - - + +
168P ILE* 3.5 13.2 - - + +
176P GLU 2.5 24.1 + - - +
177P VAL 3.2 4.7 - - - +
179P LEU* 1.3 70.9 - - - +
181P LYS* 1.3 52.3 + - - +
183P ILE* 3.2 10.1 - - - +
184P ALA* 2.7 38.3 + - - +
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Residues in contact with LYS 181 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157P ILE* 3.3 21.3 - - + +
158P ASP* 3.1 32.4 + - - +
161P SER* 2.8 25.9 + - - +
162P SER* 5.0 1.8 + - - -
165P ARG* 3.5 13.5 - - - +
177P VAL* 2.5 35.6 + - + +
178P PHE* 3.5 7.9 - - + +
180P ALA* 1.3 72.9 - - - +
182P LEU* 1.3 54.2 + - + +
185P GLN* 2.3 37.5 + - - +
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Residues in contact with LEU 182 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178P PHE* 2.8 50.2 + - + +
179P LEU* 3.1 21.0 + - + +
181P LYS* 1.3 75.7 - - + +
183P ILE* 1.3 52.1 + - - +
185P GLN* 3.0 24.2 - - - +
186P ALA* 2.6 34.1 + - - +
215P SER* 3.3 30.7 - - - +
216P SER* 4.8 1.6 - - - +
217P VAL* 3.3 23.3 - - + +
375P ILE* 4.4 5.8 - - + -
392P VAL* 5.4 0.2 - - + -
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Residues in contact with ILE 183 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164P LEU* 3.6 16.6 - - + -
168P ILE* 5.1 2.5 - - + -
179P LEU 2.7 25.2 + - - +
180P ALA* 3.2 12.8 - - - +
182P LEU* 1.3 70.9 - - - +
184P ALA* 1.3 60.2 + - - +
186P ALA* 2.7 14.7 + - + -
187P CYS* 2.3 55.0 + - + +
202P ILE* 4.0 2.7 - - + -
375P ILE* 4.0 10.9 - - + +
391P ALA 5.0 0.9 - - - +
392P VAL* 3.2 37.2 - - + +
395P GLY* 3.5 20.4 - - - -
396P VAL* 3.8 13.0 - - + -
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Residues in contact with ALA 184 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157P ILE* 3.0 40.8 - - + +
160P VAL* 3.6 7.9 - - + -
161P SER 3.3 12.8 - - - +
180P ALA 2.7 24.3 + - - +
181P LYS 3.6 2.9 - - - +
183P ILE* 1.3 72.9 - - - +
185P GLN* 1.3 63.0 + - - +
187P CYS* 3.5 11.2 - - - -
188P VAL* 3.1 22.0 - - - +
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Residues in contact with GLN 185 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157P ILE* 3.5 23.5 - - + +
181P LYS 2.3 28.4 + - - +
182P LEU* 3.0 30.5 - - - +
184P ALA* 1.3 71.0 - - - +
186P ALA* 1.3 54.5 + - - +
189P SER* 2.3 51.1 + - - +
217P VAL* 3.4 37.5 + - + +
219P HIS* 5.1 3.8 + - - -
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Residues in contact with ALA 186 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182P LEU 2.6 19.6 + - - +
183P ILE* 2.7 3.7 + - + +
185P GLN* 1.3 71.2 - - - +
187P CYS* 1.3 63.8 + - - +
189P SER* 2.9 12.8 + - - +
190P ILE* 3.0 19.1 + - - +
202P ILE* 3.7 13.5 - - + -
217P VAL* 3.6 18.8 - - + -
373P SER* 3.7 6.7 - - - +
375P ILE* 3.4 27.8 - - + -
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Residues in contact with CYS 187 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160P VAL* 3.5 7.2 - - - -
164P LEU* 3.5 6.5 - - - -
183P ILE* 2.3 52.9 + - + +
184P ALA* 3.5 15.3 - - - -
186P ALA* 1.3 69.6 - - - +
188P VAL* 1.3 71.2 + - - +
190P ILE* 3.6 1.7 - - - +
194P SER* 4.2 0.5 + - - -
197P PHE* 3.2 14.3 - - + -
202P ILE* 3.3 16.4 - - + -
395P GLY 4.1 2.0 - - - +
396P VAL* 4.6 0.2 - - - -
399P PHE* 3.2 55.5 - - + -
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Residues in contact with VAL 188 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154P LEU 3.1 29.4 - - - +
155P ARG* 3.4 24.5 - - - +
156P ASP 3.3 19.5 - - - +
157P ILE* 5.8 1.1 - - + -
160P VAL* 3.9 2.2 - - + -
184P ALA 3.1 22.2 - - - +
185P GLN 3.3 1.1 + - - +
187P CYS* 1.3 79.5 - - - +
189P SER* 1.3 63.4 + - - +
191P PHE* 2.5 46.0 + - - +
192P PRO 4.1 3.8 - - - +
194P SER* 4.3 0.2 - - - -
399P PHE* 3.6 16.2 - - + -
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Residues in contact with SER 189 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157P ILE* 5.2 2.8 - - - +
185P GLN* 2.3 53.2 + - - +
186P ALA 2.9 0.8 + - - -
188P VAL* 1.3 74.4 - - - +
190P ILE* 1.3 60.5 + - - +
191P PHE 3.2 2.0 - - - -
192P PRO* 3.2 14.7 - - - +
219P HIS* 3.1 27.8 - - - -
366P GLU* 2.8 18.9 - - - +
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Residues in contact with ILE 190 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186P ALA 3.0 17.8 + - - +
187P CYS 3.6 9.0 - - - +
188P VAL 2.7 4.4 + - - -
189P SER* 1.3 72.9 - - - +
191P PHE* 1.3 71.4 + - + +
192P PRO* 3.1 11.4 - - - +
201P ASN* 3.4 31.9 - - + -
202P ILE* 4.0 8.3 - - + -
219P HIS* 3.3 7.3 - - - +
365P HIS 3.2 19.5 - - - +
366P GLU* 3.7 11.7 - - + +
370P GLY* 4.2 1.1 - - - -
371P ALA 3.6 9.9 - - - +
372P ILE 3.1 45.1 - - - +
373P SER* 3.5 12.3 - - - -
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Residues in contact with PHE 191 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188P VAL* 2.5 27.3 + - - +
190P ILE* 1.3 83.1 - - - +
192P PRO* 1.3 70.8 - - + +
193P ASP* 3.0 17.5 + - - +
194P SER* 3.2 17.4 + - - +
195P GLY 5.3 0.4 - - - -
196P HIS* 3.0 39.5 - + - -
197P PHE* 3.7 4.0 - + - -
198P ASN* 3.7 16.8 - - + -
201P ASN* 3.1 41.5 - - - -
366P GLU 5.8 2.9 - - - -
370P GLY* 5.9 0.7 - - - -
371P ALA* 4.6 11.0 - - + -
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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