Contacts of the helix formed by residues 182 - 204 (chain B) in PDB entry 2NS7
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 ALA 182 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87B ARG* 4.2 5.2 - - - +
144B SER 5.8 0.4 - - - +
148B ASP* 3.9 36.6 - - + +
177B PHE* 4.7 9.0 - - + -
181B GLY* 1.3 73.6 - - - -
183B GLU* 1.3 59.4 + - - +
184B PRO* 3.5 0.9 - - - -
185B ALA* 3.5 8.2 + - + +
186B PHE* 3.0 27.0 + - - +
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Residues in contact with GLU 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B ARG* 3.6 33.3 + - - +
180B GLN 5.2 1.1 - - - +
181B GLY 3.4 0.2 - - - -
182B ALA* 1.3 76.1 - - - +
184B PRO* 1.3 69.5 - - + +
186B PHE* 3.3 3.5 + - + +
187B LEU* 2.8 52.0 + - + +
8C LYS* 5.9 1.9 - - - +
11C ASN* 2.9 30.3 + - - -
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Residues in contact with PRO 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A GLU* 5.0 1.3 - - - +
132A TYR* 3.6 21.6 - - + +
180B GLN* 3.3 42.6 - - + +
181B GLY 3.6 6.1 - - - +
183B GLU* 1.3 90.4 - - + +
185B ALA* 1.3 58.5 + - - +
187B LEU* 3.7 8.7 - - + +
188B HIS* 2.8 32.6 + - - +
8C LYS* 5.6 4.9 - - - +
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Residues in contact with ALA 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A TYR* 3.6 39.3 - - + +
135A SER* 4.5 10.2 + - - +
136A ALA* 5.8 0.5 - - - +
139A HIS* 5.8 5.6 - - + -
140B PHE* 4.1 3.8 - - - -
177B PHE* 3.9 18.4 - - + -
181B GLY 4.9 0.2 + - - -
182B ALA* 3.5 9.8 + - + +
183B GLU 3.3 0.6 - - - -
184B PRO* 1.3 77.1 - - - +
186B PHE* 1.3 62.6 + - - +
188B HIS* 3.4 2.1 + - - +
189B GLY* 3.0 21.0 + - - -
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Residues in contact with PHE 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B ALA 4.0 15.9 - - - -
84B LYS* 4.3 10.5 - - + -
87B ARG* 3.5 41.5 - - - +
140B PHE* 3.3 30.3 - + - -
141B THR* 3.7 29.4 - - + -
144B SER* 4.1 16.8 - - - +
182B ALA 3.0 15.9 + - - +
183B GLU* 3.4 8.3 - - + +
184B PRO 3.2 0.2 - - - -
185B ALA* 1.3 77.4 - - - +
187B LEU* 1.3 79.8 + - + +
190B LEU* 3.1 47.8 + - + +
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Residues in contact with LEU 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B LYS* 3.7 33.0 - - + +
183B GLU* 2.8 47.0 + - + +
184B PRO* 4.0 6.5 - - + +
186B PHE* 1.3 90.8 - - + +
188B HIS* 1.3 57.2 + - - +
190B LEU* 3.5 8.1 + - + +
191B GLU* 3.0 36.0 + - + +
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Residues in contact with HIS 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A ASN* 3.0 34.5 + - - -
132A TYR* 3.4 40.6 - + + +
133A ALA 4.0 11.0 - - - -
197A PHE* 4.2 12.3 - + - -
200A GLN* 4.8 12.4 - - + +
184B PRO 2.8 19.9 + - - +
185B ALA 3.6 4.0 - - - +
187B LEU* 1.3 76.4 - - - +
189B GLY* 1.3 61.2 + - - +
191B GLU* 3.3 5.9 + - - +
192B SER* 2.9 49.4 + - - -
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Residues in contact with GLY 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A TYR 5.4 0.2 - - - -
136A ALA* 4.0 17.0 - - - -
193A LEU* 4.1 1.7 - - - +
140B PHE* 3.6 22.0 - - - -
185B ALA 3.0 12.4 + - - -
188B HIS* 1.3 78.3 + - - +
190B LEU* 1.3 60.6 + - - +
192B SER* 3.5 4.5 + - - -
193B LEU* 2.9 33.1 + - - +
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Residues in contact with LEU 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B LEU 4.4 2.7 - - - +
80B ARG* 3.7 29.2 - - + +
83B ALA* 3.7 26.0 - - + -
84B LYS* 4.5 9.0 - - + -
137B VAL* 4.1 17.3 - - + -
140B PHE* 3.5 11.8 - - + -
186B PHE* 3.1 35.4 + - + +
187B LEU* 3.6 8.7 - - + +
189B GLY* 1.3 76.8 - - - +
191B GLU* 1.3 58.2 + - - +
193B LEU* 3.3 8.4 + - + +
194B ILE* 3.0 48.1 + - + +
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Residues in contact with GLU 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B ARG* 2.6 53.9 + - - +
187B LEU* 3.0 23.6 + - + +
188B HIS* 3.7 5.4 - - - +
190B LEU* 1.3 76.2 - - - +
192B SER* 1.3 60.0 + - - +
194B ILE* 4.1 5.5 - - - +
195B ARG* 2.9 36.0 + - + +
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Residues in contact with SER 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192A SER 3.4 5.3 - - - +
193A LEU* 4.2 6.7 - - - -
196A GLY* 3.3 19.7 - - - -
197A PHE* 3.3 37.2 - - - -
200A GLN* 5.7 2.6 - - - +
188B HIS* 2.9 31.3 + - - -
189B GLY* 3.5 8.3 - - - -
190B LEU 3.4 0.2 - - - -
191B GLU* 1.3 76.1 - - - +
193B LEU* 1.3 56.3 + - - +
195B ARG* 4.6 0.7 - - - -
196B GLY 2.9 23.4 + - - -
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Residues in contact with LEU 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A PHE* 5.5 2.0 - - + -
189A GLY 4.2 9.6 - - - +
192A SER* 4.3 8.9 - - - -
193A LEU* 3.6 31.2 - - + +
136B ALA* 3.7 16.6 - - + +
137B VAL* 3.7 35.4 - - + +
140B PHE* 3.9 19.5 - - + -
189B GLY 2.9 18.1 + - - +
190B LEU* 3.4 9.9 - - + +
191B GLU 3.2 0.2 - - - -
192B SER* 1.3 76.1 - - - +
194B ILE* 1.3 64.8 + - - +
196B GLY* 3.1 2.3 + - - -
197B PHE* 2.9 43.7 + - + -
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Residues in contact with ILE 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B TRP* 3.7 3.4 - - + -
76B GLN* 3.6 35.7 - - + +
79B LEU* 4.1 19.1 - - + -
80B ARG* 3.3 55.4 - - + +
137B VAL* 5.5 0.2 - - + -
190B LEU* 3.0 34.4 + - + +
191B GLU* 4.1 8.7 - - - +
193B LEU* 1.3 77.8 - - + +
195B ARG* 1.3 63.0 + - - +
197B PHE* 3.4 13.3 + - + +
198B GLU* 3.3 25.1 + - - +
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Residues in contact with ARG 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196A GLY* 4.2 6.3 - - - +
199A VAL* 3.7 44.4 - - + +
191B GLU* 2.9 20.5 + - - +
192B SER* 4.0 3.1 - - - +
194B ILE* 1.3 77.0 - - - +
196B GLY* 1.3 62.2 + - - +
198B GLU* 3.3 34.3 + - - +
199B VAL* 3.1 23.2 + - - +
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Residues in contact with GLY 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192A SER 3.2 25.1 - - - -
195A ARG* 3.8 5.7 - - - +
196A GLY* 3.6 8.9 - - - -
192B SER 2.9 12.1 + - - -
193B LEU 3.5 1.6 - - - -
195B ARG* 1.3 72.5 - - - +
197B PHE* 1.3 59.5 + - - +
199B VAL* 3.3 2.3 + - - +
200B GLN* 2.9 40.5 + - - +
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Residues in contact with PHE 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A HIS* 5.6 4.0 - + - -
189A GLY* 5.6 0.2 - - - -
192A SER* 3.5 20.9 - - - -
75B TRP* 3.7 11.7 - + + -
79B LEU* 3.9 19.1 - - + -
125B PHE* 4.5 9.2 - + + -
132B TYR 5.2 0.7 - - - -
133B ALA* 3.6 42.0 - - + -
136B ALA* 4.3 11.0 - - + -
137B VAL* 3.8 24.2 - - + -
193B LEU* 2.9 32.3 + - + -
194B ILE* 3.5 14.6 - - + +
195B ARG 3.3 0.2 - - - -
196B GLY* 1.3 76.4 - - - +
198B GLU* 1.3 53.9 + - - +
200B GLN* 3.1 17.0 + - - +
201B LEU* 2.8 41.1 + - - +
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Residues in contact with GLU 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B TRP* 3.8 20.4 - - + -
76B GLN* 3.4 26.6 + - - +
80B ARG* 5.5 2.1 + - - -
194B ILE* 3.3 15.9 + - - +
195B ARG* 3.3 43.1 + - - +
197B PHE* 1.3 75.9 - - - +
199B VAL* 1.3 60.0 + - + +
201B LEU* 3.6 4.1 + - - +
202B THR* 2.6 35.6 + - - +
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Residues in contact with VAL 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A ARG* 3.7 34.3 - - + +
199A VAL* 3.7 28.0 - - + -
195B ARG* 3.1 14.4 + - + +
196B GLY 3.6 6.7 - - - +
198B GLU* 1.3 80.9 - - + +
200B GLN* 1.3 61.2 + - - +
202B THR* 3.7 6.6 - - - -
203B ALA* 3.1 23.6 + - + +
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Residues in contact with GLN 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188A HIS* 2.9 38.5 + - + +
191A GLU* 3.8 8.1 - - + +
192A SER* 2.5 39.0 + - - -
195A ARG* 4.4 14.1 - - + +
196B GLY 2.9 22.0 + - - +
197B PHE* 3.4 17.1 - - - +
199B VAL* 1.3 74.8 - - - +
201B LEU* 1.3 66.5 + - + +
203B ALA* 3.3 5.8 + - - +
204B LEU* 3.2 40.8 + - + +
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Residues in contact with LEU 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B TRP* 4.8 6.1 - - + +
123B GLN 4.2 7.9 - - - +
124B GLY* 4.0 28.9 - - - +
125B PHE* 3.2 51.8 - - + +
129B ASN* 5.7 7.6 - - + +
197B PHE* 2.8 26.8 + - + +
198B GLU* 3.9 6.3 - - - +
200B GLN* 1.3 72.4 - - + +
202B THR* 1.3 61.8 + - - +
204B LEU* 3.1 26.2 + - - +
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Residues in contact with THR 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198B GLU* 2.6 25.1 + - - +
199B VAL* 3.7 7.7 - - - -
201B LEU* 1.3 77.8 - - - +
203B ALA* 1.3 61.1 + - - +
204B LEU 3.3 5.5 + - - +
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Residues in contact with ALA 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B VAL* 3.1 18.7 + - + +
200B GLN* 3.3 7.5 + - - +
202B THR* 1.3 76.7 - - - +
204B LEU* 1.3 64.6 + - + +
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Residues in contact with LEU 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A HIS* 4.5 14.4 - - + -
129B ASN* 4.5 20.6 - - - +
200B GLN* 3.2 32.1 - - + +
201B LEU* 3.1 18.1 + - - +
202B THR 3.7 4.7 - - - +
203B ALA* 1.3 85.9 - - + +
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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