Contacts of the helix formed by residues 184 - 199 (chain A) in PDB entry 1N35
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 ASN 184 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51A PHE* 3.7 8.1 - - - -
55A ALA* 4.0 1.3 - - - -
180A ASP 3.9 0.8 + - - -
181A LEU* 2.9 28.8 + - + +
182A SER 3.6 0.6 - - - -
183A HIS* 1.3 75.3 - - - +
185A CYS* 1.3 66.2 + - - +
186A PRO* 3.2 10.8 - - - +
187A LEU* 3.0 33.1 + - + -
188A TRP* 3.2 17.5 + - - +
237A ALA* 3.0 35.7 + - - +
240A GLN* 3.6 13.4 - - - +
241A GLN* 3.0 24.4 + - - +
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Residues in contact with CYS 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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55A ALA* 3.3 29.2 - - - +
57A LEU* 3.5 32.5 - - - -
183A HIS 3.2 7.1 + - - +
184A ASN* 1.3 69.1 - - - +
186A PRO* 1.3 76.1 - - + +
188A TRP* 3.3 1.4 + - - +
189A CYS* 3.0 24.4 + - - -
240A GLN* 4.5 3.2 + - - +
251A LYS* 3.8 34.1 - - + +
254A VAL* 4.4 7.0 - - - -
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Residues in contact with PRO 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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184A ASN* 3.2 9.4 - - - +
185A CYS* 1.3 94.9 - - + +
187A LEU* 1.3 57.2 + - - +
189A CYS* 3.2 3.3 + - - +
190A PHE* 2.9 27.8 + - - +
233A LEU* 3.2 35.1 - - + +
236A LEU* 3.6 14.4 - - + -
237A ALA 3.5 9.2 - - - +
240A GLN* 4.0 3.8 - - - +
250A VAL* 3.4 31.6 - - + -
254A VAL* 3.8 15.7 - - + -
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Residues in contact with LEU 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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46A LEU* 3.5 40.2 - - + -
49A ILE* 4.4 7.0 - - + -
51A PHE* 4.2 8.5 - - + -
155A VAL* 4.2 15.3 - - + -
158A LEU* 4.5 8.1 - - + -
159A LEU* 4.6 2.9 - - + -
181A LEU* 3.9 37.5 - - + -
184A ASN* 3.0 20.0 + - - +
185A CYS 3.3 0.2 - - - -
186A PRO* 1.3 72.0 - - - +
188A TRP* 1.3 68.2 + - - +
190A PHE* 3.1 12.1 + - + +
191A ARG* 2.9 24.3 + - - +
234A VAL* 6.3 1.6 - - + -
237A ALA* 4.0 17.6 - - + +
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Residues in contact with TRP 188 (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 PHE* 3.6 45.5 - + + -
55A ALA 3.4 27.8 - - - +
56A MET* 3.4 38.4 - - + +
57A LEU 3.6 30.3 - - - -
59A ILE* 3.8 20.4 - - + -
184A ASN 3.2 9.6 + - - +
185A CYS 3.6 2.2 - - - +
187A LEU* 1.3 77.6 - - - +
189A CYS* 1.3 77.4 + - - +
191A ARG* 3.2 13.0 + - - +
192A GLU* 2.9 60.3 + - + +
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Residues in contact with CYS 189 (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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57A LEU* 3.2 35.2 - - - -
59A ILE* 4.3 10.5 - - - -
185A CYS 3.0 16.9 + - - -
186A PRO 3.5 7.6 - - - +
188A TRP* 1.3 87.0 - - - +
190A PHE* 1.3 58.6 + - - +
193A ILE* 2.8 44.1 + - + +
233A LEU* 3.8 17.0 - - + -
254A VAL* 3.6 16.2 - - - -
258A LEU* 4.8 2.0 - - + -
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Residues in contact with PHE 190 (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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42A VAL* 6.1 0.7 - - + -
43A TYR* 3.4 41.5 - + - -
46A LEU* 3.7 20.6 - - + -
151A LEU* 4.2 11.0 - - + -
152A GLU* 5.3 1.8 - - + -
155A VAL* 4.3 17.7 - - + -
186A PRO 2.9 12.5 + - - +
187A LEU* 3.1 18.8 + - + +
189A CYS* 1.3 77.0 - - - +
191A ARG* 1.3 64.1 + - - +
193A ILE* 4.2 0.3 - - - +
194A CYS* 3.2 32.7 + - - -
230A LEU* 3.8 43.7 - - + -
233A LEU* 3.9 13.0 - - + +
234A VAL* 3.9 24.0 - - + -
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Residues in contact with ARG 191 (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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43A TYR* 5.4 2.5 - - + -
46A LEU* 2.9 55.3 + - + -
47A ASP* 3.4 26.3 + - - +
49A ILE 3.2 13.1 + - - -
51A PHE* 3.2 32.4 - - + +
56A MET* 5.8 1.2 - - - +
187A LEU 2.9 12.4 + - - +
188A TRP* 3.6 19.8 + - - +
190A PHE* 1.3 82.1 - - - +
192A GLU* 1.3 68.5 + - - +
194A CYS* 4.0 2.2 - - - +
195A ARG* 2.8 54.2 + - - +
204A ARG* 4.4 8.2 + - - +
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Residues in contact with GLU 192 (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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59A ILE* 4.1 14.6 - - + -
64A TYR* 4.5 0.9 - - - -
188A TRP* 2.9 55.4 + - + +
189A CYS 3.8 2.2 - - - +
191A ARG* 1.3 83.6 + - - +
193A ILE* 1.3 62.3 + - - +
195A ARG* 3.2 31.6 + - - +
196A HIS* 2.8 33.9 + - - +
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Residues in contact with ILE 193 (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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59A ILE* 3.8 14.8 - - + -
63A ILE* 5.2 2.5 - - + -
64A TYR* 3.3 21.4 + - + +
189A CYS* 2.8 27.6 + - + +
190A PHE 4.2 1.8 - - - +
192A GLU* 1.3 72.6 - - - +
194A CYS* 1.3 58.5 + - - +
196A HIS* 3.4 2.6 + - - +
197A ILE* 3.0 38.0 + - + +
226A ILE* 4.0 28.0 - - + -
229A LEU* 3.4 25.8 - - + -
230A LEU* 4.0 13.7 - - + -
233A LEU* 3.8 16.4 - - + -
258A LEU* 4.0 15.5 - - + -
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Residues in contact with CYS 194 (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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43A TYR* 3.9 24.9 - - + -
190A PHE* 3.2 29.6 + - - +
191A ARG 4.0 1.8 - - - +
193A ILE* 1.3 76.0 - - - +
195A ARG* 1.3 68.1 + - - +
197A ILE* 3.1 3.5 + - - +
198A SER* 2.9 26.3 + - - -
204A ARG* 4.0 6.1 - - - +
206A PRO* 3.1 38.8 - - + +
230A LEU* 3.5 23.8 - - - -
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Residues in contact with ARG 195 (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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47A ASP* 2.5 35.3 + - - +
191A ARG* 2.8 53.1 + - - +
192A GLU* 3.5 27.1 + - - +
194A CYS* 1.3 73.4 - - - +
196A HIS* 1.3 58.9 + - - +
198A SER* 3.1 7.7 + - - +
199A GLY* 2.8 32.2 + - - +
204A ARG* 4.0 18.4 - - - +
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Residues in contact with HIS 196 (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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64A TYR* 3.2 55.4 - + - +
192A GLU 2.8 18.4 + - - +
193A ILE 3.6 4.5 - - - +
195A ARG* 1.3 77.0 - - - +
197A ILE* 1.3 60.6 + - - +
199A GLY* 3.8 4.7 + - - -
221A ARG* 3.2 30.7 + - - +
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Residues in contact with ILE 197 (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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64A TYR* 3.8 15.0 - - + -
193A ILE* 3.0 20.9 + - + +
194A CYS* 3.1 6.9 + - - +
196A HIS* 1.3 75.3 - - - +
198A SER* 1.3 60.2 + - - +
206A PRO* 4.4 9.2 - - + -
217A LEU* 4.1 9.9 - - + -
219A SER* 2.7 30.3 + - - +
221A ARG* 2.6 36.1 + - - +
222A MET* 3.8 28.0 - - + +
226A ILE* 3.7 43.7 - - + -
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Residues in contact with SER 198 (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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194A CYS 2.9 15.0 + - - -
195A ARG* 3.1 17.3 + - - +
197A ILE* 1.3 77.7 - - - +
199A GLY* 1.3 58.1 + - - +
200A PRO* 3.1 2.1 - - - +
201A LEU* 2.8 41.3 + - - +
203A ASP 3.2 26.5 - - - -
204A ARG* 4.0 20.0 + - - -
217A LEU* 3.6 16.6 - - - +
221A ARG* 4.1 1.5 + - - -
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Residues in contact with GLY 199 (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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195A ARG* 2.8 19.7 + - - +
196A HIS* 4.2 4.0 - - - -
197A ILE 3.2 3.0 - - - -
198A SER* 1.3 79.5 + - - +
200A PRO* 1.3 68.9 - - - +
201A LEU 3.4 4.2 + - - +
204A ARG* 6.0 0.3 - - - -
221A ARG* 4.1 7.9 - - - -
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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
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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