Contacts of the helix formed by residues 185 - 200 (chain A) in PDB entry 3SDI
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 185 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42A ALA* 3.5 4.8 - - - +
43A THR* 4.2 2.9 - - - +
44A ASN* 2.4 37.6 + - - +
183A GLU 3.4 4.4 + - - +
184A LEU* 1.3 77.4 - - - +
186A LEU* 1.3 72.7 + - - +
187A GLU* 3.0 33.9 + - - +
188A ASP* 3.4 21.8 + - - +
189A ALA 3.2 15.8 + - - -
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Residues in contact with LEU 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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42A ALA* 3.8 6.3 - - - -
44A ASN* 3.0 32.9 + - - +
45A GLY* 4.1 2.5 - - - -
46A VAL* 4.0 26.5 - - - +
47A VAL* 4.5 2.7 - - + +
185A GLU* 1.3 80.1 - - - +
187A GLU* 1.3 67.2 + - + +
189A ALA* 3.1 6.4 + - + +
190A ILE* 3.0 38.0 + - + +
214A ILE* 3.8 44.9 - - + -
216A GLY* 4.2 10.1 - - - -
217A ASP 5.5 0.9 - - - +
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Residues in contact with GLU 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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185A GLU* 3.0 17.8 + - - +
186A LEU* 1.3 77.4 - - + +
188A ASP* 1.3 58.9 + - - +
190A ILE* 3.4 13.0 + - - +
191A HIS* 3.0 26.2 + - - +
232A ARG* 2.7 49.4 + - - +
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Residues in contact with ASP 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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183A GLU 5.3 0.5 - - - +
184A LEU* 3.7 22.3 - - + +
185A GLU* 3.4 29.3 + - - +
186A LEU 3.2 0.4 - - - -
187A GLU* 1.3 77.0 - - - +
189A ALA* 1.3 60.3 + - - +
191A HIS* 3.1 10.0 + - - +
192A ILE* 2.8 34.7 + - + +
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Residues in contact with ALA 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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40A ILE* 3.4 24.6 - - + +
42A ALA* 4.0 17.0 - - + -
47A VAL* 3.6 17.2 - - + +
184A LEU* 4.7 5.5 - - + +
185A GLU 3.2 9.4 + - - +
186A LEU* 3.1 11.7 + - + +
188A ASP* 1.3 79.4 - - - +
190A ILE* 1.3 57.1 + - - +
192A ILE* 4.4 8.1 - - - +
193A ALA* 2.9 28.4 + - - +
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Residues in contact with ILE 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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47A VAL* 4.4 6.7 - - + -
186A LEU* 3.0 36.1 + - + +
187A GLU* 3.5 24.0 - - - +
188A ASP 3.2 0.2 - - - -
189A ALA* 1.3 73.9 - - - +
191A HIS* 1.3 66.2 + - - +
193A ALA* 3.2 7.1 + - - +
194A LEU* 3.0 30.3 + - + +
212A LEU* 3.7 18.6 - - + -
214A ILE* 3.9 25.1 - - + -
224A LEU* 4.6 11.4 - - + -
232A ARG* 3.6 28.5 - - - +
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Residues in contact with HIS 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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179A ARG* 4.5 12.6 + - - -
187A GLU 3.0 13.4 + - - +
188A ASP* 3.2 13.7 - - - +
190A ILE* 1.3 75.3 - - - +
192A ILE* 1.3 65.2 + - + +
194A LEU* 3.0 20.3 + - - +
195A LEU* 3.1 37.1 + - + +
232A ARG* 5.1 6.2 + - - +
235A ALA 4.5 5.0 + - - -
236A LEU* 3.1 47.2 + - + +
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Residues in contact with ILE 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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40A ILE* 3.8 15.0 - - + -
175A PHE* 5.4 1.8 - - + +
176A LEU* 4.0 9.0 - - + -
179A ARG* 3.7 60.8 - - + +
180A TRP* 5.0 0.7 - - - +
184A LEU* 3.8 33.0 - - + -
188A ASP* 2.8 20.9 + - + +
189A ALA* 3.8 6.3 - - - +
191A HIS* 1.3 73.1 - - + +
193A ALA* 1.3 53.7 + - - +
195A LEU* 3.5 10.1 + - + +
196A THR* 2.5 46.6 + - - +
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Residues in contact with ALA 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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38A LEU* 3.9 19.0 - - + +
40A ILE* 3.4 16.1 - - + +
47A VAL* 4.2 17.3 - - + -
49A ALA* 4.6 7.9 - - + -
189A ALA 2.9 18.8 + - - +
190A ILE* 3.5 7.4 - - - +
191A HIS 3.1 0.4 - - - -
192A ILE* 1.3 77.9 - - - +
194A LEU* 1.3 62.0 + - - +
196A THR* 4.0 2.1 - - - -
197A LEU* 3.2 26.3 + - - +
212A LEU* 5.0 2.9 - - + -
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Residues in contact with LEU 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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190A ILE* 3.0 22.4 + - + +
191A HIS* 3.0 9.9 + - - +
193A ALA* 1.3 73.8 - - - +
195A LEU* 1.3 65.8 + - - +
197A LEU* 3.4 1.5 + - + -
198A LYS* 3.1 17.8 + - - +
206A PHE* 3.2 20.1 - - + -
210A ILE* 4.3 12.6 - - + -
212A LEU* 3.6 29.8 - - + -
229A ILE* 4.5 12.1 - - + +
232A ARG* 3.8 33.7 - - + +
233A LEU* 4.0 29.8 - - + -
236A LEU* 4.5 7.6 - - + -
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Residues in contact with LEU 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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175A PHE* 3.9 19.3 - - + -
179A ARG* 3.7 28.7 - - - +
191A HIS* 3.1 42.0 + - + +
192A ILE* 3.7 11.0 - - + +
194A LEU* 1.3 76.5 - - - +
196A THR* 1.3 62.7 + - - +
198A LYS* 3.0 25.9 + - - +
199A GLU* 3.6 15.5 + - - +
236A LEU* 3.7 32.1 - - + +
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Residues in contact with THR 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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38A LEU* 3.9 17.4 - - + +
172A ALA* 3.8 35.6 - - + +
175A PHE* 3.8 22.5 - - + -
176A LEU* 3.3 30.4 - - + +
192A ILE* 2.5 27.5 + - - +
193A ALA* 4.0 1.8 - - - -
194A LEU 3.4 0.2 - - - -
195A LEU* 1.3 75.1 - - - +
197A LEU* 1.3 60.9 + - - +
198A LYS 3.6 0.2 + - - -
199A GLU* 3.7 14.3 + - - +
200A SER* 3.7 8.7 + - - -
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Residues in contact with LEU 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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36A THR* 4.4 21.3 - - + +
38A LEU* 3.7 21.8 - - + -
49A ALA* 4.2 8.7 - - + -
50A THR* 3.7 26.2 - - - +
51A GLU* 4.8 1.1 - - + +
193A ALA 3.2 14.2 + - - +
194A LEU* 3.8 5.2 - - + +
195A LEU 3.2 0.6 - - - -
196A THR* 1.3 79.1 - - - +
198A LYS* 1.3 62.8 + - - +
199A GLU 3.3 0.2 - - - -
200A SER* 3.3 13.3 + - - +
202A VAL* 3.1 33.3 + - + +
206A PHE* 3.8 8.3 - - + -
210A ILE* 3.7 38.1 - - + -
212A LEU* 5.2 1.1 - - + -
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Residues in contact with LYS 198 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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194A LEU 3.1 12.0 + - - +
195A LEU* 3.0 18.4 + - - +
197A LEU* 1.3 75.6 - - - +
199A GLU* 1.3 74.0 + - - +
202A VAL 3.2 19.3 + - - +
206A PHE* 3.7 38.4 - - + +
233A LEU* 5.1 2.6 - - - +
236A LEU* 4.3 31.8 - - - +
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Residues in contact with GLU 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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171A ALA* 6.4 1.6 - - + -
175A PHE* 4.6 19.5 - - + -
195A LEU* 3.8 17.2 - - - +
196A THR 3.8 8.1 - - - +
197A LEU 3.3 0.4 - - - -
198A LYS* 1.3 88.5 - - - +
200A SER* 1.3 60.0 + - - +
202A VAL 3.5 2.1 + - - +
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Residues in contact with SER 200 (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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36A THR* 3.6 36.4 + - - +
51A GLU* 4.4 2.3 - - - +
167A LYS* 6.2 0.2 - - - -
168A GLY* 4.8 13.5 - - - -
196A THR 3.7 9.7 + - - -
197A LEU* 3.3 15.6 + - - +
199A GLU* 1.3 78.3 - - - +
202A VAL* 1.3 62.0 + - - +
203A GLU* 3.1 18.8 - - - +
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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
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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