Contacts of the helix formed by residues 183 - 200 (chain A) in PDB entry 3HS3
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 LEU 183 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A TRP* 4.0 12.3 - - + -
180A PRO* 3.1 18.0 + - + +
181A LEU 3.0 3.1 - - - +
182A SER* 1.3 82.1 - - - +
184A PRO* 1.3 71.6 - - + +
185A THR* 3.3 4.7 - - - +
186A ILE* 3.0 27.4 + - + +
187A ARG 3.0 19.1 + - - -
211A GLU* 3.1 29.2 - - - +
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Residues in contact with PRO 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A THR* 5.3 9.4 - - - +
143A ALA* 3.5 24.9 - - + +
145A ILE* 5.1 10.8 - - + -
182A SER 3.2 11.2 - - - +
183A LEU* 1.3 85.1 - - + +
185A THR* 1.3 62.3 + - + +
187A ARG* 3.4 9.6 + - + +
188A GLU* 3.1 28.2 + - - +
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Residues in contact with THR 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A ASP* 3.5 37.0 + - - +
142A SER 3.7 23.3 - - - +
143A ALA 3.8 1.1 - - - +
156A ASN* 3.6 34.3 + - - +
183A LEU* 4.7 3.5 + - - +
184A PRO* 1.3 75.9 - - + +
186A ILE* 1.3 79.4 + - - +
188A GLU* 3.5 3.3 + - - -
189A ARG* 3.1 18.9 + - - +
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Residues in contact with ILE 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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178A HIS* 4.5 1.1 - - + -
179A TRP* 3.4 57.7 - - + +
180A PRO 4.0 4.9 - - - +
181A LEU* 4.3 2.5 - - + -
183A LEU* 3.0 35.3 + - + +
185A THR* 1.3 82.8 - - - +
187A ARG* 1.3 66.5 + - - +
189A ARG* 3.0 30.6 + - + +
190A ILE* 2.9 39.4 + - + +
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Residues in contact with ARG 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A LEU* 3.1 65.2 + - + +
182A SER* 4.6 2.4 - - - +
183A LEU 3.0 6.9 + - - +
184A PRO* 3.7 11.6 - - + +
186A ILE* 1.3 77.6 - - - +
188A GLU* 1.3 62.7 + - + +
191A GLU* 2.9 61.4 + - + +
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Residues in contact with GLU 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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143A ALA* 3.6 15.0 - - + +
144A ASN* 2.9 37.1 + - - +
153A VAL* 4.5 4.0 - - - +
154A SER 4.6 0.3 - - - +
156A ASN* 3.0 32.9 + - + +
157A THR* 4.0 17.2 + - - +
184A PRO 3.1 17.5 + - - +
185A THR* 3.6 6.2 - - - +
186A ILE 3.2 0.2 - - - -
187A ARG* 1.3 77.4 - - + +
189A ARG* 1.3 62.2 + - - +
191A GLU* 4.2 6.6 - - - +
192A ALA* 3.2 23.9 + - - +
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Residues in contact with ARG 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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156A ASN* 3.5 21.2 - - + +
160A GLY* 3.4 26.2 - - - +
179A TRP* 4.7 7.3 - - - -
185A THR 3.1 10.6 + - - +
186A ILE* 3.0 35.7 + - - +
188A GLU* 1.3 79.7 - - - +
190A ILE* 1.3 63.3 + - - +
192A ALA 3.3 2.4 + - - -
193A MET* 3.1 48.1 + - + +
233A THR 4.7 2.4 + - - -
234A VAL* 3.0 32.5 + - - +
262A TYR* 3.4 49.5 + - + +
263A ASP* 5.0 1.0 + - - -
280A GLN* 4.5 7.1 + - - +
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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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176A ILE* 4.0 11.2 - - + -
177A GLN 5.2 0.9 - - - +
178A HIS* 3.6 32.8 - - + -
181A LEU* 3.9 22.2 - - + -
186A ILE* 2.9 26.2 + - + +
187A ARG 4.2 0.7 - - - +
189A ARG* 1.3 76.5 - - - +
191A GLU* 1.3 67.1 + - + +
193A MET* 3.0 28.3 + - + +
194A THR* 2.9 23.2 + - + +
206A LEU* 3.9 36.8 - - + -
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Residues in contact with GLU 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A LEU* 6.3 1.6 - - + -
187A ARG* 2.9 63.3 + - + +
188A GLU* 4.2 5.5 - - - +
190A ILE* 1.3 76.5 - - + +
192A ALA* 1.3 61.5 + - - +
194A THR* 3.1 9.6 + - - -
195A ALA* 3.1 23.9 + - - +
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Residues in contact with ALA 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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157A THR* 3.0 43.7 - - + +
161A LYS* 3.9 9.6 + - + +
188A GLU 3.2 18.0 + - - +
189A ARG 3.5 5.2 - - - +
190A ILE 3.1 0.6 - - - -
191A GLU* 1.3 77.2 - - - +
193A MET* 1.3 63.7 + - - +
195A ALA* 3.4 6.8 + - - +
196A GLU* 3.0 25.1 + - - +
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Residues in contact with MET 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A GLY* 3.3 21.8 - - - +
163A SER* 4.1 12.1 - - - +
164A ILE* 3.5 15.5 - - + +
176A ILE* 3.7 37.5 - - + -
189A ARG* 3.1 44.6 + - + +
190A ILE* 3.0 20.7 + - + +
192A ALA* 1.3 76.5 - - - +
194A THR* 1.3 57.7 + - - +
196A GLU 3.4 0.7 + - - -
197A ALA* 2.9 30.4 + - - +
232A ILE* 3.8 31.4 - - + -
233A THR 5.7 1.3 - - - +
262A TYR* 5.3 1.3 - - + -
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Residues in contact with THR 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A ILE* 5.0 0.9 - - + -
190A ILE* 2.9 17.3 + - + +
191A GLU* 3.1 17.2 + - - -
193A MET* 1.3 77.3 - - + +
195A ALA* 1.3 52.9 + - - +
197A ALA* 3.7 2.0 - - - +
198A SER* 2.7 37.9 + - - -
204A TYR* 3.6 46.5 - - + +
206A LEU* 4.0 24.0 - - + -
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Residues in contact with ALA 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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191A GLU 3.1 18.4 + - - +
192A ALA* 3.6 8.3 - - - +
193A MET 3.2 0.2 - - - -
194A THR* 1.3 79.7 + - - +
196A GLU* 1.3 58.1 + - - +
198A SER* 3.3 6.7 + - - -
199A LYS* 3.0 26.7 + - - +
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Residues in contact with GLU 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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161A LYS* 3.5 45.1 - - + +
164A ILE* 3.7 26.2 - - + -
165A LYS* 3.8 15.4 - - + +
192A ALA 3.0 16.9 + - - +
193A MET 4.0 2.9 - - - +
195A ALA* 1.3 73.2 - - - +
197A ALA* 1.3 65.5 + - - +
199A LYS* 3.2 25.8 + - - +
200A LEU* 3.0 39.2 + - + +
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Residues in contact with ALA 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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164A ILE* 4.1 19.2 - - + +
174A VAL* 5.3 0.4 - - + -
176A ILE* 5.6 0.4 - - + -
193A MET 2.9 18.1 + - - +
194A THR* 3.7 4.9 - - - +
196A GLU* 1.3 77.0 - - - +
198A SER* 1.3 56.5 + - - +
200A LEU 3.2 1.7 + - - -
201A LYS 2.9 9.0 + - - -
202A ILE* 2.8 54.2 + - + +
204A TYR* 3.9 17.7 - - + -
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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 THR* 2.7 22.0 + - - -
195A ALA* 3.5 6.7 - - - -
196A GLU 3.2 0.2 - - - -
197A ALA* 1.3 77.6 - - - +
199A LYS* 1.3 62.5 + - - +
201A LYS* 3.1 17.2 + - - +
202A ILE 5.0 1.3 - - - -
204A TYR* 4.4 11.7 + - - -
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Residues in contact with LYS 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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161A LYS* 5.2 9.5 - - - +
195A ALA 3.0 14.1 + - - +
196A GLU* 3.4 34.6 + - - +
198A SER* 1.3 77.1 - - - +
200A LEU* 1.3 69.6 + - + +
201A LYS* 3.3 5.4 + - - +
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Residues in contact with LEU 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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164A ILE* 3.8 32.1 - - + +
165A LYS* 5.2 5.2 - - + -
169A LYS* 6.1 9.2 - - + -
196A GLU* 3.0 34.8 + - + +
198A SER 3.2 0.2 - - - -
199A LYS* 1.3 88.2 - - + +
201A LYS* 1.3 71.7 + - - +
202A ILE* 3.4 22.0 + - + +
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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