Contacts of the helix formed by residues 188 - 200 (chain A) in PDB entry 1DXK
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 188 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147A LYS* 3.4 42.8 + - + +
185A TYR* 3.2 30.0 + - + +
187A ASN* 1.3 83.7 - - + +
189A TRP* 1.3 65.6 + - - +
190A SER 3.2 3.4 - - - -
191A THR* 3.1 12.4 + - - +
192A SER* 3.0 22.6 + - - +
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Residues in contact with TRP 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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147A LYS 3.4 9.4 + - - -
148A GLY* 3.4 16.8 - - - -
149A HIS* 3.7 28.5 - - + -
168A SER 3.8 12.8 - - - -
169A LEU* 3.0 44.2 + - + +
171A LYS* 4.3 9.9 - - + -
178A LEU* 4.0 37.0 - - + -
180A ASN 5.4 0.4 - - - -
181A VAL* 4.4 4.5 - - + -
184A ALA* 4.0 15.3 - - + -
185A TYR 2.9 15.7 + - - +
186A VAL* 4.2 6.3 - - + +
187A ASN 3.6 0.2 - - - -
188A GLU* 1.3 76.6 - - - +
190A SER* 1.3 57.4 + - - +
192A SER* 3.4 1.2 + - - -
193A ILE* 3.0 31.8 + - + +
222A THR* 3.6 11.3 - - + +
226A LEU* 3.7 28.9 - - + -
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Residues in contact with SER 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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186A VAL 4.7 5.7 + - - -
187A ASN 5.2 4.7 - - - -
188A GLU 3.2 1.0 - - - -
189A TRP* 1.3 74.8 - - - +
191A THR* 1.3 62.6 + - - +
193A ILE* 3.3 2.8 + - - +
194A GLU* 2.9 34.2 + - - +
223A LEU* 3.6 21.7 + - - +
226A LEU* 3.4 26.0 + - - +
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Residues in contact with THR 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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187A ASN 4.8 6.6 + - - -
188A GLU* 3.1 12.0 + - - -
190A SER* 1.3 78.6 - - - +
192A SER* 1.3 57.9 + - - +
194A GLU* 3.1 10.6 + - + +
195A ASN* 2.8 43.6 + - - +
198A LYS* 6.0 2.5 - - - +
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Residues in contact with SER 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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145A PRO* 3.4 26.8 + - - +
146A GLY* 3.1 23.1 - - - -
147A LYS 2.7 30.5 + - - -
169A LEU* 4.2 11.4 - - - -
188A GLU* 3.0 6.0 + - - +
189A TRP 3.6 5.8 - - - -
191A THR* 1.3 77.0 - - - +
193A ILE* 1.3 61.7 + - - +
195A ASN* 3.1 12.7 + - - +
196A VAL* 3.1 11.7 + - - +
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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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169A LEU* 3.5 35.2 - - + +
170A VAL* 4.3 0.9 - - + -
189A TRP* 3.0 29.1 + - + +
190A SER 3.6 7.6 - - - +
191A THR 3.3 0.2 - - - -
192A SER* 1.3 75.4 - - - +
194A GLU* 1.3 63.6 + - - +
196A VAL* 3.1 8.9 + - - +
197A LEU* 3.0 21.5 + - + +
219A LEU* 3.6 49.1 - - + +
222A THR* 4.0 15.9 - - + -
223A LEU* 3.6 22.2 - - + -
226A LEU* 4.7 0.4 - - + -
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Residues in contact with GLU 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 SER* 2.9 21.0 + - - +
191A THR* 3.1 13.0 + - + +
193A ILE* 1.3 74.5 - - - +
195A ASN* 1.3 59.7 + - - +
197A LEU* 3.2 14.6 + - - +
198A LYS* 2.8 55.3 + - - +
223A LEU* 3.3 28.3 - - + +
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Residues in contact with ASN 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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143A PHE* 3.8 12.6 - - + -
145A PRO* 2.9 31.1 + - + +
191A THR* 2.8 29.8 + - - +
192A SER* 3.1 9.6 + - - +
194A GLU* 1.3 76.9 - - - +
196A VAL* 1.3 57.6 + - - +
198A LYS* 3.5 19.9 + - - +
199A ARG* 3.1 29.1 + - - +
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Residues in contact with VAL 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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143A PHE* 4.2 6.3 - - + -
145A PRO* 3.7 22.9 - - + -
155A VAL* 4.2 13.0 - - + -
164A LEU* 3.6 33.0 - - + -
169A LEU* 4.1 13.9 - - + -
192A SER 3.1 13.6 + - - +
193A ILE* 3.1 9.7 + - - +
195A ASN* 1.3 75.4 - - - +
197A LEU* 1.3 60.1 + - - +
199A ARG* 3.2 1.0 + - - -
200A TYR* 2.8 41.2 + - + +
203A ILE* 5.1 0.9 - - + -
219A LEU* 4.4 15.0 - - + -
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Residues in contact with LEU 197 (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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193A ILE* 3.0 31.1 + - + +
194A GLU* 3.6 23.8 - - - +
196A VAL* 1.3 75.6 - - - +
198A LYS* 1.3 63.2 + - + +
200A TYR 3.4 20.4 - - - +
201A ARG* 3.7 15.2 + - - -
203A ILE* 5.2 3.1 - - + -
216A LYS* 3.9 27.8 - - + -
219A LEU* 3.5 32.5 - - + -
220A LEU* 4.2 12.1 - - + -
223A LEU* 4.1 13.7 - - + -
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Residues in contact with LYS 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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191A THR* 6.0 2.6 - - - +
194A GLU* 2.8 40.9 + - - +
195A ASN* 3.8 19.6 + - - +
197A LEU* 1.3 78.0 - - + +
199A ARG* 1.3 61.1 + - - +
201A ARG* 4.1 15.4 - - - +
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Residues in contact with ARG 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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130A VAL* 3.5 28.2 - - - +
141A GLU* 3.0 38.0 + - - -
143A PHE* 3.6 29.8 - - + -
195A ASN 3.1 18.8 + - - +
196A VAL 3.8 3.4 - - - +
198A LYS* 1.3 79.7 - - - +
200A TYR* 1.3 85.2 + - + +
201A ARG 3.8 2.0 + - - -
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Residues in contact with TYR 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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141A GLU* 2.6 30.3 + - - +
143A PHE* 3.4 30.5 + + - +
155A VAL* 4.2 3.3 - - + +
157A TRP* 3.4 51.4 - + + +
164A LEU* 3.8 28.5 - - + -
196A VAL* 2.8 27.2 + - + +
197A LEU* 3.4 12.1 - - - +
199A ARG* 1.3 94.4 + - + +
201A ARG* 1.3 63.9 + - - +
202A ASN 3.3 2.0 - - - +
203A ILE* 3.4 32.2 - - + +
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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