Contacts of the helix formed by residues 183 - 197 (chain A) in PDB entry 5KRE
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
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Residue Dist Surf HB Arom Phob DC
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175A HIS* 3.8 2.6 + - - -
179A ASP 3.8 14.1 - - - +
180A GLU* 4.2 26.7 - - - +
182A VAL* 1.3 74.9 - - - +
184A HIS* 1.3 65.3 + - - +
185A SER* 3.7 16.8 - - - +
186A TRP* 3.0 57.0 + - + +
187A ALA 3.4 7.8 + - - -
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Residues in contact with HIS 184 (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 HIS* 3.6 24.2 + + + -
176A GLY 3.7 7.9 - - - +
177A THR* 3.5 43.3 + - + +
179A ASP 4.4 3.0 + - - -
182A VAL 3.5 2.6 + - - -
183A LEU* 1.3 71.4 - - - +
185A SER* 1.3 56.6 + - - +
187A ALA* 3.2 3.1 + - - +
188A GLU* 2.8 78.5 + - + +
203A PHE* 3.9 10.1 - + - -
205A SER* 2.8 32.2 + - - -
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Residues in contact with SER 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A ASN* 5.6 0.2 - - - -
183A LEU* 3.7 13.2 - - - +
184A HIS* 1.3 78.7 + - - +
186A TRP* 1.4 72.0 + - - +
188A GLU* 3.9 12.2 + - - +
189A GLU* 3.0 30.1 + - - +
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Residues in contact with TRP 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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83A ILE* 3.5 30.3 - - + -
84A THR* 3.7 15.8 + - - -
85A ASN* 3.5 39.9 + - - +
150A PHE* 3.8 43.9 - + + +
151A LEU 4.9 0.5 - - - +
181A LEU 3.5 23.3 - - - -
182A VAL* 3.9 2.9 - - - -
183A LEU* 3.0 49.9 + - + +
185A SER* 1.4 84.0 + - - +
187A ALA* 1.4 64.7 + - - +
189A GLU* 3.8 2.5 - - - +
190A THR* 2.9 27.9 + - - -
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Residues in contact with ALA 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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149A SER 3.4 19.5 - - - +
150A PHE* 4.2 0.8 - - - +
173A GLN* 3.4 17.8 + - - +
175A HIS* 3.2 43.7 - - + +
183A LEU 3.4 2.2 + - - -
184A HIS 3.2 5.1 + - - +
186A TRP* 1.4 76.4 - - - +
188A GLU* 1.3 58.4 + - - +
190A THR* 3.3 3.0 + - - -
191A ASN* 3.0 25.5 + - - +
203A PHE* 4.0 3.6 - - + -
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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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184A HIS* 2.8 58.3 + - + +
185A SER* 3.9 9.2 + - - +
187A ALA* 1.3 74.1 - - - +
189A GLU* 1.3 57.7 + - - +
191A ASN* 3.4 3.5 + - - +
192A SER* 2.8 38.3 + - - +
203A PHE* 3.6 20.4 - - + -
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Residues in contact with GLU 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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85A ASN* 3.0 22.8 + - - -
151A LEU 5.4 2.5 - - - +
153A LYS* 3.1 42.2 + - - +
158A TYR* 5.2 4.0 + - - +
185A SER 3.0 18.3 + - - +
186A TRP 3.8 5.2 - - - +
188A GLU* 1.3 74.8 - - - +
190A THR* 1.4 59.9 + - - +
192A SER* 3.3 6.2 + - - -
193A MET* 2.8 49.1 + - + +
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Residues in contact with THR 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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131A MET* 4.2 10.8 - - + -
150A PHE* 3.6 4.1 - - - -
151A LEU* 2.9 62.2 + - + +
158A TYR* 3.6 9.4 + - - -
173A GLN* 4.5 6.1 - - - +
186A TRP 2.9 13.7 + - - -
187A ALA 3.4 9.2 - - - -
189A GLU* 1.4 78.0 - - - +
191A ASN* 1.3 57.6 + - - +
193A MET* 3.4 2.1 + - - +
194A LEU* 3.0 44.6 + - + +
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Residues in contact with ASN 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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171A LEU* 4.1 0.4 - - - +
173A GLN* 2.9 27.2 + - - +
187A ALA 3.0 11.9 + - - +
188A GLU* 3.7 5.4 - - - +
189A GLU 3.3 0.2 - - - -
190A THR* 1.3 75.7 - - - +
192A SER* 1.3 58.7 + - - +
194A LEU* 3.4 6.3 + - - +
195A LYS* 3.0 33.6 + - - +
201A THR* 2.8 39.3 + - - +
203A PHE* 3.4 35.9 - - + +
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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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188A GLU* 2.8 24.4 + - - +
189A GLU* 3.7 6.7 - - - -
191A ASN* 1.3 73.6 + - - +
193A MET* 1.3 60.0 + - - +
195A LYS* 3.4 9.1 + - - +
196A SER* 3.0 30.5 + - - -
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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
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158A TYR* 3.5 57.4 - - + +
189A GLU* 2.8 34.9 + - + +
190A THR 3.5 2.2 - - - +
192A SER* 1.3 75.6 - - - +
194A LEU* 1.4 62.5 + - - +
196A SER* 2.7 25.1 + - - +
197A LEU* 3.1 24.9 + - + +
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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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131A MET* 3.8 20.4 - - - -
135A TYR* 4.8 8.7 - - + -
151A LEU* 4.2 0.7 - - + -
157A VAL* 3.8 17.5 - - + -
158A TYR* 3.9 13.7 - - + -
161A LEU* 3.4 27.6 - - + -
171A LEU* 3.6 28.5 - - + -
190A THR* 3.0 27.9 + - + +
191A ASN* 3.9 4.0 - - - +
193A MET* 1.4 74.5 - - - +
195A LYS* 1.3 62.4 + - - +
197A LEU* 3.0 15.2 + - - +
198A GLY 3.3 0.5 + - - -
199A VAL* 3.1 34.0 + - + +
201A THR* 4.7 3.6 - - - +
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Residues in contact with LYS 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 ASN* 3.0 24.8 + - - +
192A SER* 3.6 9.0 - - - +
194A LEU* 1.3 75.5 - - - +
196A SER* 1.3 60.6 + - - +
198A GLY* 3.1 15.1 + - - -
199A VAL 3.5 17.1 + - - +
201A THR* 4.4 17.4 + - - +
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Residues in contact with SER 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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192A SER 3.0 14.9 + - - -
193A MET* 2.7 27.7 + - - +
195A LYS* 1.3 74.8 - - - +
197A LEU* 1.4 62.6 + - - +
198A GLY 3.4 0.7 + - - -
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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
----------------------------------------------------------
158A TYR* 3.6 45.8 - - + +
161A LEU* 4.0 27.8 - - + +
162A GLN* 3.7 44.2 - - + +
168A LEU* 4.4 8.8 - - - +
193A MET* 3.1 23.8 + - + +
194A LEU 3.0 11.2 + - - +
196A SER* 1.4 81.6 - - - +
198A GLY* 1.3 56.0 + - - +
199A VAL* 3.6 1.1 - - - -
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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