Contacts of the helix formed by residues 187 - 197 (chain A) in PDB entry 3LKB
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 187 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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180A VAL* 4.1 5.4 - - - +
184A ASN* 2.9 46.5 + - - +
186A ASP* 1.3 73.5 - - - +
188A THR* 1.3 64.0 + - - +
189A ALA 3.4 2.7 - - - -
190A LEU* 3.1 15.7 + - + +
191A LEU* 2.9 36.3 + - + +
213A ASN* 3.4 18.8 + - - +
214A ILE* 3.5 21.7 - - + +
217A ASP* 2.9 25.6 + - + +
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Residues in contact with THR 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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186A ASP* 2.8 26.9 + - - -
187A ASN* 1.3 76.3 - - - +
189A ALA* 1.3 59.3 + - - +
190A LEU 3.2 0.2 + - - -
191A LEU* 3.2 1.6 + - - +
192A LYS* 2.8 55.6 + - + +
217A ASP* 4.3 5.6 + - - -
221A LEU* 4.3 23.0 - - + +
220B ARG* 5.8 1.2 + - - -
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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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186A ASP* 5.1 2.6 + - - +
187A ASN 3.4 0.8 - - - -
188A THR* 1.3 79.7 - - - +
190A LEU* 1.3 63.3 + - - +
192A LYS* 3.8 6.1 - - - +
193A ARG* 3.0 26.6 + - - +
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Residues in contact with LEU 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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149A VAL* 4.4 12.8 - - + -
176A ASP* 5.5 0.2 - - - +
178A GLN* 3.2 40.2 - - + +
180A VAL* 3.9 26.7 - - + -
187A ASN* 3.1 20.3 + - + +
189A ALA* 1.3 78.6 - - - +
191A LEU* 1.3 69.3 + - + +
193A ARG* 3.3 10.8 + - + +
194A PHE* 3.1 42.7 + - + -
214A ILE* 4.6 11.7 - - + -
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Residues in contact with LEU 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* 2.9 26.7 + - + +
188A THR 3.8 3.1 - - - +
190A LEU* 1.3 81.4 - - + +
192A LYS* 1.3 56.3 + - - +
194A PHE* 3.2 15.4 + - + +
195A GLU* 2.9 29.4 + - - +
202A VAL* 5.6 0.2 - - + -
214A ILE* 3.7 27.8 - - + +
217A ASP* 3.8 12.6 - - + -
218A ALA* 3.6 30.5 - - + +
221A LEU* 4.3 8.5 - - + -
223A LEU* 3.8 16.7 - - + +
225A MET* 3.4 30.5 - - + -
227A HIS* 4.4 2.2 - - - +
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Residues in contact with LYS 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 THR* 2.8 36.3 + - + +
189A ALA* 3.8 6.3 - - - +
191A LEU* 1.3 69.4 - - - +
193A ARG* 1.3 64.7 + - - +
195A GLU* 3.4 20.1 + - + +
196A GLN* 3.0 34.4 + - + +
221A LEU* 3.7 36.7 - - + +
223A LEU* 5.3 5.8 - - + +
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Residues in contact with ARG 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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176A ASP* 5.0 10.5 - - - +
189A ALA 3.0 14.3 + - - +
190A LEU* 3.3 13.9 - - + +
192A LYS* 1.3 75.1 - - - +
194A PHE* 1.3 68.7 + - + +
196A GLN* 3.0 43.7 + - - +
197A ALA* 3.2 33.6 + - - +
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Residues in contact with PHE 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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147A ALA* 3.6 24.2 - - + -
148A LEU 4.6 2.0 - - - -
149A VAL* 3.7 26.0 - - + -
175A VAL* 5.9 0.2 - - + -
176A ASP* 4.0 29.8 - - + -
178A GLN* 4.1 5.2 - - + -
190A LEU* 3.1 41.7 + - + -
191A LEU* 3.4 13.2 - - + +
193A ARG* 1.3 79.3 - - + +
195A GLU* 1.3 65.3 + - - +
197A ALA* 3.3 2.3 + - + -
198A GLY 3.1 4.5 + - - -
199A VAL* 2.9 49.3 + - + +
202A VAL* 4.0 20.2 - - + -
225A MET* 3.9 13.2 - - + -
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Residues in contact with GLU 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 LEU 2.9 16.5 + - - +
192A LYS* 3.8 19.8 + - + +
193A ARG 3.4 0.2 - - - -
194A PHE* 1.3 75.3 - - - +
196A GLN* 1.3 67.2 + - + +
198A GLY* 3.1 12.9 + - - -
199A VAL 4.9 4.5 - - - +
223A LEU* 3.9 29.5 - - + +
225A MET* 4.9 5.8 - - + -
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Residues in contact with GLN 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 LYS* 3.0 24.5 + - + +
193A ARG* 3.0 42.4 + - - +
194A PHE 3.3 0.4 - - - -
195A GLU* 1.3 79.2 - - + +
197A ALA* 1.3 58.6 + - - +
198A GLY 3.1 3.9 + - - -
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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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145A LYS* 3.3 21.8 - - - +
175A VAL* 4.0 25.2 - - + +
193A ARG* 3.2 25.5 + - - +
194A PHE* 3.9 4.9 - - + +
195A GLU 3.3 0.4 - - - -
196A GLN* 1.3 78.1 - - - +
198A GLY* 1.3 61.3 + - - +
199A VAL* 3.4 2.2 + - + +
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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