Contacts of the helix formed by residues 194 - 208 (chain A) in PDB entry 4B90
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 194 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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161A MET 4.4 0.2 - - - -
168A MET* 5.4 1.0 - - - +
193A GLU* 1.3 69.7 - - - +
195A GLY* 1.3 58.1 + - - +
196A GLU* 3.2 9.9 + - - +
197A LEU* 3.0 44.7 + - + +
198A VAL* 2.9 29.3 + - - +
224A LEU* 3.1 18.6 + - + +
227A GLU* 2.7 31.9 + - - +
228A ALA* 3.5 0.6 - - - +
231A ARG* 3.2 17.9 - - - +
171B ASP* 4.5 11.0 + - - +
231B ARG* 4.6 4.6 - - - +
235B ILE* 5.4 1.8 - - - +
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Residues in contact with GLY 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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161A MET 3.0 24.8 + - - -
162A THR* 3.5 21.3 - - - -
163A TYR 4.7 0.4 - - - -
164A LYS* 4.1 6.1 + - - +
168A MET* 3.9 13.8 - - - +
193A GLU 3.1 0.4 + - - -
194A ASN* 1.3 74.3 + - - +
196A GLU* 1.3 62.1 + - - +
198A VAL* 3.6 1.8 - - - +
199A ALA* 3.0 23.4 + - - +
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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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164A LYS* 2.8 41.7 + - - +
168A MET* 3.9 18.9 - - + +
170A ARG* 5.7 6.6 - - - +
194A ASN* 3.2 8.5 + - - +
195A GLY* 1.3 76.2 - - - +
197A LEU* 1.3 62.5 + - + +
199A ALA* 3.4 5.5 + - - +
200A GLU* 3.0 38.7 + - + +
170B ARG* 5.9 0.3 + - - -
171B ASP* 4.5 23.0 - - + +
172B SER* 3.7 26.5 + - - +
175B TYR* 6.3 2.0 - - + -
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Residues in contact with LEU 197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194A ASN* 3.0 34.1 + - + +
196A GLU* 1.3 80.2 - - + +
198A VAL* 1.3 59.5 + - - +
200A GLU* 4.0 1.7 - - - +
201A GLY* 2.8 27.4 + - - -
219A SER 4.4 0.2 - - - +
224A LEU* 3.7 36.5 - - + +
175B TYR* 3.6 35.4 - - + -
231B ARG 5.3 0.2 - - - +
234B THR* 3.8 19.5 - - + -
235B ILE* 4.1 24.7 - - + +
238B ARG* 4.2 18.2 + - + -
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Residues in contact with VAL 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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162A THR* 3.7 19.3 - - - +
163A TYR 5.5 1.3 - - - +
193A GLU* 4.3 9.9 - - + -
194A ASN 2.9 21.8 + - - +
195A GLY 3.6 4.3 - - - +
197A LEU* 1.3 77.6 - - - +
199A ALA* 1.3 65.7 + - - +
201A GLY* 3.2 1.0 + - - -
202A ALA* 2.9 27.1 + - + +
219A SER* 4.5 5.4 - - - +
220A ARG* 3.5 46.7 - - + +
224A LEU* 3.6 18.8 - - + -
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Residues in contact with ALA 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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164A LYS* 4.0 26.7 - - + +
195A GLY 3.0 17.8 + - - +
196A GLU 3.5 4.9 - - - +
198A VAL* 1.3 80.0 - - - +
200A GLU* 1.3 65.9 + - + +
202A ALA* 3.8 4.5 - - - +
203A LYS* 3.1 30.3 + - - +
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Residues in contact with GLU 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 LYS* 5.0 9.4 + - - -
196A GLU* 3.0 26.4 + - + +
197A LEU* 4.0 3.4 - - + +
199A ALA* 1.3 78.8 - - - +
201A GLY* 1.3 59.1 + - - +
203A LYS* 2.8 32.6 + - - +
204A GLU* 2.8 32.0 + - - +
172B SER* 5.8 3.3 - - - -
175B TYR* 3.6 56.6 + - + +
176B GLN* 4.0 13.5 + - - -
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Residues in contact with GLY 201 (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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197A LEU 2.8 18.4 + - - -
198A VAL 3.2 1.3 + - - -
200A GLU* 1.3 79.2 - - - +
202A ALA* 1.3 51.3 + - - +
204A GLU* 3.3 8.1 + - - +
205A ALA* 2.8 36.0 + - - +
219A SER* 3.7 19.3 - - - -
238B ARG* 3.8 14.4 - - - -
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Residues in contact with ALA 202 (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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198A VAL* 2.9 20.4 + - + +
199A ALA* 3.8 5.8 - - - +
201A GLY* 1.3 74.7 - - - +
203A LYS* 1.3 65.2 + - - +
205A ALA* 3.2 1.4 + - - +
206A LEU* 3.0 28.7 + - - +
219A SER* 3.7 16.0 - - - +
220A ARG* 6.3 0.4 - - - +
341A PHE* 4.2 5.5 - - + -
342A THR* 3.7 24.7 - - + -
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Residues in contact with LYS 203 (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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199A ALA* 3.1 17.5 + - - +
200A GLU* 2.8 38.3 + - - +
202A ALA* 1.3 79.4 - - - +
204A GLU* 1.3 64.1 + - - +
206A LEU* 3.5 8.9 + - - +
207A ASP* 3.1 37.0 + - - +
176B GLN* 5.8 0.4 - - - +
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Residues in contact with GLU 204 (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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200A GLU 2.8 22.0 + - - +
201A GLY* 3.8 4.2 - - - +
203A LYS* 1.3 74.3 - - - +
205A ALA* 1.3 64.4 + - - +
207A ASP* 3.2 8.4 + - - +
208A LEU* 3.0 41.6 + - + +
175B TYR* 4.8 11.9 + - - +
179B HIS* 5.3 6.2 + - - -
238B ARG* 4.4 28.5 + - - -
240B HIS* 4.9 14.2 + - - -
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Residues in contact with ALA 205 (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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201A GLY 2.8 21.1 + - - +
202A ALA 3.7 3.1 - - - +
204A GLU* 1.3 74.9 - - - +
206A LEU* 1.3 62.9 + - - +
208A LEU* 3.0 17.8 + - - +
209A GLY 3.3 0.2 + - - -
210A ILE* 3.1 37.2 + - + +
215A GLY 5.0 0.7 - - - +
218A ILE* 4.8 10.1 - - + -
219A SER* 4.2 8.5 - - - -
341A PHE* 4.1 19.3 - - + -
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Residues in contact with LEU 206 (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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202A ALA 3.0 18.1 + - - +
203A LYS* 3.8 8.1 - - - +
205A ALA* 1.3 74.7 - - - +
207A ASP* 1.3 60.2 - - - +
209A GLY* 2.9 20.6 + - - -
210A ILE 3.6 17.4 - - - +
211A THR* 4.4 17.2 - - + +
339A GLU 5.2 0.2 - - - +
340A ASP* 3.4 39.0 - - - +
341A PHE* 3.8 14.4 - - + -
342A THR* 4.0 13.2 - - + +
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Residues in contact with ASP 207 (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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203A LYS* 3.1 21.9 + - - +
204A GLU* 3.2 11.8 + - - +
206A LEU* 1.3 78.1 - - - +
208A LEU* 1.3 64.3 + - + +
209A GLY 3.2 1.3 + - - -
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Residues in contact with LEU 208 (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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204A GLU* 3.0 37.2 + - + +
205A ALA* 3.0 10.7 + - - +
207A ASP* 1.3 80.5 - - + +
209A GLY* 1.3 58.6 + - - +
210A ILE* 3.3 12.2 + - + +
484B VAL* 3.5 33.7 - - + +
485B ARG* 6.1 0.2 - - - -
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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