Contacts of the helix formed by residues 190 - 206 (chain A) in PDB entry 5M7T
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 SER 190 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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180A MET* 3.7 15.0 - - - +
188A PHE* 3.3 3.3 - - - +
189A SER* 1.3 80.5 + - - +
191A PHE* 1.3 64.0 + - - +
192A ALA* 3.4 9.5 + - - +
193A HIS* 3.1 41.6 + - - +
194A ALA 3.3 9.0 + - - -
232A PRO 5.5 0.7 + - - -
233A TYR* 5.9 0.3 - - - -
236A THR* 4.5 3.3 + - - -
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Residues in contact with PHE 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A GLY 5.5 1.1 - - - -
145A PHE* 4.0 22.9 - + - -
176A ILE* 3.9 15.3 - - + -
177A ASP 3.4 27.1 - - - -
178A HIS* 3.6 39.9 - + + +
179A ASN 5.5 1.3 - - - -
180A MET* 3.5 33.0 - - + +
190A SER* 1.3 74.0 - - - +
192A ALA* 1.3 61.3 + - - +
194A ALA* 3.5 2.1 + - - +
195A GLN* 3.2 50.1 + - - +
217A THR* 3.7 12.8 - - + -
233A TYR* 4.5 8.7 - + + -
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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
----------------------------------------------------------
190A SER* 3.2 6.0 + - - +
191A PHE* 1.3 77.0 - - - +
193A HIS* 1.3 65.2 + - - +
194A ALA 3.2 0.2 - - - -
195A GLN* 3.3 4.1 + - - +
196A VAL* 2.9 28.5 + - - +
233A TYR* 3.6 50.8 - - + +
236A THR* 3.7 19.1 - - + +
237A VAL* 4.5 5.2 - - + -
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Residues in contact with HIS 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A PHE* 3.7 14.7 - - + -
189A SER* 3.2 26.4 + - - +
190A SER* 3.1 37.2 + - - +
192A ALA* 1.3 78.5 - - - +
194A ALA* 1.3 60.5 + - - +
196A VAL* 4.2 2.7 - - - +
197A SER* 3.2 24.1 + - - -
236A THR* 3.7 18.3 + - + +
240A LYS* 3.5 39.1 - - + +
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Residues in contact with ALA 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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145A PHE* 3.6 29.3 - - + -
180A MET* 4.0 17.5 - - - -
188A PHE* 3.5 33.1 - - + -
190A SER 3.3 2.8 + - - +
191A PHE 3.7 8.7 - - - +
192A ALA 3.2 0.6 - - - -
193A HIS* 1.3 77.6 - - - +
195A GLN* 1.3 65.3 + - - +
197A SER* 3.3 4.5 + - - -
198A ILE* 3.2 19.9 + - - +
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Residues in contact with GLN 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A PHE* 3.9 23.6 - - + -
173A PHE* 3.7 23.7 - - + +
191A PHE* 3.2 39.6 + - + +
192A ALA* 3.3 7.1 + - - +
194A ALA* 1.3 80.2 - - - +
196A VAL* 1.3 54.7 + - - +
198A ILE* 3.7 2.2 + - - +
199A THR* 2.6 38.5 + - - -
214A PHE* 3.5 21.3 - - + -
217A THR* 3.0 22.8 + - - -
233A TYR* 2.5 28.5 + - - -
237A VAL* 5.6 0.2 - - - +
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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
----------------------------------------------------------
192A ALA 2.9 20.7 + - - +
193A HIS* 4.3 3.8 - - - +
195A GLN* 1.3 73.9 - - - +
197A SER* 1.3 60.3 + - - +
199A THR* 4.4 4.7 - - - -
200A ASN* 2.9 49.0 + - - +
214A PHE* 4.8 3.8 - - + -
236A THR* 4.5 4.0 - - + +
237A VAL* 4.1 32.5 - - + +
240A LYS* 3.5 31.2 - - + +
241A LEU* 3.6 17.3 - - + +
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Residues in contact with SER 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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188A PHE* 3.4 28.4 - - - -
193A HIS 3.2 20.5 + - - -
194A ALA 3.4 3.1 - - - -
195A GLN 3.3 0.2 - - - -
196A VAL* 1.3 74.9 - - - +
198A ILE* 1.3 67.1 + - - +
200A ASN* 3.9 2.9 - - - +
201A GLU* 3.1 27.6 + - - +
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Residues in contact with ILE 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A PRO* 5.0 1.3 - - + -
143A ILE* 3.9 20.2 - - + -
145A PHE* 3.4 48.0 - - + +
151A VAL* 3.7 31.0 - - + -
154A LEU* 4.3 15.9 - - + -
171A LEU* 4.6 2.7 - - + -
173A PHE* 4.0 15.9 - - + -
188A PHE* 5.7 1.1 - - + -
194A ALA 3.2 5.6 + - - +
195A GLN 3.7 8.3 - - - +
197A SER* 1.3 78.9 - - - +
199A THR* 1.3 60.3 + - - +
201A GLU* 3.6 7.0 - - - +
202A ILE* 2.9 37.4 + - + +
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Residues in contact with THR 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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171A LEU* 3.5 20.5 - - + +
173A PHE* 3.7 2.8 - - - -
195A GLN 2.6 23.8 + - - -
196A VAL 4.0 2.5 - - - -
198A ILE* 1.3 76.1 - - - +
200A ASN* 1.3 64.0 + - - +
202A ILE* 3.3 2.1 + - - +
203A TYR* 3.0 23.0 + - - +
212A PHE* 3.9 23.7 - - + -
214A PHE* 3.5 36.6 - - + -
241A LEU* 3.9 15.0 - - + -
245A ILE* 4.2 6.1 - - + -
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Residues in contact with ASN 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A VAL* 2.9 31.4 + - - +
197A SER* 4.0 2.9 - - - +
199A THR* 1.3 74.1 - - - +
201A GLU* 1.3 62.2 + - - +
203A TYR* 3.6 6.1 - - - +
204A GLN* 3.1 31.5 + - - +
240A LYS 2.9 27.1 + - - -
241A LEU* 3.8 2.8 - - - +
242A LEU* 2.9 42.1 + - + +
245A ILE* 3.3 12.8 - - - +
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Residues in contact with GLU 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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151A VAL* 3.4 20.0 - - + +
155A LYS* 3.1 29.4 + - - +
197A SER* 3.1 21.6 + - - +
198A ILE* 3.6 8.0 - - - +
200A ASN* 1.3 75.5 - - - +
202A ILE* 1.3 61.5 + - + +
204A GLN* 3.2 10.0 + - - +
205A TYR* 2.9 28.5 + - + +
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Residues in contact with ILE 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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151A VAL* 4.5 6.1 - - + +
154A LEU* 3.7 35.4 - - + -
155A LYS* 3.6 36.6 - - + +
158A LEU* 3.5 24.9 - - + -
171A LEU* 4.4 6.5 - - + -
198A ILE* 2.9 23.7 + - + +
199A THR 3.9 3.4 - - - +
201A GLU* 1.3 75.3 - - + +
203A TYR* 1.3 62.4 + - - +
205A TYR* 3.3 5.0 + - + +
206A LEU* 3.0 38.1 + - + +
212A PHE* 4.0 13.0 - - + -
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Residues in contact with TYR 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 THR 3.0 18.2 + - - +
200A ASN 3.6 3.1 - - - +
202A ILE* 1.3 77.7 - - - +
204A GLN* 1.3 60.2 + - + +
206A LEU 3.6 0.2 + - - -
207A GLY 3.6 1.2 + - - -
208A GLU* 2.9 74.5 + - + +
209A PRO* 3.5 25.8 + - + +
212A PHE* 3.7 37.8 - + + -
242A LEU* 4.3 23.6 - - + -
244A GLY* 3.6 30.4 + - - -
245A ILE* 3.9 24.2 - - + -
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Residues in contact with GLN 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 ASN* 3.1 21.5 + - - +
201A GLU* 3.2 6.7 + - - +
203A TYR* 1.3 75.3 - - + +
205A TYR* 1.3 61.5 + - - +
207A GLY* 2.9 21.7 + - - -
208A GLU* 3.9 28.3 + - + +
242A LEU* 4.0 22.8 - - + +
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Residues in contact with TYR 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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155A LYS* 3.7 58.4 - - + +
159A ASP* 2.6 32.2 + - + -
201A GLU* 2.9 17.7 + - + +
202A ILE* 3.3 5.8 + - + +
204A GLN* 1.3 77.0 - - - +
206A LEU* 1.3 75.5 + - + +
207A GLY 3.2 3.8 + - - -
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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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158A LEU* 4.4 26.7 - - + +
159A ASP* 4.8 2.7 - - + +
162A SER* 4.7 8.3 - - - +
169A PHE* 3.8 38.1 - - + -
202A ILE* 3.0 37.2 + - + +
203A TYR 3.6 0.2 + - - -
204A GLN 3.2 0.4 - - - -
205A TYR* 1.3 93.4 - - + +
207A GLY* 1.3 61.1 + - - +
208A GLU 3.5 1.3 - - - -
209A PRO* 3.6 20.8 - - + +
212A PHE* 3.9 8.3 - - + -
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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
------------------------------------------------------------
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