Contacts of the helix formed by residues 176 - 196 (chain A) in PDB entry 6XPD
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 THR 176 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A GLN* 2.4 42.5 + - - +
175A ALA* 1.3 73.0 - - + +
177A VAL* 1.3 63.2 + - - +
178A MET 3.0 1.3 - - - -
179A ILE* 2.9 29.2 + - + +
180A ILE* 3.6 5.2 + - - +
239A TYR* 3.5 34.5 - - + -
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Residues in contact with VAL 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A ALA* 5.9 7.6 - - + -
173A ILE* 5.4 5.8 - - + -
174A GLN* 2.6 39.7 + - + +
176A THR* 1.3 77.1 + - - +
178A MET* 1.3 63.2 + - - +
179A ILE 3.1 0.9 + - - -
180A ILE* 3.2 23.6 - - + +
181A VAL* 3.1 16.2 - - + +
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Residues in contact with MET 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A ALA 5.6 4.5 - - - +
173A ILE* 3.7 34.3 - - + -
174A GLN 3.2 20.7 + - - +
175A ALA* 4.1 11.0 - - - +
176A THR 3.0 0.6 - - - -
177A VAL* 1.3 78.4 - - - +
179A ILE* 1.3 57.8 + - - +
181A VAL* 3.1 24.5 - - + +
182A SER* 3.5 11.6 + - - -
231A VAL* 5.2 19.8 - - + +
235A ALA* 4.4 13.3 - - + +
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Residues in contact with ILE 179 (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 ALA 3.3 25.8 - - - +
176A THR* 2.9 11.6 + - - +
178A MET* 1.3 77.1 - - - +
180A ILE* 1.3 53.9 + - - +
181A VAL 3.2 1.3 - - - -
182A SER* 2.5 38.9 + - - +
183A SER* 2.7 13.0 + - - -
232A LEU* 4.6 11.2 - - + -
235A ALA* 3.7 17.3 - - + -
236A LEU* 3.5 36.8 - - + +
239A TYR* 4.4 12.1 - - + -
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Residues in contact with ILE 180 (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 THR 3.6 2.8 + - - +
177A VAL* 3.2 34.8 - - + +
179A ILE* 1.3 76.6 - - - +
181A VAL* 1.3 61.8 + - + +
183A SER* 3.1 26.7 + - - +
184A CYS* 3.4 9.0 + - - +
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Residues in contact with VAL 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A ALA* 4.3 10.5 - - + +
100A VAL* 3.6 31.0 - - + -
103A ASP* 4.3 21.4 - - + +
177A VAL* 3.1 20.6 - - + +
178A MET* 3.1 32.1 - - + +
180A ILE* 1.3 81.7 - - + +
182A SER* 1.3 57.9 + - - +
184A CYS* 3.0 27.3 - - - -
185A ALA* 3.5 7.3 + - - +
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Residues in contact with SER 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A MET 3.6 11.2 - - - -
179A ILE* 2.5 26.8 + - - -
181A VAL* 1.3 76.2 - - - +
183A SER* 1.3 58.0 + - - -
185A ALA* 3.1 8.6 + - - +
186A VAL* 2.8 32.5 + - - +
228A SER* 4.2 0.4 + - - -
231A VAL* 3.8 27.6 - - - -
232A LEU* 3.2 31.4 - - - +
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Residues in contact with SER 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A ILE* 2.7 17.4 + - - -
180A ILE* 3.1 18.5 + - - +
182A SER* 1.3 75.0 + - - +
184A CYS* 1.3 62.3 + - - +
186A VAL* 3.1 5.2 + - - +
187A ALA* 2.6 36.2 + - - +
232A LEU* 4.2 13.5 - - - -
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Residues in contact with CYS 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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88A GLU* 2.9 41.1 - - - +
100A VAL* 6.2 0.9 - - - -
103A ASP* 4.6 5.4 - - - -
180A ILE 3.4 6.0 + - - +
181A VAL* 3.0 26.5 - - - -
183A SER* 1.3 82.3 + - - +
185A ALA* 1.3 70.0 + - - +
187A ALA* 2.9 7.8 + - - -
188A ALA* 2.3 41.6 + - + +
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Residues in contact with ALA 185 (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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103A ASP* 3.2 31.0 - - - +
107A LEU* 6.5 1.6 - - - -
181A VAL 3.6 9.4 - - - +
182A SER* 3.1 11.6 + - - +
184A CYS* 1.3 82.0 - - - +
186A VAL* 1.3 57.6 + - - +
188A ALA* 4.1 5.3 - - - +
189A ASN* 3.0 30.4 + - - +
228A SER* 2.9 20.6 + - - +
231A VAL* 6.2 1.1 - - + -
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Residues in contact with VAL 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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182A SER 2.8 22.7 + - - +
183A SER* 3.4 8.3 - - - +
185A ALA* 1.3 71.0 - - - +
187A ALA* 1.3 54.9 + - - +
189A ASN* 3.2 4.1 + - - +
190A ILE* 2.7 42.8 + - + +
225A LEU* 4.1 7.4 - - + +
228A SER* 3.5 15.5 - - - +
229A ILE* 3.5 44.0 - - + +
232A LEU* 4.4 13.0 - - + -
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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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183A SER 2.6 21.8 + - - +
184A CYS* 3.5 7.4 - - - +
186A VAL* 1.3 73.3 - - - +
188A ALA* 1.3 63.3 + - - +
190A ILE* 3.0 11.9 + - - +
191A VAL* 2.9 29.6 + - + +
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Residues in contact with ALA 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A PHE* 4.1 39.5 - - + -
88A GLU* 5.4 4.3 - - - +
107A LEU* 5.2 12.6 - - + -
184A CYS* 2.3 32.9 + - + +
185A ALA* 4.1 5.2 - - - +
187A ALA* 1.3 67.9 - - - +
189A ASN* 1.3 54.6 + - - +
191A VAL* 3.1 5.7 + - - +
192A LEU* 2.7 38.6 + - + +
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Residues in contact with ASN 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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107A LEU* 4.4 8.0 - - - +
110A ASN* 3.9 15.1 + - - -
185A ALA* 3.0 19.2 + - - +
186A VAL* 3.6 3.1 - - - +
188A ALA* 1.3 73.8 - - - +
190A ILE* 1.3 67.6 + - - +
192A LEU* 3.8 11.6 - - - +
193A THR* 2.8 31.5 + - - +
221A ALA 4.9 1.8 - - - +
224A ASN* 3.0 45.1 + - - +
225A LEU* 4.1 17.3 - - + -
228A SER* 3.3 12.3 + - - -
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Residues in contact with ILE 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* 2.7 32.9 + - + +
187A ALA* 3.0 13.9 + - - +
189A ASN* 1.3 73.2 - - - +
191A VAL* 1.3 67.3 + - + +
193A THR* 3.8 2.8 - - - -
194A VAL* 3.1 40.9 + - + +
225A LEU* 4.3 22.2 - - + +
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Residues in contact with VAL 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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80A ILE* 4.8 17.5 - - + -
84A PHE* 4.6 14.4 - - + -
187A ALA* 2.9 18.5 + - + +
188A ALA* 3.6 6.5 - - - +
190A ILE* 1.3 79.2 - - + +
192A LEU* 1.3 65.6 + - - +
193A THR 3.0 0.9 + - - -
194A VAL* 3.2 15.0 + - + +
195A VAL* 3.1 33.4 - - + +
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Residues in contact with LEU 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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77A ALA* 3.5 31.9 - - + +
80A ILE* 4.4 11.7 - - + -
81A CYS* 3.8 26.7 - - + +
84A PHE* 5.2 3.6 - - + -
107A LEU* 4.0 22.4 - - + -
110A ASN* 4.5 6.3 - - - +
114A PHE* 3.8 22.2 - - + -
188A ALA* 2.7 21.5 + - + +
189A ASN* 3.2 14.6 + - - +
191A VAL* 1.3 74.1 - - - +
193A THR* 1.3 57.8 + - - +
195A VAL* 4.2 4.0 + - + +
196A LEU* 3.2 31.5 + - - +
221A ALA* 4.4 7.9 - - + -
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Residues in contact with THR 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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189A ASN 2.8 18.6 + - - -
190A ILE* 3.8 5.8 - - - +
192A LEU* 1.3 76.2 - - - +
194A VAL* 1.3 64.1 + - + +
195A VAL 3.0 4.3 - - - -
196A LEU* 2.8 22.8 + - - +
197A HIS* 3.1 9.3 + - + -
218A PHE* 3.5 26.9 - - + -
221A ALA* 3.7 10.6 + - - +
222A LEU* 3.5 33.7 + - + -
225A LEU* 4.6 9.0 - - + +
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Residues in contact with VAL 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 ILE* 3.1 31.8 + - + +
191A VAL* 3.2 20.9 - - + +
193A THR* 1.3 80.6 - - + +
195A VAL* 1.3 63.6 + - + +
197A HIS* 3.6 20.0 - - - +
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Residues in contact with VAL 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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73A LYS* 3.3 27.3 - - + +
76A SER* 3.9 21.5 - - - +
77A ALA* 4.6 13.0 - - + +
80A ILE* 4.4 19.3 - - + -
191A VAL* 3.1 23.3 - - + +
192A LEU* 4.5 6.1 - - + +
193A THR 3.0 0.6 - - - -
194A VAL* 1.3 84.5 - - + +
196A LEU* 1.3 59.9 + - + +
197A HIS 3.2 6.0 + - - +
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Residues in contact with LEU 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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73A LYS* 3.3 26.7 - - - +
74A LEU* 4.5 11.9 - - + -
77A ALA* 3.6 15.9 - - + -
114A PHE* 3.6 23.6 - - + -
192A LEU 3.2 20.0 - - - +
193A THR* 2.8 9.4 + - - +
195A VAL* 1.3 76.6 - - - +
197A HIS* 1.3 57.3 + - - +
198A GLN* 3.0 9.5 + - - +
214A VAL* 4.3 17.7 - - + +
217A ALA* 3.6 25.1 - - + +
218A PHE* 3.2 31.7 - - + +
221A ALA* 3.7 5.2 - - + -
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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
------------------------------------------------------------
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