Contacts of the helix formed by residues 180 - 195 (chain w) in PDB entry 5XTD
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 ARG 180 (chain w).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124w ASN* 3.8 28.9 + - - +
174w TYR* 4.5 0.4 - - - -
179w ILE* 1.3 81.9 - - - +
181w LYS* 1.3 68.2 + - + +
182w GLN* 2.9 46.7 + - + +
183w CYS* 3.3 18.4 - - + +
184w VAL* 3.5 10.4 + - - +
315w PRO* 5.9 2.2 - - - -
316w GLU* 3.9 14.7 + - - +
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Residues in contact with LYS 181 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174w TYR* 4.1 31.0 - - + +
179w ILE 4.0 0.2 + - - -
180w ARG* 1.3 73.1 - - + +
182w GLN* 1.3 59.3 + - - +
183w CYS 3.1 1.8 - - - -
184w VAL* 2.7 41.2 + - + +
185w ASP* 3.0 35.4 + - - +
188w ASN* 4.8 4.6 - - - +
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Residues in contact with GLN 182 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180w ARG* 2.9 44.8 + - - +
181w LYS* 1.3 79.2 - - - +
183w CYS* 1.3 64.0 + - + +
185w ASP* 3.0 18.7 + - + +
186w HIS* 3.0 22.0 + - - +
314w LEU* 4.6 8.9 - - + +
315w PRO* 4.3 23.4 - - - +
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Residues in contact with CYS 183 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129w TYR* 3.2 40.2 + - - -
170w LEU* 5.5 0.9 - - - -
179w ILE* 3.6 13.9 - - + -
180w ARG* 3.3 15.7 + - + +
182w GLN* 1.3 85.6 - - + +
184w VAL* 1.3 57.2 + - - +
186w HIS* 3.1 5.2 + - - +
187w TYR* 3.0 24.8 + - - +
314w LEU* 4.0 13.0 - - + -
316w GLU* 3.1 32.1 - - - +
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Residues in contact with VAL 184 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170w LEU* 3.6 30.3 - - + -
171w GLU* 5.3 5.8 - - - +
174w TYR* 4.0 25.1 - - + -
179w ILE* 4.2 5.8 - - + -
180w ARG 3.5 15.0 + - - +
181w LYS* 2.7 27.3 + - + +
183w CYS* 1.3 70.6 - - - +
185w ASP* 1.3 58.8 + - - +
187w TYR* 3.2 8.0 + - + +
188w ASN* 2.9 50.5 + - - +
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Residues in contact with ASP 185 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181w LYS* 3.0 45.0 + - - +
182w GLN* 3.0 19.8 + - + +
184w VAL* 1.3 77.7 - - - +
186w HIS* 1.3 56.6 + - - +
188w ASN* 3.1 14.0 + - - +
189w GLU* 3.0 34.0 + - + +
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Residues in contact with HIS 186 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308i SER* 5.8 2.4 - - - -
310i ASN* 5.5 4.6 + - - -
129w TYR* 3.0 30.1 + + - -
133w SER* 5.4 0.2 + - - -
182w GLN 3.0 8.8 + - - +
183w CYS 3.1 3.1 + - - +
185w ASP* 1.3 73.9 - - - +
187w TYR* 1.3 63.8 + - - +
189w GLU* 3.1 7.4 + - - +
190w VAL* 3.0 44.3 + - + +
308w THR 5.5 1.6 + - - -
310w ILE* 3.6 15.0 + - + +
312w ILE* 3.3 51.6 - - + +
314w LEU* 3.4 34.8 - - + -
317w VAL* 4.9 8.1 - - + +
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Residues in contact with TYR 187 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129w TYR* 3.9 19.5 + + - +
132w GLN* 4.6 7.7 + - + -
133w SER* 4.5 3.6 - - - -
136w TYR* 2.9 50.1 - + + -
163w ILE 4.8 0.3 + - - -
166w ASP* 3.7 18.4 + - - +
167w PHE* 3.9 22.7 + - + +
170w LEU* 3.5 38.8 - - + -
183w CYS 3.0 12.6 + - - +
184w VAL* 3.2 8.7 + - - +
186w HIS* 1.3 76.9 - - - +
188w ASN* 1.3 60.9 + - - +
190w VAL* 3.4 6.2 + - + +
191w LYS* 3.0 56.3 + - + +
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Residues in contact with ASN 188 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181w LYS* 4.8 4.6 - - - +
184w VAL* 2.9 40.6 + - - +
185w ASP* 3.1 18.3 + - - +
187w TYR* 1.3 80.1 - - - +
189w GLU* 1.3 58.5 + - + +
191w LYS* 3.2 32.8 + - - +
192w SER* 2.9 29.9 + - - -
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Residues in contact with GLU 189 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66Q TRP* 5.2 5.6 + - + -
185w ASP* 3.0 19.5 + - - +
186w HIS* 3.1 9.7 + - - +
188w ASN* 1.3 75.5 - - + +
190w VAL* 1.3 65.4 + - - +
192w SER* 2.3 27.3 + - - +
193w VAL* 3.0 14.4 + - + +
310w ILE* 5.1 4.7 - - + +
312w ILE* 3.2 35.5 - - + +
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Residues in contact with VAL 190 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310i ASN* 5.7 1.6 - - - +
129w TYR* 5.0 1.6 - - - +
133w SER* 5.9 0.9 - - - +
136w TYR* 4.1 21.8 - - + -
186w HIS* 3.0 33.2 + - + +
187w TYR* 3.8 7.6 - - + +
189w GLU* 1.3 76.9 - - - +
191w LYS* 1.3 61.1 + - - +
193w VAL* 3.2 6.8 + - - +
194w THR* 2.8 29.3 + - + +
307w TYR 4.5 1.8 - - - +
308w THR* 4.0 30.3 - - - +
310w ILE* 3.6 28.7 - - + -
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Residues in contact with LYS 191 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136w TYR* 3.3 31.0 - - + +
167w PHE* 4.3 23.4 - - + +
187w TYR* 3.0 33.0 + - + +
188w ASN* 3.2 37.1 + - - +
190w VAL* 1.3 78.3 - - - +
192w SER* 1.3 67.4 + - - +
195w ILE* 2.9 38.7 + - + +
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Residues in contact with SER 192 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70Q ASP* 4.5 13.2 - - - +
188w ASN 2.9 15.7 + - - -
189w GLU* 2.3 32.3 + - - +
191w LYS* 1.3 79.2 - - - +
193w VAL* 1.3 61.8 + - - +
195w ILE* 5.5 0.4 - - - -
196w CYS* 3.2 29.1 - - - -
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Residues in contact with VAL 193 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66Q TRP* 4.4 28.7 - - + +
67Q ASN* 3.2 36.8 + - + +
189w GLU* 3.0 15.3 + - + +
190w VAL* 3.7 6.7 - - - +
192w SER* 1.3 87.5 + - - +
194w THR* 1.3 60.2 + - - +
195w ILE 3.9 0.2 + - - -
196w CYS* 4.2 9.2 + - - +
197w ASP* 4.7 6.4 - - - +
307w TYR* 3.5 33.5 - - + +
310w ILE* 4.9 5.8 - - + -
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Residues in contact with THR 194 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136w TYR* 2.9 26.9 + - + -
140w LEU* 4.3 26.5 - - + +
190w VAL* 2.8 24.1 + - + +
191w LYS* 3.2 0.4 + - - -
193w VAL* 1.3 76.5 - - - +
195w ILE* 1.3 63.5 + - - +
196w CYS 3.3 3.0 + - - -
197w ASP* 3.9 10.0 + - - +
198w TYR* 3.9 17.8 - - - -
304w VAL 5.0 2.7 - - - +
307w TYR* 3.6 31.6 - - + -
308w THR* 4.2 10.1 - - - +
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Residues in contact with ILE 195 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136w TYR* 3.1 25.1 - - + +
140w LEU* 5.6 4.3 - - + -
143w TYR* 5.4 1.6 - - + -
163w ILE* 3.5 30.1 - - + +
164w PHE* 3.5 26.2 - - + -
191w LYS* 2.9 28.8 + - + +
192w SER* 5.5 0.2 - - - -
194w THR* 1.3 77.7 - - - +
196w CYS* 1.3 66.4 + - - +
197w ASP 3.2 1.0 + - - -
198w TYR* 3.4 22.4 + - - +
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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