Contacts of the helix formed by residues 237 - 251 (chain p) in PDB entry 6QXT
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 237 (chain p).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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235p HIS 4.0 0.4 + - - -
236p ASN* 1.3 78.3 - - - +
238p PHE* 1.3 61.7 + - - +
239p VAL* 3.1 9.0 + - + +
240p LYS* 3.2 10.0 + - + +
241p ILE* 2.9 24.4 + - - +
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Residues in contact with PHE 238 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172p ASP* 4.4 24.1 - - + +
176p ALA* 6.4 1.6 - - + -
236p ASN 3.9 0.4 + - - -
237p ASN* 1.3 73.2 - - - +
239p VAL* 1.3 57.5 + - - +
241p ILE* 3.5 9.1 + - - +
242p LYS* 2.9 27.9 + - - +
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Residues in contact with VAL 239 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237p ASN* 3.1 6.7 - - + +
238p PHE* 1.3 75.1 - - - +
240p LYS* 1.3 60.4 + - - +
242p LYS* 3.1 8.5 + - - +
243p LYS* 2.9 27.0 + - - +
110q TYR* 6.0 0.7 - - - +
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Residues in contact with LYS 240 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233p ASN* 5.3 1.3 - - - +
236p ASN* 4.1 16.8 - - + -
237p ASN* 3.2 13.3 + - + +
239p VAL* 1.3 78.2 - - - +
241p ILE* 1.3 56.3 + - - +
243p LYS* 3.3 8.2 + - - +
244p GLU* 2.9 28.9 + - - +
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Residues in contact with ILE 241 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176p ALA* 4.9 17.8 - - + +
230p VAL* 6.3 2.5 - - - -
233p ASN* 4.4 26.9 - - + +
234p ARG* 6.2 0.2 - - - -
236p ASN* 4.9 1.7 - - - +
237p ASN 2.9 17.0 + - - +
238p PHE* 3.7 10.3 - - - +
240p LYS* 1.3 76.3 - - - +
242p LYS* 1.3 58.3 + - - +
244p GLU* 3.5 2.6 + - - +
245p LEU* 2.9 28.2 + - - +
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Residues in contact with LYS 242 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176p ALA* 6.1 0.6 - - - +
238p PHE 2.9 18.5 + - - +
239p VAL* 3.1 8.0 + - - +
241p ILE* 1.3 75.8 - - - +
243p LYS* 1.3 59.1 + - - +
245p LEU* 3.2 8.7 + - - +
246p PHE* 2.9 26.0 + - - +
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Residues in contact with LYS 243 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239p VAL 2.9 12.4 + - - +
240p LYS* 3.3 11.6 + - - +
242p LYS* 1.3 77.0 - - - +
244p GLU* 1.3 56.5 + - - +
246p PHE* 3.0 10.7 + - - +
247p SER* 2.9 25.6 + - - -
110q TYR* 4.9 19.1 - - + +
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Residues in contact with GLU 244 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229p ILE* 4.9 17.6 - - + +
233p ASN* 4.8 12.6 - - + -
240p LYS 2.9 16.7 + - - +
241p ILE* 3.8 7.9 - - - +
243p LYS* 1.3 76.1 - - - +
245p LEU* 1.3 61.2 + - - +
247p SER* 3.2 22.0 + - - -
248p ILE* 3.7 4.9 + - - +
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Residues in contact with LEU 245 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176p ALA 6.1 0.9 - - - +
180p GLY* 5.7 9.0 - - - -
229p ILE* 5.5 4.7 - - - +
241p ILE 2.9 18.1 + - - +
242p LYS* 3.4 9.6 - - - +
243p LYS 3.2 0.4 - - - -
244p GLU* 1.3 76.5 - - - +
246p PHE* 1.3 61.0 + - - +
248p ILE* 3.4 20.6 + - - +
249p PHE 4.6 0.5 + - - -
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Residues in contact with PHE 246 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242p LYS 2.9 13.0 + - - +
243p LYS* 3.0 13.6 + - - +
245p LEU* 1.3 71.4 - - - +
247p SER* 1.3 59.9 + - - +
248p ILE 3.1 6.3 + - - -
249p PHE* 3.5 18.0 + - - +
250p SER 4.2 1.4 + - - -
103q LEU* 4.9 9.2 - - - +
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Residues in contact with SER 247 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243p LYS 2.9 11.2 + - - -
244p GLU* 3.2 17.4 + - - -
246p PHE* 1.3 74.0 - - - +
248p ILE* 1.3 58.8 + - - +
249p PHE 3.2 0.4 - - - -
250p SER* 3.2 12.1 + - - +
251p GLU* 3.0 27.8 + - - +
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Residues in contact with ILE 248 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244p GLU 3.7 4.6 + - - +
245p LEU* 3.4 16.7 + - - +
246p PHE 3.1 0.6 - - - -
247p SER* 1.3 79.5 - - - +
249p PHE* 1.3 61.3 + - - +
251p GLU* 3.2 23.6 + - - +
262p LEU* 4.5 9.9 - - - +
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Residues in contact with PHE 249 (chain p).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6p THR* 4.9 17.5 - - - -
245p LEU 4.6 0.4 + - - -
246p PHE 3.5 12.1 + - - +
247p SER 3.2 0.8 - - - -
248p ILE* 1.3 79.5 - - - +
250p SER* 1.3 59.0 + - - +
251p GLU 3.8 4.0 - - - +
261p TYR* 5.4 6.9 - - - +
262p LEU* 5.3 8.2 + - - +
102q ARG* 4.4 9.3 - - + +
103q LEU* 5.6 4.9 - - + -
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Residues in contact with SER 250 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246p PHE 4.2 1.5 + - - -
247p SER* 3.2 15.2 + - - -
249p PHE* 1.3 79.4 - - - +
251p GLU* 1.3 64.9 + - - +
252p THR* 3.8 1.7 + - - -
102q ARG* 4.0 22.9 - - - +
103q LEU* 5.1 9.3 - - - +
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Residues in contact with GLU 251 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247p SER 3.0 16.8 + - - +
248p ILE* 3.2 20.1 + - - +
249p PHE 3.8 4.9 - - - +
250p SER* 1.3 80.3 - - - +
252p THR* 1.3 63.4 + - - +
253p TYR 4.5 0.2 + - - -
261p TYR* 4.8 1.9 - - - +
262p LEU* 4.5 9.5 + - - +
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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