Contacts of the helix formed by residues 187 - 202 (chain A) in PDB entry 1P4X
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 LYS 187 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A PHE* 5.7 10.3 - - + -
181A ILE* 5.0 1.3 - - - -
185A HIS 3.6 5.6 + - - +
186A HIS* 1.3 74.8 - - - +
188A TYR* 1.3 66.9 + - - +
189A PRO* 3.5 7.0 - - + -
190A GLN* 3.3 22.4 + - - +
191A THR* 2.8 25.0 + - - -
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Residues in contact with TYR 188 (chain A).
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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177A LEU* 4.6 8.4 - - + +
181A ILE* 3.4 39.8 - - + +
187A LYS* 1.3 73.8 - - - +
189A PRO* 1.3 79.5 - - + +
191A THR* 3.1 1.9 + - - -
192A VAL* 2.9 56.7 + - + +
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Residues in contact with PRO 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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187A LYS* 3.5 10.1 - - + -
188A TYR* 1.3 108.4 - - + +
190A GLN* 1.3 77.0 + - - +
192A VAL* 4.1 2.1 - - + +
193A ARG* 3.1 49.3 + - - +
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Residues in contact with GLN 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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159A VAL* 4.5 13.9 - - + +
186A HIS* 4.9 8.5 - - + +
187A LYS* 3.3 35.5 - - - +
189A PRO* 1.3 86.1 - - - +
191A THR* 1.3 58.3 + - - +
193A ARG* 3.5 28.3 + - - +
194A ALA* 3.0 29.7 + - - +
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Residues in contact with THR 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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159A VAL* 5.3 1.1 - - - -
163A ILE* 3.8 15.2 - - + +
177A LEU* 4.4 1.3 - - + -
180A LEU* 3.3 34.1 - - + -
181A ILE* 3.9 13.7 - - + +
184A ILE* 3.3 19.4 - - - +
186A HIS* 3.7 4.9 + - - +
187A LYS 2.8 24.5 + - - -
188A TYR* 3.5 7.0 - - - -
190A GLN* 1.3 74.5 - - - +
192A VAL* 1.3 60.7 + - - +
194A ALA* 3.1 4.7 + - - +
195A LEU* 2.9 35.7 + - + +
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Residues in contact with VAL 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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177A LEU* 4.4 19.3 - - + -
181A ILE* 4.8 0.7 - - + -
188A TYR* 2.9 63.8 + - + +
189A PRO* 4.1 2.9 - - + +
191A THR* 1.3 73.8 - - - +
193A ARG* 1.3 60.8 + - + +
195A LEU* 3.1 8.3 + - - +
196A ASN* 2.8 50.1 + - - +
206A LYS* 5.2 2.7 - - - +
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Residues in contact with ARG 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 PRO* 3.1 44.6 + - - +
190A GLN* 3.5 36.3 - - - +
192A VAL* 1.3 79.8 - - + +
194A ALA* 1.3 61.3 + - - +
196A ASN* 3.4 9.3 + - - +
197A ASN* 2.9 38.2 + - - +
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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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159A VAL* 4.2 6.3 - - + -
160A GLU* 3.7 31.9 - - + +
163A ILE* 3.5 21.1 - - + -
190A GLN 3.0 16.3 + - - +
191A THR 3.1 8.9 + - - +
193A ARG* 1.3 78.1 - - - +
195A LEU* 1.3 55.3 + - - +
197A ASN* 3.4 2.6 + - - +
198A LEU* 3.0 34.5 + - - +
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Residues in contact with LEU 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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163A ILE* 3.5 29.6 - - + -
177A LEU* 3.3 34.3 - - + -
180A LEU* 4.6 2.7 - - + -
191A THR* 2.9 23.0 + - + +
192A VAL* 3.1 8.7 + - - +
194A ALA* 1.3 75.4 - - - +
196A ASN* 1.3 60.5 + - - +
198A LEU* 3.1 3.7 + - + +
199A LYS* 2.8 32.7 + - - +
204A LEU* 4.2 14.0 - - + +
206A LYS* 4.6 17.2 - - + +
218A ILE* 3.4 36.8 - - + -
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Residues in contact with ASN 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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192A VAL* 2.8 41.1 + - - +
193A ARG* 3.8 9.1 - - - +
194A ALA 3.4 0.2 - - - -
195A LEU* 1.3 73.1 - - - +
197A ASN* 1.3 59.3 + - - +
199A LYS* 3.8 7.2 - - - +
200A LYS* 3.0 28.6 + - - +
206A LYS* 2.4 35.5 + - - -
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Residues in contact with ASN 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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156A LEU* 6.3 1.1 - - + -
160A GLU* 3.4 27.3 + - - +
193A ARG* 2.9 32.3 + - - +
194A ALA* 3.8 1.1 - - - +
196A ASN* 1.3 76.3 - - - +
198A LEU* 1.3 66.4 + - - +
200A LYS* 3.4 11.1 + - - +
201A GLN* 3.0 38.0 + - + +
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Residues in contact with LEU 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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156A LEU* 3.9 31.6 - - + -
160A GLU* 3.6 32.8 - - + +
163A ILE* 3.8 24.5 - - + -
164A LEU* 4.1 9.0 - - + +
194A ALA 3.0 25.5 + - - +
195A LEU* 3.1 5.6 + - - +
197A ASN* 1.3 78.0 - - - +
199A LYS* 1.3 62.1 + - - +
201A GLN* 3.5 0.4 + - - -
202A GLY 3.2 3.1 + - - -
203A TYR* 3.0 44.2 + - + +
204A LEU* 4.0 24.7 - - + -
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Residues in contact with LYS 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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195A LEU 2.8 20.3 + - - +
196A ASN* 3.8 6.3 - - - +
198A LEU* 1.3 73.5 - - - +
200A LYS* 1.3 57.4 + - - +
202A GLY* 2.7 26.9 + - - -
204A LEU* 3.6 22.1 - - + +
205A ILE* 5.3 0.7 - - - -
206A LYS* 3.2 54.2 + - + +
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Residues in contact with LYS 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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196A ASN 3.0 15.9 + - - +
197A ASN* 3.7 11.9 - - - +
199A LYS* 1.3 83.0 - - - +
201A GLN* 1.3 73.7 + - - +
202A GLY* 3.4 0.7 + - - -
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Residues in contact with GLN 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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155A THR* 4.5 12.4 + - - +
156A LEU* 4.3 13.4 - - - +
197A ASN* 3.0 24.2 + - + +
200A LYS* 1.3 91.9 - - - +
202A GLY* 1.3 57.8 - - - +
203A TYR* 3.0 40.1 + - + -
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Residues in contact with GLY 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 LEU 3.2 0.2 + - - -
199A LYS 2.7 15.8 + - - -
200A LYS 3.2 0.8 - - - -
201A GLN* 1.3 79.5 - - - +
203A TYR* 1.3 60.0 + - - +
204A LEU 3.3 3.1 - - - -
224A GLN* 3.0 27.2 + - - +
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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