Contacts of the helix formed by residues 209 - 220 (chain A) in PDB entry 4P4J
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 PHE 209 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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208A VAL* 1.3 75.0 - - - +
210A ARG* 1.3 89.7 + - - +
211A GLY* 3.3 18.4 - - - -
212A ASN* 3.0 37.5 + - - +
213A LYS 3.4 6.9 + - - -
257A ASN* 3.8 26.7 - - - -
259A LEU 3.4 21.8 - - - -
260A ASN* 5.3 1.3 - - - -
698A ASN* 2.9 13.0 + - - +
699A LYS* 3.6 32.5 - - + -
700A TYR* 3.5 34.8 - + + -
818A 2H9 4.0 29.2 - - + -
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Residues in contact with ARG 210 (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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205A TYR* 3.6 34.0 + - + -
208A VAL 3.5 2.6 + - - -
209A PHE* 1.3 83.2 - - + +
211A GLY* 1.3 62.1 + - - +
213A LYS* 3.2 17.3 + - + +
214A VAL* 3.2 25.0 + - - +
227A LEU* 4.3 7.8 - - + +
254A GLN* 3.0 28.1 + - - -
256A GLY* 3.6 26.1 - - - -
257A ASN 3.1 37.0 + - - +
258A ILE* 3.9 9.9 - - + -
552A TYR* 3.2 25.3 + - - -
553A HIS* 3.4 11.7 + - - -
700A TYR* 3.8 7.5 + - - -
818A 2H9 2.7 21.4 + - - -
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Residues in contact with GLY 211 (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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209A PHE* 3.2 21.4 + - - -
210A ARG* 1.3 82.9 - - - +
212A ASN* 1.3 54.5 - - - +
214A VAL* 3.3 1.9 + - - +
215A LYS 3.0 16.8 + - - -
258A ILE* 3.9 15.5 - - - -
259A LEU 3.7 10.3 - - - -
260A ASN* 2.9 24.1 + - - -
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Residues in contact with ASN 212 (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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208A VAL* 4.5 3.4 - - + -
209A PHE* 3.0 23.7 + - - +
211A GLY* 1.3 73.9 - - - +
213A LYS* 1.3 58.4 + - - +
215A LYS* 3.6 7.3 - - - +
216A ASN* 2.9 43.0 + - - +
260A ASN* 4.1 11.2 + - - -
695A SER 4.5 0.8 + - - -
696A SER* 3.2 26.3 + - - +
697A HIS* 3.5 26.2 - - - +
698A ASN* 3.5 3.9 - - - +
699A LYS* 2.9 24.7 + - - +
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Residues in contact with LYS 213 (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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179A TYR* 2.7 32.2 + - - +
180A ALA* 3.7 24.8 - - + +
203A ALA* 4.9 0.7 - - + -
204A ARG 2.8 24.2 + - - +
205A TYR* 3.9 8.1 - - - +
206A GLY 2.8 28.4 + - - +
208A VAL* 3.5 31.1 - - + +
209A PHE 3.9 3.4 - - - +
210A ARG* 3.2 15.4 + - + +
212A ASN* 1.3 76.1 - - - +
214A VAL* 1.3 59.3 + - + +
216A ASN* 3.3 3.1 + - - +
217A ALA* 2.9 29.4 + - - +
225A VAL* 5.7 1.6 - - + -
227A LEU* 4.0 26.2 - - + -
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Residues in contact with VAL 214 (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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210A ARG 3.2 12.2 + - - +
211A GLY 3.7 6.7 - - - +
212A ASN 3.3 0.2 - - - -
213A LYS* 1.3 74.2 - - + +
215A LYS* 1.3 61.5 + - - +
217A ALA* 3.2 6.1 + - - +
218A GLN* 2.9 50.2 + - + +
225A VAL* 4.6 12.1 - - + -
227A LEU* 4.8 3.8 - - + -
258A ILE* 3.9 29.2 - - + +
260A ASN* 5.4 1.3 - - - +
290A PRO* 3.9 17.3 - - + -
292A ILE* 4.8 1.1 - - + +
294A VAL* 3.9 29.4 - - + -
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Residues in contact with LYS 215 (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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211A GLY 3.0 14.0 + - - +
212A ASN* 3.3 14.3 + - - +
214A VAL* 1.3 76.1 - - - +
216A ASN* 1.3 65.5 + - - +
218A GLN* 3.5 12.9 - - - +
219A LEU* 3.0 53.8 + - + +
260A ASN* 3.7 28.9 - - + +
696A SER* 4.5 14.5 + - - +
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Residues in contact with ASN 216 (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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180A ALA 2.9 20.2 + - - +
181A ARG* 3.6 1.8 - - - +
182A THR* 3.3 33.4 + - - +
185A PHE* 3.6 24.7 - - + -
208A VAL* 5.7 0.6 - - - +
212A ASN* 2.9 30.8 + - - +
213A LYS 3.6 0.4 - - - +
215A LYS* 1.3 90.1 + - - +
217A ALA* 1.3 61.2 + - - +
219A LEU* 3.5 8.6 + - - +
220A ALA* 3.1 22.9 + - - +
697A HIS* 5.0 4.8 + - - +
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Residues in contact with ALA 217 (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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180A ALA* 5.6 0.9 - - + -
185A PHE* 3.7 15.8 - - + -
201A VAL* 3.6 19.3 - - + -
213A LYS 2.9 17.2 + - - +
214A VAL 3.7 1.6 - - - +
216A ASN* 1.3 76.5 - - - +
218A GLN* 1.3 63.3 + - - +
220A ALA* 3.1 8.7 + - - +
221A GLY 3.3 0.2 + - - -
222A ALA* 3.1 26.5 + - + +
225A VAL* 3.6 31.0 - - + -
292A ILE* 4.5 0.2 - - - -
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Residues in contact with GLN 218 (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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214A VAL* 2.9 24.9 + - - +
215A LYS* 3.5 11.3 + - - +
217A ALA* 1.3 77.0 - - - +
219A LEU* 1.3 61.5 + - + +
221A GLY* 3.0 19.9 + - - -
222A ALA 4.7 2.6 - - - +
260A ASN* 6.1 0.6 - - - +
289A LEU 5.0 2.2 + - - -
290A PRO* 3.0 18.8 - - - +
291A SER* 2.7 49.1 + - - +
292A ILE* 3.6 23.8 + - + -
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Residues in contact with LEU 219 (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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215A LYS* 3.0 49.5 + - + +
216A ASN* 4.0 8.3 - - - +
218A GLN* 1.3 81.1 - - + +
220A ALA* 1.3 58.7 + - - +
221A GLY 3.1 1.1 + - - -
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Residues in contact with ALA 220 (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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185A PHE* 3.7 30.1 - - + -
189A GLU* 6.2 0.2 - - - -
195A ASN* 4.6 1.4 - - - +
196A CYS* 3.7 13.8 + - + +
197A SER* 3.6 18.5 + - - -
216A ASN 3.1 13.5 + - - +
217A ALA 3.1 10.0 + - - +
219A LEU* 1.3 75.4 - - - +
221A GLY* 1.3 60.0 + - - +
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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