Contacts of the helix formed by residues 208 - 222 (chain A) in PDB entry 4X4W
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 SER 208 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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206A GLY 4.0 1.8 + - - -
207A ILE* 1.3 77.0 - - - +
209A GLY* 1.3 65.3 - - - +
210A GLU* 3.7 15.4 + - - +
211A ARG* 3.3 32.6 + - - +
212A ILE* 3.2 19.1 + - - +
286A ARG* 4.7 0.4 - - - +
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Residues in contact with GLY 209 (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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207A ILE 3.6 1.6 + - - -
208A SER* 1.3 73.0 - - - +
210A GLU* 1.3 59.1 + - - +
212A ILE* 3.4 1.0 + - - -
213A TRP* 2.9 31.4 + - - +
286A ARG* 3.3 33.9 + - - +
287A LEU* 3.6 21.2 - - - +
288A LYS* 5.0 1.9 - - - +
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Residues in contact with GLU 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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208A SER* 3.7 18.4 - - - +
209A GLY* 1.3 79.2 + - - +
211A ARG* 1.3 62.9 + - + +
213A TRP* 3.3 4.4 + - - +
214A VAL* 3.2 28.5 + - - +
287A LEU 4.1 4.7 + - - +
288A LYS* 3.9 36.9 + - + +
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Residues in contact with ARG 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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168A ASP* 2.7 43.4 + - - -
170A LEU* 3.4 37.5 - - + +
207A ILE* 3.9 27.6 - - + +
208A SER* 3.3 22.6 + - - +
210A GLU* 1.3 77.0 - - + +
212A ILE* 1.3 66.7 + - - +
214A VAL* 3.5 8.9 + - - +
215A GLU* 3.5 15.8 + - - +
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Residues in contact with ILE 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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170A LEU* 4.1 12.3 - - + -
173A LEU* 3.9 13.1 - - + +
204A LEU* 3.8 10.8 - - + +
207A ILE* 3.6 25.1 - - + +
208A SER 3.2 7.0 + - - +
209A GLY 3.7 5.8 - - - +
211A ARG* 1.3 78.1 - - - +
213A TRP* 1.3 59.9 + - - +
215A GLU* 3.2 4.2 + - - +
216A LEU* 2.8 29.8 + - + +
241A ILE* 3.8 31.4 - - + +
286A ARG* 3.2 34.8 - - - +
287A LEU* 3.6 20.0 - - + -
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Residues in contact with TRP 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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209A GLY 2.9 18.4 + - - +
210A GLU* 3.8 5.6 - - - +
211A ARG 3.3 0.4 - - - -
212A ILE* 1.3 79.9 - - - +
214A VAL* 1.3 64.1 + - + +
216A LEU* 4.1 13.5 - - + -
217A LYS* 3.0 62.6 + - + +
220A LEU* 4.4 4.7 - - + -
266A PRO* 4.6 5.2 - - + -
267A VAL* 3.9 25.4 - - + -
270A LEU* 3.7 27.6 - - + -
283A LEU* 5.0 0.9 - - + -
287A LEU* 3.7 28.0 - - + +
288A LYS 5.1 1.1 - - - -
289A ILE* 3.6 27.8 - - + +
293A GLU* 2.9 36.7 + - - -
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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 GLU* 3.2 16.9 + - + +
211A ARG* 3.8 9.9 - - - +
213A TRP* 1.3 78.5 - - + +
215A GLU* 1.3 65.6 + - + +
217A LYS* 3.9 12.2 - - - +
218A LYS* 3.4 47.8 + - - +
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Residues in contact with GLU 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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170A LEU* 4.0 30.7 - - + +
173A LEU* 4.0 18.8 - - + -
174A ARG* 3.4 32.4 + - + +
177A ARG* 3.1 49.8 + - - +
211A ARG 3.5 3.0 + - - +
212A ILE 3.2 8.1 + - - +
214A VAL* 1.3 79.8 - - + +
216A LEU* 1.3 66.8 + - - +
218A LYS* 3.1 11.6 + - - +
219A ILE* 3.0 26.7 + - + +
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Residues in contact with LEU 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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173A LEU* 4.6 3.5 - - + +
212A ILE* 2.8 23.9 + - + +
213A TRP* 4.0 14.4 - - + +
215A GLU* 1.3 73.7 - - - +
217A LYS* 1.3 58.1 + - - +
219A ILE* 3.2 15.3 + - + +
220A LEU* 2.8 52.5 + - + +
229A ILE* 4.5 17.5 - - + -
232A ILE* 4.8 6.1 - - + -
241A ILE* 4.4 24.2 - - + +
243A LEU* 4.4 21.1 - - + -
270A LEU* 4.7 2.2 - - + -
287A LEU* 4.0 25.1 - - + -
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Residues in contact with LYS 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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213A TRP* 3.0 60.7 + - + +
214A VAL* 3.9 11.3 - - - +
216A LEU* 1.3 77.6 - - - +
218A LYS* 1.3 62.9 + - + +
220A LEU* 3.3 1.9 + - - +
221A VAL* 3.2 30.7 + - - +
266A PRO* 3.5 31.2 - - + -
293A GLU* 3.0 29.8 + - - +
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Residues in contact with LYS 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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177A ARG* 3.5 55.4 - - + +
214A VAL* 3.4 35.1 + - + +
215A GLU* 3.1 12.1 + - - +
217A LYS* 1.3 75.1 - - + +
219A ILE* 1.3 65.5 + - - +
221A VAL* 3.5 9.0 + - + +
222A GLY* 3.1 21.7 + - - -
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Residues in contact with ILE 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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173A LEU* 3.6 35.7 - - + +
176A PHE* 4.0 12.6 - - + -
177A ARG* 3.7 24.9 - - + +
215A GLU 3.0 18.0 + - - +
216A LEU* 3.5 15.9 - - + +
218A LYS* 1.3 76.2 - - - +
220A LEU* 1.3 65.7 + - - +
222A GLY* 3.3 12.1 + - - +
225A VAL* 3.6 18.5 - - + +
228A LEU* 4.0 29.7 - - + +
229A ILE* 4.8 7.0 - - + -
232A ILE* 4.5 19.1 - - + -
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Residues in contact with LEU 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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213A TRP* 4.4 3.6 - - + -
216A LEU* 2.8 38.5 + - + +
217A LYS 3.7 4.3 - - - +
218A LYS 3.3 0.2 - - - -
219A ILE* 1.3 79.4 - - - +
221A VAL* 1.3 58.8 + - - +
222A GLY 3.4 0.8 + - - +
225A VAL* 3.8 24.2 - - + +
229A ILE* 4.0 26.5 - - + -
252A PHE* 5.4 1.1 - - + -
264A PRO* 5.1 5.2 - - - +
266A PRO* 3.8 37.2 - - + +
269A LEU* 3.9 27.1 - - + +
270A LEU* 4.1 30.1 - - + +
273A LEU* 6.1 0.2 - - + -
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Residues in contact with VAL 221 (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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217A LYS 3.2 17.4 + - - +
218A LYS* 3.9 9.9 - - - +
220A LEU* 1.3 76.4 - - - +
222A GLY* 1.3 63.3 + - - +
264A PRO* 3.9 20.2 - - + +
266A PRO* 3.8 30.5 - - + -
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Residues in contact with GLY 222 (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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218A LYS 3.1 16.0 + - - -
219A ILE* 3.3 10.1 + - - +
220A LEU 4.5 0.2 - - - +
221A VAL* 1.3 82.9 - - - +
223A ASN* 1.3 69.0 + - - -
224A HIS 3.9 0.5 + - - -
225A VAL* 4.1 11.6 + - - +
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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