Contacts of the helix formed by residues 217 - 226 (chain A) in PDB entry 6D6U
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 217 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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182A GLU* 5.7 2.2 + - - -
183A LEU 5.4 0.4 + - - -
184A PRO 4.5 5.5 + - - -
185A GLN* 3.1 32.0 + - + +
186A PHE 4.0 9.1 + - - -
187A SER* 4.7 11.0 + - - -
216A ARG* 1.3 75.6 - - - +
218A ILE* 1.3 66.7 + - - +
219A GLY 3.2 2.7 - - - +
220A TYR* 3.3 24.6 + - + +
221A PHE* 4.0 9.2 + - - -
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Residues in contact with ILE 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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144A PRO* 4.9 8.3 - - + +
145A LEU* 3.8 44.9 - - + -
215A LYS* 5.5 9.6 - - - -
216A ARG* 3.4 12.6 + - + +
217A ASN* 1.3 72.8 - - - +
219A GLY* 1.3 57.6 + - - +
221A PHE* 2.9 27.3 + - + +
222A ILE* 2.9 37.3 + - + +
226A TYR* 5.7 0.2 - - + -
336A TRP* 5.4 2.2 - - + -
340A VAL* 5.1 7.2 - - + -
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Residues in contact with GLY 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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217A ASN* 3.2 1.8 - - - +
218A ILE* 1.3 79.1 - - - +
220A TYR* 1.3 59.0 + - - +
222A ILE* 4.0 13.9 + - - +
223A LEU* 4.4 17.3 + - - +
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Residues in contact with TYR 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 GLN* 5.8 5.4 - - + -
217A ASN* 3.3 19.8 + - + +
218A ILE 3.1 1.0 - - - -
219A GLY* 1.3 77.2 - - - +
221A PHE* 1.3 81.0 + + + +
223A LEU* 5.0 1.0 - - - +
224A GLN* 3.5 27.9 + - + +
292E TYR* 3.5 42.2 - + - -
293E VAL 4.4 8.5 + - - -
294E THR* 4.8 3.1 - - - -
295E ALA* 5.0 4.0 + - - +
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Residues in contact with PHE 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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143A TYR* 3.9 15.7 - + - -
144A PRO* 3.5 39.9 - - + -
185A GLN* 3.1 31.6 - - + -
216A ARG* 4.5 10.8 - - + -
217A ASN 4.6 8.7 - - - -
218A ILE* 2.9 12.7 + - + +
220A TYR* 1.3 107.2 - + + +
222A ILE* 1.3 61.3 + - + +
223A LEU 3.4 0.7 - - - -
224A GLN* 3.9 4.5 - - + +
225A THR* 2.6 47.9 + - + +
226A TYR* 5.5 2.0 - - + -
292E TYR* 3.5 24.5 - - + -
293E VAL 5.3 3.1 - - - -
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Residues in contact with ILE 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 ILE* 2.9 43.7 + - + +
219A GLY* 4.0 8.7 + - - +
220A TYR 3.7 0.2 - - - -
221A PHE* 1.3 75.0 - - + +
223A LEU* 1.3 68.1 + - + +
225A THR* 4.5 1.3 - - - -
226A TYR* 2.9 53.6 + - + +
227A MET* 3.6 30.0 + - + -
336A TRP* 4.0 12.8 - - + -
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Residues in contact with LEU 223 (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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219A GLY 4.4 13.9 + - - +
220A TYR 5.5 0.4 - - - +
221A PHE 4.9 0.2 - - - +
222A ILE* 1.3 84.4 - - + +
224A GLN* 1.3 72.2 + - + +
225A THR 3.5 0.3 + - - -
227A MET* 3.6 37.7 - - + +
228A PRO* 4.1 12.8 - - - +
298E LEU* 4.6 6.2 - - - +
353E SER* 4.2 22.7 - - - +
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Residues in contact with GLN 224 (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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220A TYR* 3.5 29.1 + - + +
221A PHE* 3.3 5.5 + - + +
222A ILE 3.2 0.8 - - - -
223A LEU* 1.3 87.7 - - + +
225A THR* 1.3 66.7 + - + +
228A PRO* 4.7 2.2 - - - +
268A LEU* 4.8 2.8 - - - +
293E VAL* 4.0 24.8 + - + +
294E THR 3.7 7.3 + - - -
295E ALA* 3.4 36.0 - - - +
298E LEU* 4.0 42.7 - - - +
350E TYR* 5.5 4.1 - - - -
353E SER* 6.2 0.2 - - - -
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Residues in contact with THR 225 (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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144A PRO* 6.0 0.3 - - - +
221A PHE* 2.6 35.3 + - + +
222A ILE 3.3 0.2 + - - -
224A GLN* 1.3 86.6 - - + +
226A TYR* 1.3 89.1 + - - +
227A MET 3.6 1.1 - - - -
228A PRO* 3.2 14.0 - - - +
229A SER* 4.6 4.5 + - - -
264A ILE* 5.4 1.9 - - - +
268A LEU* 3.8 37.1 - - + +
272A LEU* 5.2 3.6 - - + -
281A ILE* 4.1 13.8 - - + +
285A LEU* 5.6 1.2 - - - +
293E VAL* 4.2 13.2 - - + -
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Residues in contact with TYR 226 (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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144A PRO* 3.4 30.4 - - + +
145A LEU* 3.9 11.7 - - + +
221A PHE* 5.6 1.6 - - + -
222A ILE* 2.9 40.9 + - + +
225A THR* 1.3 88.3 + - - +
227A MET* 1.3 67.3 + - - +
228A PRO 3.2 1.6 - - - -
229A SER* 3.2 15.9 + - - -
230A ILE* 3.3 25.4 + - + +
268A LEU* 5.9 0.4 - - + -
280A ALA* 6.1 0.2 - - - +
281A ILE* 3.6 34.1 - - + +
284A TYR* 4.5 23.5 - + + -
285A LEU* 6.0 3.1 - - + -
335A TYR* 4.2 15.0 + + - -
336A TRP* 3.6 32.1 - + + -
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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