Contacts of the helix formed by residues 213 - 225 (chain A) in PDB entry 3HF8
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 GLN 213 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162A PRO 4.5 1.6 - - - +
163A LYS* 3.4 33.8 - - + +
164A VAL* 2.7 49.5 + - - +
166A PHE* 3.7 18.0 - - - -
204A CYS 4.7 1.2 + - - -
211A ILE 4.0 7.3 + - - +
212A PRO* 1.3 74.0 - - - +
214A LEU* 1.3 67.5 + - - +
215A GLU 4.3 1.3 - - - +
216A ASP* 3.2 26.5 + - - +
217A VAL* 3.1 25.1 + - - +
254A GLN* 4.9 1.9 + - - -
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Residues in contact with LEU 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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161A ILE* 3.8 25.4 - - + +
162A PRO 5.9 0.2 + - - -
212A PRO 4.0 1.2 + - - +
213A GLN* 1.3 74.3 + - - +
215A GLU* 1.3 57.5 + - - +
217A VAL* 3.2 7.7 - - + +
218A SER* 2.8 32.4 + - - -
229A ILE* 4.2 11.9 - - + +
231A PRO* 4.4 4.9 - - + -
252A CYS* 4.0 40.8 - - + +
253A THR 4.0 2.7 - - - +
254A GLN* 3.9 36.8 - - + +
270A THR* 4.0 17.5 - - - +
273A GLU* 5.2 1.6 - - + -
274A LEU* 4.1 17.7 - - + -
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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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159A ASP 4.6 0.7 - - - +
160A PRO* 3.5 19.4 - - + +
161A ILE* 2.8 58.9 + - - +
162A PRO 5.9 0.2 + - - -
163A LYS* 4.1 22.4 - - + +
213A GLN* 3.3 1.4 - - - +
214A LEU* 1.3 77.4 - - - +
216A ASP* 1.3 57.9 - - - +
218A SER* 3.5 3.9 + - - -
219A ASN* 3.0 59.1 + - - +
222A LYS* 5.8 0.3 + - - -
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Residues in contact with ASP 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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163A LYS* 3.0 31.7 + - - -
203A TYR 5.3 3.4 - - - +
204A CYS* 3.8 25.4 - - + +
213A GLN* 3.2 25.9 + - + +
215A GLU* 1.3 77.3 - - - +
217A VAL* 1.3 58.0 + - - +
219A ASN* 3.3 8.3 + - - +
220A PHE* 3.0 27.7 + - - +
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Residues in contact with VAL 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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204A CYS* 3.9 18.6 - - + -
206A TYR* 3.8 35.9 - - + +
212A PRO* 4.3 2.9 - - + -
213A GLN 3.1 13.3 + - - +
214A LEU* 3.2 20.2 - - - +
216A ASP* 1.3 71.7 - - - +
218A SER* 1.3 60.6 + - - +
220A PHE* 3.3 2.4 + - - +
221A LEU* 2.9 34.6 + - - +
229A ILE* 3.4 20.2 - - + -
274A LEU* 3.9 17.5 - - + -
278A VAL* 4.3 14.8 - - + -
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Residues in contact with SER 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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161A ILE* 4.1 9.3 - - - +
214A LEU 2.8 18.5 + - - -
215A GLU* 3.7 7.4 - - - -
217A VAL* 1.3 77.3 - - - +
219A ASN* 1.3 59.3 + - - +
221A LEU* 3.2 5.5 + - - +
222A LYS* 2.9 37.1 + - - +
227A PHE 3.7 0.3 - - - +
228A SER* 3.4 9.2 - - - -
229A ILE* 2.8 43.0 + - - +
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Residues in contact with ASN 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 GLU* 3.0 49.8 + - - +
216A ASP* 3.8 7.1 + - - +
218A SER* 1.3 75.5 - - - +
220A PHE* 1.3 61.9 + - - +
222A LYS* 3.5 26.8 + - - +
223A GLU* 3.4 25.0 + - - +
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Residues in contact with PHE 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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196A ASN* 5.1 1.8 - - + -
199A LEU* 3.8 28.3 - - + -
200A LEU* 3.7 25.6 - - + -
203A TYR* 4.0 31.4 - + + -
204A CYS* 3.5 30.1 - - - -
216A ASP 3.0 7.1 + - - +
217A VAL 3.5 6.1 - - - +
218A SER 3.3 0.2 - - - -
219A ASN* 1.3 77.2 - - - +
221A LEU* 1.3 70.4 + - + +
223A GLU* 3.2 33.6 - - - +
224A ARG* 3.3 44.6 - - + +
282A ALA* 4.0 18.2 - - + -
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Residues in contact with LEU 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 VAL 2.9 19.3 + - - +
218A SER 3.7 2.0 - - - +
220A PHE* 1.3 77.8 - - + +
222A LYS* 1.3 67.2 + - - +
224A ARG* 3.1 1.7 + - - +
225A THR* 2.9 26.0 + - - +
226A GLY 3.2 4.5 + - - -
227A PHE* 3.2 22.9 - - + +
228A SER 5.3 0.4 - - - +
229A ILE* 4.2 23.1 - - + -
278A VAL* 3.8 23.6 - - + +
281A LEU* 3.7 31.4 - - + +
282A ALA* 3.5 40.2 - - + +
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Residues in contact with LYS 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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157A HIS* 6.4 0.2 - - - -
215A GLU* 5.8 0.4 + - - -
218A SER* 2.9 26.1 + - - +
219A ASN* 3.7 25.0 + - - +
220A PHE 3.3 0.2 - - - -
221A LEU* 1.3 75.7 - - - +
223A GLU* 1.3 61.0 + - - +
226A GLY* 3.3 23.1 + - - +
227A PHE 2.9 13.8 + - - +
228A SER* 3.6 23.8 - - - -
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Residues in contact with GLU 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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203A TYR* 6.2 0.2 - - - -
219A ASN 3.4 12.4 + - - +
220A PHE* 3.2 30.8 - - + +
222A LYS* 1.3 79.6 - - - +
224A ARG* 1.3 67.2 + - + +
226A GLY 4.8 0.2 - - - -
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Residues in contact with ARG 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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196A ASN* 5.1 5.4 - - - -
199A LEU* 4.8 17.9 - - - +
203A TYR* 6.0 2.4 - - - -
220A PHE* 3.3 48.6 + - + +
221A LEU* 3.1 6.3 + - - +
223A GLU* 1.3 87.7 + - + +
225A THR* 1.3 64.5 + - + +
282A ALA* 4.1 24.2 + - - +
284A PRO* 4.8 7.4 - - - +
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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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221A LEU 2.9 8.1 + - - -
224A ARG* 1.3 76.2 - - - +
226A GLY* 1.3 61.4 + - - +
227A PHE* 3.1 15.1 + - - +
248A ARG* 2.8 30.6 + - - +
281A LEU 2.7 29.2 + - - +
282A ALA* 3.4 25.2 - - - +
283A GLU 3.7 1.6 - - - -
284A PRO* 3.6 24.7 - - + -
287A ALA* 3.8 11.4 - - + -
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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