Contacts of the helix formed by residues 254 - 265 (chain F) in PDB entry 2HAK
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 254 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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255E LEU* 4.6 10.3 - - + -
259E ARG* 5.1 6.3 - - - +
210F CYS* 4.0 11.9 - - - -
252F GLY 3.1 2.5 - - - -
253F GLN* 1.3 88.7 - - - +
255F LEU* 1.3 67.3 + - - +
256F LYS* 3.1 30.5 + - - +
257F GLU* 3.1 23.4 + - - +
258F LEU* 3.0 20.8 + - - +
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Residues in contact with LEU 255 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255E LEU* 5.0 3.4 - - + +
210F CYS* 3.3 37.3 - - - +
211F GLY* 5.2 4.3 - - - -
212F SER* 4.0 15.3 - - - +
221F PHE* 3.9 26.2 - - + -
254F ASN* 1.3 74.7 - - - +
256F LYS* 1.3 63.2 + - - +
258F LEU* 3.3 3.8 + - + -
259F ARG* 2.9 25.4 + - + +
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Residues in contact with LYS 256 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254F ASN* 3.1 13.3 + - - +
255F LEU* 1.3 76.7 - - - +
257F GLU* 1.3 62.5 + - - +
259F ARG* 3.3 8.6 + - - +
260F GLU* 3.1 29.2 + - - +
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Residues in contact with GLU 257 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251F ASP 4.0 2.3 - - - +
252F GLY* 3.7 3.3 - - - -
253F GLN* 2.6 57.5 + - - +
254F ASN* 3.1 20.3 + - - +
256F LYS* 1.3 77.2 - - - +
258F LEU* 1.3 69.2 + - - +
260F GLU* 3.5 8.4 + - + +
261F ARG* 2.4 61.5 + - - +
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Residues in contact with LEU 258 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209E PHE* 4.4 17.7 - - + -
210F CYS* 4.5 8.7 - - - -
212F SER 3.7 22.2 - - - +
214F PRO* 4.1 19.5 - - + -
221F PHE* 4.1 9.6 - - + -
250F PHE* 3.7 26.9 - - + +
251F ASP 3.9 13.0 - - - +
252F GLY* 4.2 3.6 - - - +
254F ASN 3.0 12.5 + - - +
255F LEU* 3.7 9.9 - - + +
257F GLU* 1.3 75.5 - - - +
259F ARG* 1.3 56.4 + - - +
261F ARG* 2.8 22.9 + - - +
262F VAL* 2.8 33.9 + - + +
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Residues in contact with ARG 259 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221F PHE* 3.3 57.5 + - + -
222F GLN* 3.7 16.7 - - - +
255F LEU* 2.9 20.4 + - + +
256F LYS* 3.9 7.0 - - - +
258F LEU* 1.3 75.6 - - - +
260F GLU* 1.3 59.4 + - - +
262F VAL* 3.5 1.3 + - - +
263F LEU* 2.8 65.7 + - + +
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Residues in contact with GLU 260 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256F LYS* 3.1 19.5 + - - +
257F GLU* 3.6 9.8 - - + +
259F ARG* 1.3 81.6 - - - +
261F ARG* 1.3 61.5 + - - +
263F LEU* 3.4 7.6 + - - +
264F ARG* 2.9 31.5 + - + +
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Residues in contact with ARG 261 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250F PHE* 3.4 21.3 - - + -
251F ASP* 3.3 39.4 + - - +
252F GLY 5.0 0.4 - - - +
253F GLN* 5.6 0.2 - - - +
257F GLU* 2.4 54.0 + - - +
258F LEU 2.8 7.0 + - - +
260F GLU* 1.3 80.7 - - - +
262F VAL* 1.3 63.0 + - - +
264F ARG* 3.3 10.4 + - + +
265F GLY 2.8 23.9 + - - -
266F LYS 4.5 4.2 + - - +
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Residues in contact with VAL 262 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214F PRO 4.8 4.5 - - - +
216F ALA 3.7 20.0 - - - +
218F PRO* 3.9 12.1 - - + -
221F PHE* 3.6 27.4 - - + -
234F TRP* 3.8 18.8 - - + -
250F PHE* 3.8 21.3 - - + -
258F LEU* 2.8 37.7 + - + +
259F ARG 3.8 1.8 - - - +
261F ARG* 1.3 77.1 - - - +
263F LEU* 1.3 64.0 + - - +
265F GLY* 2.9 14.7 + - - -
287F LEU* 3.8 6.9 - - - +
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Residues in contact with LEU 263 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218F PRO* 3.5 36.1 - - + +
221F PHE* 4.5 3.6 - - + -
222F GLN* 3.6 25.1 - - + +
259F ARG* 2.8 65.3 + - + +
260F GLU* 3.9 5.4 - - - +
262F VAL* 1.3 72.4 - - - +
264F ARG* 1.3 61.4 + - - +
287F LEU* 3.3 23.5 - - - +
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Residues in contact with ARG 264 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260F GLU* 2.9 21.6 + - + +
261F ARG* 3.6 11.7 - - + +
263F LEU* 1.3 80.9 - - - +
265F GLY* 1.3 61.5 + - - +
266F LYS* 3.1 22.5 + - + +
287F LEU* 3.7 11.3 - - - +
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Residues in contact with GLY 265 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234F TRP* 4.5 4.1 - - - -
250F PHE* 3.7 13.7 - - - -
261F ARG 2.8 11.7 + - - -
262F VAL 2.9 12.8 + - - -
264F ARG* 1.3 75.7 - - - +
266F LYS* 1.4 61.7 + - - -
267F TYR* 3.3 19.9 - - - -
285F LEU 5.0 3.3 - - - +
287F LEU* 4.4 12.1 - - - -
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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