Contacts of the helix formed by residues 254 - 265 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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252C GLY 3.9 5.2 - - - +
253C GLN* 1.3 82.3 - - + +
255C LEU* 1.3 58.0 + - - +
256C LYS* 2.4 42.6 + - - +
257C GLU* 2.8 28.1 + - - +
258C LEU* 3.1 21.2 + - - +
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Residues in contact with LEU 255 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213C PRO* 5.4 6.7 - - + -
221C PHE* 4.0 29.6 - - + -
254C ASN* 1.3 67.8 + - - +
256C LYS* 1.3 67.5 + - - +
257C GLU 3.0 1.8 - - - -
258C LEU* 3.1 10.5 + - + -
259C ARG* 2.8 45.6 + - + +
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Residues in contact with LYS 256 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254C ASN* 2.4 26.0 + - - +
255C LEU* 1.3 73.2 - - - +
257C GLU* 1.3 57.2 + - - +
259C ARG* 3.3 32.7 + - - +
260C GLU* 2.9 41.1 + - - +
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Residues in contact with GLU 257 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122B GLU* 5.8 1.6 - - - +
123B LYS* 5.7 6.1 + - - +
251C ASP 4.5 2.2 - - - -
252C GLY* 3.4 3.8 - - - -
253C GLN* 2.9 41.1 + - - +
254C ASN* 2.8 30.2 + - - +
256C LYS* 1.3 75.3 - - - +
258C LEU* 1.3 65.6 + - - +
260C GLU* 3.3 19.3 + - + +
261C ARG* 2.5 61.3 + - - +
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Residues in contact with LEU 258 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213C PRO 4.1 7.0 - - - -
214C PRO* 3.9 29.4 - - + -
221C PHE* 3.6 27.1 - - + -
250C PHE* 3.6 31.0 - - + +
251C ASP* 4.0 9.9 - - - +
252C GLY* 4.4 9.5 - - - +
254C ASN 3.1 10.9 + - - +
255C LEU* 3.1 14.3 + - + +
257C GLU* 1.3 74.9 - - - +
259C ARG* 1.3 56.4 - - - +
261C ARG* 3.0 2.9 + - - +
262C VAL* 2.8 47.9 + - + +
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Residues in contact with ARG 259 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221C PHE* 4.1 46.0 - - + -
255C LEU* 2.8 48.5 + - + +
256C LYS* 3.3 34.7 + - - +
258C LEU* 1.3 77.6 - - - +
260C GLU* 1.3 65.6 + - - +
262C VAL* 3.5 1.5 + - - +
263C LEU* 3.0 41.9 + - + +
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Residues in contact with GLU 260 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256C LYS* 2.9 33.0 + - - +
257C GLU* 3.3 24.8 - - + +
259C ARG* 1.3 80.8 + - - +
261C ARG* 1.3 58.6 + - - +
263C LEU* 4.0 5.8 - - - +
264C ARG* 3.1 29.3 + - - +
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Residues in contact with ARG 261 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B THR* 4.1 22.0 - - - +
122B GLU* 3.9 32.4 - - - +
250C PHE* 3.6 24.9 - - + -
251C ASP 3.2 29.1 + - - +
252C GLY* 4.5 0.8 - - - -
257C GLU* 2.5 48.1 + - - +
258C LEU 3.0 7.7 + - - +
260C GLU* 1.3 77.1 - - - +
262C VAL* 1.3 67.2 + - - +
264C ARG* 3.2 6.1 + - + +
265C GLY 3.0 18.2 + - - -
266C LYS 4.6 3.7 + - - +
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Residues in contact with VAL 262 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214C PRO 5.0 4.0 - - - +
216C ALA 4.4 3.4 - - - +
218C PRO* 3.8 37.7 - - + -
221C PHE* 3.6 28.7 - - + -
234C TRP* 3.8 14.6 - - + +
250C PHE* 3.9 22.4 - - + -
258C LEU* 2.8 37.0 + - + +
259C ARG 4.0 3.1 - - - +
261C ARG* 1.3 71.2 - - - +
263C LEU* 1.3 57.3 + - + +
265C GLY* 3.0 22.0 + - - -
287C LEU* 3.7 6.2 - - - +
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Residues in contact with LEU 263 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218C PRO* 3.5 40.6 - - + +
221C PHE* 4.7 4.3 - - + -
222C GLN* 3.9 30.5 - - + +
259C ARG* 3.0 40.5 + - + +
260C GLU* 4.4 4.7 - - - +
262C VAL* 1.3 71.0 - - + +
264C ARG* 1.3 64.9 + - - +
287C LEU* 3.6 20.6 - - + +
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Residues in contact with ARG 264 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122B GLU* 5.4 9.3 + - - -
260C GLU 3.1 19.7 + - - +
261C ARG* 3.2 7.4 + - + +
263C LEU* 1.3 76.1 - - - +
265C GLY* 1.3 58.9 + - - +
266C LYS* 3.0 53.9 + - - +
287C LEU* 4.0 8.2 - - - +
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Residues in contact with GLY 265 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234C TRP* 4.7 1.7 - - - -
250C PHE* 3.8 11.9 - - - -
261C ARG 3.0 6.1 + - - -
262C VAL 3.0 16.5 + - - -
264C ARG* 1.3 76.4 - - - +
266C LYS* 1.3 59.9 + - - +
267C TYR* 3.5 21.0 - - - -
285C LEU 5.0 4.7 - - - +
287C LEU* 4.2 15.7 - - - +
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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