Contacts of the helix formed by residues 254 - 265 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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252A GLY 3.3 1.7 - - - -
253A GLN* 1.3 91.1 - - - +
255A LEU* 1.3 69.0 + - + +
256A LYS* 2.8 33.3 + - - +
257A GLU* 3.0 17.1 + - - +
258A LEU* 3.0 25.6 + - - +
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Residues in contact with LEU 255 (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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211A GLY* 4.3 12.6 - - - +
212A SER* 4.1 32.1 - - - +
221A PHE* 5.2 8.7 - - + -
254A ASN* 1.3 76.4 - - + +
256A LYS* 1.3 54.2 + - - +
258A LEU* 4.7 7.0 - - + -
259A ARG* 3.2 35.6 + - + +
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Residues in contact with LYS 256 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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254A ASN* 2.8 17.7 + - - +
255A LEU* 1.3 73.5 - - - +
257A GLU* 1.3 57.7 + - - -
259A ARG* 5.0 2.0 - - - -
260A GLU* 3.2 27.0 + - - +
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Residues in contact with GLU 257 (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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251A ASP 4.3 2.2 - - - -
252A GLY* 3.6 14.8 - - - -
253A GLN* 2.2 52.2 + - - +
254A ASN* 3.0 14.0 + - - +
256A LYS* 1.3 73.3 - - - +
258A LEU* 1.3 59.6 + - - +
260A GLU* 3.4 3.7 + - - +
261A ARG* 2.8 49.6 + - - +
49D HIS* 3.6 32.9 + - - +
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Residues in contact with LEU 258 (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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212A SER 4.6 5.6 - - - +
214A PRO* 4.1 35.7 - - + -
221A PHE* 3.7 22.2 - - + -
250A PHE 4.7 2.2 - - - +
251A ASP* 3.5 39.9 - - - +
252A GLY* 4.4 3.9 - - - +
254A ASN 3.0 17.9 + - - +
255A LEU* 4.1 8.7 - - + +
257A GLU* 1.3 76.8 - - - +
259A ARG* 1.3 52.2 + - - +
261A ARG* 3.3 1.7 - - - +
262A VAL* 2.7 61.9 + - + +
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Residues in contact with ARG 259 (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 PHE* 3.4 32.5 - - + -
255A LEU* 3.2 21.5 + - + +
256A LYS* 4.7 1.8 - - - +
258A LEU* 1.3 75.5 - - - +
260A GLU* 1.3 68.0 + - - +
262A VAL* 4.5 0.9 - - - +
263A LEU* 2.9 38.8 + - + +
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Residues in contact with GLU 260 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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256A LYS 3.2 21.6 + - - +
257A GLU* 3.7 4.7 - - - +
259A ARG* 1.3 79.4 - - - +
261A ARG* 1.3 64.8 + - - +
263A LEU* 3.9 3.6 - - - +
264A ARG* 3.0 22.8 + - - +
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Residues in contact with ARG 261 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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250A PHE* 4.0 16.8 - - + -
251A ASP 2.7 42.2 + - - +
252A GLY* 3.4 16.8 - - - -
257A GLU* 2.8 40.3 + - - +
258A LEU* 3.3 3.6 - - - +
260A GLU* 1.3 71.5 - - - +
262A VAL* 1.3 67.7 + - - +
264A ARG* 3.1 7.4 + - - +
265A GLY* 2.8 19.4 + - - -
266A LYS 4.5 4.0 + - - +
49D HIS* 5.7 5.9 - - - -
51D GLY 5.0 10.3 + - - -
52D ASN* 5.4 5.1 + - - -
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Residues in contact with VAL 262 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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214A PRO 5.2 3.4 - - - +
216A ALA 4.6 5.4 - - - +
218A PRO* 3.7 29.8 - - + -
221A PHE* 4.4 9.6 - - + -
234A TRP* 3.9 18.8 - - + +
250A PHE* 3.8 25.3 - - + -
258A LEU* 2.7 47.8 + - + +
259A ARG* 3.9 4.5 - - - +
261A ARG* 1.3 71.0 - - - +
263A LEU* 1.3 61.5 + - + +
265A GLY* 2.9 21.1 + - - -
287A LEU* 3.4 7.8 - - - +
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Residues in contact with LEU 263 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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218A PRO* 3.1 41.1 - - + +
221A PHE* 4.0 14.1 - - + +
222A GLN* 3.9 33.7 - - + +
259A ARG* 2.9 33.4 + - + +
260A GLU* 4.3 2.9 - - - +
262A VAL* 1.3 74.1 - - + +
264A ARG* 1.3 59.2 - - - +
287A LEU* 3.4 20.2 - - - +
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Residues in contact with ARG 264 (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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260A GLU 3.0 17.6 + - - +
261A ARG* 3.7 4.0 - - - +
263A LEU* 1.3 76.5 - - - +
265A GLY* 1.3 63.0 + - - +
266A LYS* 3.1 38.8 + - + +
287A LEU* 3.5 11.8 - - - +
353D GLU* 5.5 4.6 + - - -
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Residues in contact with GLY 265 (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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234A TRP* 4.6 1.8 - - - -
250A PHE* 3.7 18.0 - - - -
261A ARG 2.8 9.5 + - - -
262A VAL 2.9 14.6 + - - -
264A ARG* 1.3 77.0 - - - +
266A LYS* 1.3 70.3 + - - +
267A TYR* 3.6 16.6 - - - -
285A LEU 4.9 4.3 - - - +
287A LEU* 4.0 13.2 - - - +
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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