Contacts of the helix formed by residues 257 - 266 (chain E) in PDB entry 6ACQ
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 HIS 257 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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204B GLU* 4.4 12.0 + - - -
196E ASN* 2.8 22.6 + - - +
199E VAL* 3.6 21.3 - - + -
200E GLY* 3.4 27.4 + - - -
203E ALA* 3.4 26.4 - - + +
204E GLU* 5.5 2.8 - - - +
255E ARG* 3.6 2.5 + - - -
256E PRO* 1.3 75.2 - - - +
258E THR* 1.3 91.2 + - + +
259E LEU* 3.1 17.3 + - + +
260E LEU* 3.0 14.7 + - + +
261E LYS* 3.2 12.6 + - - +
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Residues in contact with THR 258 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204B GLU* 5.2 8.1 - - - +
181C GLU 5.9 1.1 - - - +
182C ALA* 5.5 5.4 - - + -
183C PRO* 4.0 28.1 - - + +
248C GLU* 3.9 19.2 + - - +
249C THR* 4.5 8.2 - - - +
256E PRO 3.6 1.8 + - - -
257E HIS* 1.3 88.5 + - + +
259E LEU* 1.3 66.0 + - + +
261E LYS* 3.2 16.6 + - - +
262E LYS* 3.1 19.2 + - - +
265E ARG* 5.6 0.2 + - - -
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Residues in contact with LEU 259 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155C ILE* 5.0 0.9 - - + -
199E VAL* 4.1 11.2 - - + +
202E LEU* 4.2 16.6 - - + -
203E ALA* 3.5 34.8 - - + +
257E HIS* 3.1 17.3 + - + +
258E THR* 1.3 78.6 - - + +
260E LEU* 1.3 65.2 + - - +
262E LYS* 3.0 20.7 + - + +
263E TYR* 2.9 57.5 + - + +
277E PHE* 5.0 1.1 - - + -
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Residues in contact with LEU 260 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195E ILE* 6.1 2.9 - - + -
196E ASN* 4.1 17.7 - - + +
199E VAL* 4.1 19.9 - - + +
235E LEU* 3.9 44.6 - - + +
238E CYS* 4.5 7.2 - - + +
239E LEU* 3.8 38.8 - - + +
242E MET* 4.9 3.1 - - + -
256E PRO* 4.7 3.1 - - + -
257E HIS* 3.0 13.6 + - + +
259E LEU* 1.3 79.0 - - - +
261E LYS* 1.3 63.4 + - - +
263E TYR* 3.4 4.6 + - - +
264E VAL* 3.1 24.4 + - + +
277E PHE* 4.7 8.5 - - + -
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Residues in contact with LYS 261 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247C SER 3.6 14.1 + - - -
248C GLU* 2.9 43.1 + - - +
250C GLY* 5.4 0.8 - - - +
239E LEU* 4.0 26.5 - - + +
243E ASP* 4.8 4.3 + - - -
256E PRO* 3.9 30.7 - - - +
257E HIS 3.2 10.0 + - - +
258E THR* 3.2 14.8 + - - +
259E LEU 3.1 0.2 - - - -
260E LEU* 1.3 80.8 - - - +
262E LYS* 1.3 56.7 + - - +
264E VAL* 3.5 2.3 + - - +
265E ARG* 3.0 52.8 + - - +
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Residues in contact with LYS 262 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206B ILE* 6.0 1.6 - - - +
122C THR* 3.6 26.8 - - - +
153C ARG 5.1 0.4 + - - -
154C GLY 5.5 0.2 - - - -
155C ILE* 3.8 31.0 - - + +
180C ALA* 4.6 7.9 - - - +
181C GLU* 2.8 52.3 + - + +
258E THR 3.1 7.9 + - - +
259E LEU* 3.0 22.1 + - + +
261E LYS* 1.3 78.3 - - - +
263E TYR* 1.3 66.6 + - - +
265E ARG* 3.2 11.4 + - - +
266E ALA* 3.0 19.2 + - - +
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Residues in contact with TYR 263 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155C ILE* 3.8 19.7 - - + +
202E LEU* 4.7 5.5 - - - +
209E VAL* 6.0 1.4 - - - +
235E LEU* 4.2 13.7 - - + -
259E LEU* 2.9 47.1 + - + +
260E LEU* 3.8 8.1 - - + +
262E LYS* 1.3 75.5 - - - +
264E VAL* 1.3 63.5 + - - +
266E ALA* 3.3 8.4 + - - +
268E TRP* 3.0 58.0 + + - +
276E GLY 3.4 35.9 - - - -
277E PHE* 3.8 31.2 + + - -
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Residues in contact with VAL 264 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235E LEU* 3.5 39.3 - - + +
236E ASP* 3.9 11.4 - - + +
239E LEU* 3.7 24.9 - - + -
260E LEU* 3.1 19.0 + - + +
261E LYS 3.8 4.3 - - - +
263E TYR* 1.3 76.5 - - - +
265E ARG* 1.3 61.0 + - + +
267E GLY* 2.9 20.4 + - - -
269E LEU* 3.7 17.6 - - + +
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Residues in contact with ARG 265 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120C SER* 3.5 31.4 + - - -
122C THR* 3.8 12.4 - - + +
123C GLU* 3.4 38.9 + - + +
126C SER* 2.7 30.0 + - - -
181C GLU* 4.4 4.4 + - - -
248C GLU* 2.9 41.4 + - - -
261E LYS* 3.0 39.9 + - - +
262E LYS* 3.2 10.1 + - - +
264E VAL* 1.3 80.6 - - + +
266E ALA* 1.3 49.9 + - - +
267E GLY 3.1 1.1 + - - -
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Residues in contact with ALA 266 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122C THR* 3.4 19.7 - - + +
126C SER* 3.5 13.6 + - - -
155C ILE* 3.5 20.9 - - + -
156C ALA* 5.5 3.4 - - + -
262E LYS 3.0 6.1 + - - +
263E TYR 3.6 10.3 - - - +
264E VAL 3.1 0.2 - - - -
265E ARG* 1.3 74.9 - - - +
267E GLY* 1.3 58.3 + - - +
268E TRP* 3.2 28.6 + - + +
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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