Contacts of the helix formed by residues 256 - 264 (chain C) in PDB entry 4K9N
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 GLY 256 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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254C PRO* 3.0 6.1 + - - +
255C ALA* 1.3 78.1 - - - +
257C ILE* 1.3 66.5 + - - -
258C ALA 3.4 2.2 - - - -
259C ALA* 3.5 2.2 + - - -
260C ILE* 2.9 27.2 + - - +
280C TYR* 3.5 6.8 - - - -
282C GLN* 4.0 7.3 - - - +
284C ASP* 3.5 23.8 - - - -
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Residues in contact with ILE 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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102A ALA 5.9 2.0 - - - +
103A MET* 4.7 17.9 - - + -
106A VAL* 5.8 2.5 - - + -
256C GLY* 1.3 71.4 - - - +
258C ALA* 1.3 64.5 + - - +
260C ILE* 3.4 1.9 + - - +
261C SER 3.1 17.3 + - - -
280C TYR* 3.5 38.2 + - + -
282C GLN 5.3 0.6 + - - -
284C ASP* 3.4 15.0 + - - +
285C PRO* 5.1 6.1 - - + -
286C GLY 3.7 20.0 - - - +
287C GLN 3.4 23.0 - - - +
288C TYR* 3.9 32.0 - - + +
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Residues in contact with ALA 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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257C ILE* 1.3 75.3 - - - +
259C ALA* 1.3 63.4 + - - +
261C SER* 3.1 9.6 + - - -
262C GLN* 3.0 26.2 + - - +
284C ASP* 2.9 32.0 + - - +
285C PRO 3.5 16.2 - - - +
286C GLY* 4.2 5.2 - - - -
287C GLN 4.4 1.6 - - - +
290C LYS* 5.6 0.5 + - - -
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Residues in contact with ALA 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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254C PRO* 3.6 29.4 - - + +
256C GLY* 3.8 6.1 - - - +
257C ILE 3.4 0.2 - - - -
258C ALA* 1.3 76.7 - - - +
260C ILE* 1.3 58.1 + - - +
262C GLN* 3.7 6.2 - - - +
263C LEU* 3.0 29.8 + - - +
282C GLN* 5.9 0.9 - - - +
284C ASP* 2.9 18.9 + - - +
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Residues in contact with ILE 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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235C PRO* 3.8 29.4 - - + -
253C MET* 3.9 20.6 - - + -
254C PRO* 3.3 26.9 - - + +
256C GLY 2.9 12.7 + - - +
257C ILE 4.0 2.5 - - - +
259C ALA* 1.3 75.3 - - - +
261C SER* 1.3 65.7 + - - +
263C LEU* 3.3 5.2 + - - +
264C LEU* 3.0 35.3 + - + +
278C PHE* 3.8 29.8 - - + -
280C TYR* 3.8 22.0 - - + +
288C TYR 5.0 4.9 - - - +
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Residues in contact with SER 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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257C ILE 3.1 5.7 + - - -
258C ALA* 3.1 14.2 + - - -
260C ILE* 1.3 78.0 - - - +
262C GLN* 1.3 60.6 + - - +
264C LEU* 3.4 6.5 + - - +
265C GLU 3.1 17.2 + - - -
287C GLN* 2.8 35.2 + - - +
288C TYR 3.5 17.9 + - - -
289C LEU* 3.8 13.9 - - - +
290C LYS* 3.4 23.1 + - - +
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Residues in contact with GLN 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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258C ALA 3.0 17.9 + - - +
259C ALA* 3.7 7.2 - - - +
261C SER* 1.3 76.5 + - - +
263C LEU* 1.3 66.9 + - + +
265C GLU* 3.1 36.6 + - - +
290C LYS* 3.8 23.4 + - - +
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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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232C TRP* 3.6 55.5 + - + +
253C MET* 4.3 12.8 - - + -
254C PRO* 3.7 33.0 - - + -
259C ALA 3.0 15.2 + - - +
260C ILE* 3.6 7.2 - - - +
262C GLN* 1.3 77.7 - - + +
264C LEU* 1.3 64.6 + - + +
265C GLU 3.5 2.6 + - - +
267C HIS* 4.0 11.8 + - - -
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Residues in contact with LEU 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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204C ALA* 4.6 10.1 - - + -
206C VAL* 4.6 4.7 - - + -
232C TRP* 4.9 7.6 - - + -
253C MET* 4.0 20.6 - - + -
260C ILE* 3.0 37.2 + - + +
261C SER* 3.7 5.4 - - - +
262C GLN 3.2 0.2 - - - -
263C LEU* 1.3 77.0 - - - +
265C GLU* 1.3 66.2 + - - +
266C GLY 3.3 0.2 + - - -
267C HIS* 3.1 23.3 + - + +
270C VAL* 4.1 39.3 - - + -
278C PHE* 4.7 8.7 - - + -
289C LEU* 4.2 20.6 - - + -
293C THR* 3.4 15.4 + - + +
295C LEU* 5.1 0.2 - - + -
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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