Contacts of the helix formed by residues 295 - 303 (chain C) in PDB entry 3QI6
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 295 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135C ALA* 6.3 2.0 - - - -
163C ILE* 3.6 27.4 - - - +
293C HIS* 3.2 0.4 + - - -
294C PRO* 1.3 72.6 - - - +
296C HIS* 1.3 66.5 + - - +
297C ALA 3.2 2.2 - - - -
298C VAL* 3.2 11.4 + - - -
299C ALA* 2.8 20.4 + - - +
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Residues in contact with HIS 296 (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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288C PRO 2.7 28.9 + - - +
289C GLY 3.1 26.3 + - - -
290C LEU 3.4 13.2 - - - +
291C PRO* 3.8 28.0 - - + +
293C HIS* 2.9 19.4 + - - +
294C PRO 3.8 0.2 + - - -
295C GLY* 1.3 77.6 - - - +
297C ALA* 1.3 62.6 + - + +
299C ALA* 3.0 5.1 + - - +
300C ALA* 2.9 33.3 + - + +
306C PHE* 3.7 21.8 - + - -
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Residues in contact with ALA 297 (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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295C GLY 3.2 0.6 - - - -
296C HIS* 1.3 84.5 - - + +
298C VAL* 1.3 66.1 + - + +
300C ALA* 3.2 14.5 + - - +
301C ARG* 3.2 19.8 + - - +
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Residues in contact with VAL 298 (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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163C ILE* 3.6 21.1 - - + +
165C ASP* 3.8 37.2 - - + +
295C GLY* 3.2 12.7 + - - +
297C ALA* 1.3 80.0 - - + +
299C ALA* 1.3 63.3 + - - +
301C ARG* 3.2 29.7 + - - +
302C GLN* 3.1 27.6 + - - +
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Residues in contact with ALA 299 (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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163C ILE* 3.7 21.0 - - + +
288C PRO* 4.2 9.4 - - + +
295C GLY 2.8 18.2 + - - +
296C HIS 3.5 7.4 - - - +
298C VAL* 1.3 73.9 - - - +
300C ALA* 1.3 58.1 + - - +
302C GLN* 4.5 0.7 - - - -
303C MET* 2.9 58.3 + - - +
306C PHE* 3.9 13.0 - - + -
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Residues in contact with ALA 300 (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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296C HIS* 2.9 24.6 + - + +
297C ALA* 3.7 7.4 - - - +
298C VAL 3.2 0.6 - - - -
299C ALA* 1.3 76.2 - - - +
301C ARG* 1.3 60.8 + - - +
303C MET 3.6 11.1 - - - +
306C PHE* 3.9 23.5 - - + -
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Residues in contact with ARG 301 (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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165C ASP* 2.6 40.6 + - - +
167C ALA* 5.8 2.6 - - - +
297C ALA* 3.2 14.0 + - - +
298C VAL* 3.2 33.3 + - - +
299C ALA 3.2 0.6 - - - -
300C ALA* 1.3 80.6 - - - +
302C GLN* 1.4 63.0 + - + +
303C MET 3.7 0.9 + - - +
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Residues in contact with GLN 302 (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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155C THR* 3.7 10.1 + - - +
163C ILE* 3.7 14.8 - - - +
164C ALA 2.6 23.9 + - - -
165C ASP* 3.8 6.4 - - - +
166C ILE* 3.1 33.5 + - - +
167C ALA 4.5 0.3 + - - -
191C LEU 3.9 2.4 - - - +
192C GLN* 3.5 35.4 + - - +
193C GLN 4.9 0.7 + - - -
197C LEU* 3.4 26.2 - - + +
298C VAL* 3.1 22.9 + - + +
299C ALA* 4.1 2.4 - - - +
301C ARG* 1.4 81.6 - - + +
303C MET* 1.3 58.9 + - + +
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Residues in contact with MET 303 (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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155C THR* 5.7 0.2 - - - -
156C PRO* 4.1 24.0 - - + -
163C ILE* 4.7 3.1 - - - -
187C ALA* 3.9 29.2 - - + -
191C LEU* 3.1 9.6 - - + +
192C GLN* 3.4 21.1 - - - +
288C PRO* 5.0 1.6 - - - -
299C ALA* 2.9 39.5 + - - +
300C ALA* 3.6 17.3 - - - +
301C ARG 3.7 0.8 - - - +
302C GLN* 1.3 76.6 - - + +
304C ARG* 1.3 62.6 + - - +
305C GLY* 3.3 23.5 - - - +
306C PHE* 4.5 19.5 - - + -
307C GLY* 5.4 0.4 - - - -
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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