Contacts of the helix formed by residues 296 - 304 (chain A) in PDB entry 2FQ6
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 296 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135A LEU* 4.2 8.4 - - - +
163A VAL* 3.5 30.0 - - - +
294A SER 3.0 1.4 + - - -
295A LYS* 1.3 71.6 - - - +
297A HIS* 1.3 65.6 + - - +
298A GLU* 3.1 3.8 - - - -
299A PHE* 2.9 29.0 + - - -
300A TRP 3.0 10.0 + - - -
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Residues in contact with HIS 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A PRO* 2.8 31.9 - - - +
290A ALA 3.3 25.3 + - - -
291A LEU 3.5 12.8 - - - +
292A PRO* 3.5 27.0 - - + +
293A GLY 4.2 3.6 + - - +
294A SER* 2.8 21.6 + - - +
295A LYS 3.3 1.2 + - - -
296A GLY* 1.3 77.2 - - - +
298A GLU* 1.3 70.4 + - + +
300A TRP* 3.2 17.1 + + - +
301A LYS* 2.8 51.5 + - + +
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Residues in contact with GLU 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A GLY* 3.1 0.9 - - - -
297A HIS* 1.3 95.8 + - + +
299A PHE* 1.3 69.7 + - + +
301A LYS* 3.6 15.4 + - - +
302A ARG* 3.1 28.2 + - - +
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Residues in contact with PHE 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A LEU* 4.6 11.2 - - + -
163A VAL* 3.6 24.7 - - + -
164A HIS 3.3 21.5 - - - +
165A ASP* 3.4 33.9 - - + -
296A GLY* 2.9 18.5 + - - +
298A GLU* 1.3 84.2 - - + +
300A TRP* 1.3 59.0 + - - +
302A ARG* 3.7 27.6 - - - -
303A ASP* 2.8 44.3 + - - +
304A PHE* 5.0 0.2 - - - -
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Residues in contact with TRP 300 (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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163A VAL* 3.8 12.6 - - + +
188A TRP* 4.0 9.3 - + - -
267A HIS* 4.2 11.4 - + - -
289A PRO* 3.5 41.3 - - + +
290A ALA* 3.8 29.2 - - + -
296A GLY 3.0 10.4 + - - +
297A HIS* 3.2 17.0 + + - +
299A PHE* 1.3 75.7 - - - +
301A LYS* 1.3 88.3 + - + +
304A PHE* 2.9 70.3 + + + +
305A THR 5.6 0.2 - - - -
306A GLY* 2.9 40.7 + - - -
307A SER* 3.9 3.1 - - - -
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Residues in contact with LYS 301 (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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297A HIS* 2.8 38.2 + - + +
298A GLU* 3.8 17.9 - - - +
300A TRP* 1.3 94.7 - - + +
302A ARG* 1.3 59.3 + - - +
304A PHE 4.2 7.3 - - - +
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Residues in contact with ARG 302 (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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165A ASP* 2.9 29.1 + - - -
167A PRO* 3.4 15.5 - - - +
298A GLU 3.1 18.0 + - - +
299A PHE* 3.7 25.7 - - - +
301A LYS* 1.3 79.9 - - - +
303A ASP* 1.3 91.3 + - - +
304A PHE 3.7 1.8 - - - +
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Residues in contact with ASP 303 (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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164A HIS 4.8 0.9 - - - +
166A VAL* 4.5 2.1 + - - +
167A PRO* 3.5 11.4 - - - +
193A LEU 4.2 1.9 - - - +
194A PHE* 3.5 27.4 - - + -
195A LYS 5.0 0.5 + - - -
199A PHE* 3.6 38.9 - - + -
299A PHE* 2.8 24.3 + - - +
302A ARG* 1.3 121.3 + - - +
304A PHE* 1.3 63.5 + - + +
305A THR* 5.3 2.5 - - - +
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Residues in contact with PHE 304 (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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155A SER* 3.9 26.2 - - - -
156A PRO* 4.2 5.8 - - + -
163A VAL* 3.9 21.3 - - + -
164A HIS 5.8 0.2 - - - -
188A TRP* 3.7 29.6 - + - -
189A ALA* 4.0 6.7 - - + -
193A LEU 3.2 15.7 - - - -
194A PHE* 3.8 32.1 - + + -
299A PHE 5.0 0.2 - - - -
300A TRP* 2.9 57.8 + + + +
301A LYS 4.2 8.1 - - - +
302A ARG 4.8 1.2 - - - +
303A ASP* 1.3 87.2 + - + +
305A THR* 1.3 65.3 + - - +
306A GLY 3.4 6.3 - - - +
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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