Contacts of the helix formed by residues 246 - 257 (chain A) in PDB entry 1F4J
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 SER 246 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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244A ASN 4.2 1.0 + - - -
245A LEU* 1.3 75.3 - - - +
247A VAL* 1.3 65.1 + - - +
248A GLU* 3.9 8.1 + - - +
249A ASP* 3.1 33.3 + - - +
250A ALA* 2.8 20.8 + - - +
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Residues in contact with VAL 247 (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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127A ARG* 3.7 19.3 - - - +
205A ILE* 4.8 5.8 - - + -
245A LEU 3.8 1.2 + - - +
246A SER* 1.3 72.2 - - - +
248A GLU* 1.3 65.0 + - + +
250A ALA* 3.3 8.8 + - - +
251A ALA* 2.8 31.2 + - - +
458A ARG* 6.3 1.3 - - + -
462A ASN* 3.5 25.8 - - - +
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Residues in contact with GLU 248 (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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246A SER* 3.1 8.8 + - - +
247A VAL* 1.3 85.5 - - + +
249A ASP* 1.3 61.4 + - - +
251A ALA* 3.2 7.2 + - - +
252A ARG* 2.9 28.7 + - + +
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Residues in contact with ASP 249 (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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245A LEU* 4.0 21.9 - - + +
246A SER* 3.1 26.7 + - - +
248A GLU* 1.3 82.6 - - - +
250A ALA* 1.3 54.1 + - - +
252A ARG* 3.1 30.4 + - - +
253A LEU* 2.8 40.5 + - - +
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Residues in contact with ALA 250 (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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125A THR* 2.9 36.5 + - - +
126A VAL* 5.3 0.2 - - - -
205A ILE* 3.8 31.9 - - + -
245A LEU* 4.4 5.3 - - + +
246A SER 2.8 16.4 + - - +
247A VAL* 3.4 5.8 - - - +
249A ASP* 1.3 77.1 - - - +
251A ALA* 1.3 56.7 + - - +
253A LEU* 4.7 0.2 - - - -
254A SER* 2.8 25.1 + - - -
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Residues in contact with ALA 251 (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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247A VAL 2.8 13.8 + - - +
248A GLU* 3.4 10.8 - - - +
250A ALA* 1.3 73.6 - - - +
252A ARG* 1.3 68.9 + - - +
254A SER* 2.8 27.2 + - - -
255A GLN* 3.2 2.9 + - - +
255D GLN* 3.3 31.5 - - - +
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Residues in contact with ARG 252 (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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245A LEU* 6.1 0.4 - - - +
248A GLU* 2.9 14.0 + - + +
249A ASP* 3.5 29.8 + - - +
251A ALA* 1.3 75.7 - - - +
253A LEU* 1.3 82.7 + - - +
255A GLN* 3.1 10.3 - - - +
256A GLU* 2.8 69.6 + - - +
255D GLN* 4.8 2.4 - - - +
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Residues in contact with LEU 253 (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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125A THR* 3.4 14.6 - - + +
245A LEU* 3.9 31.0 - - + -
249A ASP 2.8 23.2 + - - +
250A ALA 3.7 0.2 - - - +
252A ARG* 1.3 103.4 - - - +
254A SER* 1.3 57.3 + - - +
255A GLN 2.9 5.8 - - - -
256A GLU* 4.0 9.0 - - + +
257A ASP* 2.5 42.5 + - + +
260A TYR* 3.5 40.8 - - + +
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Residues in contact with SER 254 (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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123A ALA* 3.6 29.2 - - - +
125A THR* 3.2 14.0 + - - -
126A VAL* 4.5 4.9 - - - -
250A ALA 2.8 18.2 + - - -
251A ALA* 2.8 17.3 + - - -
253A LEU* 1.3 73.5 - - - +
255A GLN* 1.3 60.6 + - - +
257A ASP 4.6 1.6 - - - -
258A PRO* 3.6 17.2 - - - +
254D SER* 5.0 5.4 + - - +
255D GLN* 3.2 20.8 + - - +
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Residues in contact with GLN 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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251A ALA 3.7 2.2 - - - +
252A ARG* 3.1 12.7 + - - +
253A LEU 2.9 0.4 - - - -
254A SER* 1.3 82.5 + - - +
256A GLU* 1.3 84.0 + - - +
257A ASP 3.4 0.3 + - - -
258A PRO* 4.0 9.0 - - - +
251D ALA* 3.1 48.2 - - - +
252D ARG* 5.0 1.7 - - - +
254D SER* 3.7 11.5 + - - +
255D GLN* 3.6 22.0 - - + +
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Residues in contact with GLU 256 (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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252A ARG* 2.8 68.0 + - - +
253A LEU* 4.0 7.3 - - + +
255A GLN* 1.3 95.8 + - - +
257A ASP* 1.3 61.3 + - + +
258A PRO* 4.1 2.3 - - - +
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Residues in contact with ASP 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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124A ASP 5.3 0.2 + - - -
125A THR* 4.9 1.2 + - - -
253A LEU* 2.5 25.2 + - + +
254A SER* 4.6 0.5 - - - -
255A GLN 3.4 0.2 - - - -
256A GLU* 1.3 79.3 - - + +
258A PRO* 1.3 66.5 - - - +
259A ASP* 3.0 15.2 + - - +
260A TYR* 3.1 40.9 + - + +
263A ARG* 2.8 46.2 + - - -
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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