Contacts of the helix formed by residues 245 - 250 (chain A) in PDB entry 1JV2
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 ARG 245 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218A ASP 5.5 0.2 - - - +
219A ASP* 3.0 35.4 + - - +
220A SER* 3.0 15.1 + - - +
221A TYR* 3.8 21.9 - - + -
243A VAL 3.0 0.2 + - - -
244A PRO* 1.3 80.1 - - + +
246A ALA* 1.3 69.9 + - - +
247A ALA 3.7 7.3 - - - +
249A THR* 3.7 18.9 + - + +
275A TYR* 4.4 4.9 - - + -
219B PRO* 3.6 27.0 - - - +
253B LYS* 4.3 12.5 - - - +
254B THR 3.0 21.8 + - - -
255B HIS* 4.1 2.6 - - - +
256B ILE* 4.1 14.4 - - + +
259B ASP* 2.6 50.6 + - - +
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Residues in contact with ALA 246 (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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220A SER* 3.8 13.6 + - - -
243A VAL* 3.0 27.4 + - + +
244A PRO 3.5 0.6 - - - -
245A ARG* 1.3 85.2 - - - +
247A ALA* 1.3 68.5 + - - +
248A ARG 3.2 1.7 + - - -
249A THR 3.3 1.9 + - - -
251A GLY* 3.1 13.3 + - - -
252A MET* 3.4 37.9 - - + +
254A TYR* 4.6 3.6 - - - +
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Residues in contact with ALA 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A SER* 5.4 0.2 + - - -
245A ARG 3.7 5.0 - - - +
246A ALA* 1.3 79.5 - - + +
248A ARG* 1.3 78.2 + - - +
249A THR 3.7 0.2 + - - -
250A LEU* 3.6 29.8 - - + -
251A GLY 4.6 0.2 - - - +
252A MET* 4.2 17.8 - - + +
268A THR* 5.1 1.6 - - + -
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Residues in contact with ARG 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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247A ALA* 1.3 91.6 - - - +
249A THR* 1.3 69.4 + - - +
250A LEU* 2.9 46.1 + - - +
272A MET* 3.2 24.5 - - + +
317B LEU* 4.1 21.3 - - + -
3320B NAG 3.4 65.3 + - + +
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Residues in contact with THR 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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244A PRO 3.9 6.9 - - - +
245A ARG* 3.7 23.7 + - + +
246A ALA 3.3 7.4 + - - -
247A ALA 3.5 1.4 + - - -
248A ARG* 1.3 76.7 + - - +
250A LEU* 1.3 61.9 + - - +
251A GLY 3.3 2.4 + - - -
272A MET* 3.7 0.6 - - - -
273A ALA* 2.9 37.5 + - - -
274A ALA 4.1 2.6 + - - -
275A TYR 4.8 0.7 + - - -
256B ILE* 3.3 34.5 - - + -
317B LEU* 4.7 6.9 - - - +
321B TYR* 2.8 32.3 + - - +
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Residues in contact with LEU 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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244A PRO 4.4 0.2 - - - -
246A ALA 3.3 0.6 + - - -
247A ALA* 3.6 17.7 - - + -
248A ARG* 2.9 42.9 + - - +
249A THR* 1.3 80.0 - - - +
251A GLY* 1.3 68.2 + - - +
268A THR* 4.1 13.0 - - + -
269A GLY* 3.5 25.0 - - - +
270A GLU* 3.8 22.7 - - - +
271A GLN 3.8 18.0 - - - +
272A MET* 4.1 10.1 - - + +
275A TYR 5.2 0.3 + - - -
276A PHE* 3.4 18.4 + - - +
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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