Contacts of the strand formed by residues 246 - 250 (chain J) in PDB entry 6QX2
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 246 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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222J GLY* 4.2 3.4 + - - -
223J LEU* 3.6 27.5 - - + +
244J ARG 3.7 1.6 + - - -
245J SER* 1.3 69.6 - - - +
247J ALA* 1.3 62.5 + - - +
248J VAL* 5.5 6.3 - - + -
260J VAL 4.0 0.5 - - - +
261J VAL* 3.5 2.1 - - - -
262J THR* 3.0 37.8 + - - +
263J GLU* 2.9 52.6 + - + +
485J ARG 5.3 2.6 + - - -
487J GLU* 2.9 46.1 + - - +
250T GLU* 4.9 14.3 + - - -
258T ARG* 5.8 0.6 - - - +
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Residues in contact with ALA 247 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245J SER* 3.4 5.7 + - - +
246J ARG* 1.3 74.9 - - - +
248J VAL* 1.3 69.2 + - - +
259J ILE* 4.3 3.1 - - + -
260J VAL 3.2 10.1 - - - +
261J VAL* 3.9 18.8 - - + -
318J LEU* 3.9 25.5 - - + +
322J TYR* 3.9 20.3 + - + +
327J LEU* 5.3 0.2 - - + -
250T GLU* 4.3 10.0 - - - +
251T GLU* 4.9 3.8 + - - +
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Residues in contact with VAL 248 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246J ARG* 5.5 7.6 - - + -
247J ALA* 1.3 79.8 - - - +
249J ILE* 1.3 64.1 + - - +
250J GLU* 4.1 11.6 + - - +
258J ARG 3.9 0.3 - - - +
259J ILE* 3.3 5.6 - - - +
260J VAL* 2.8 44.6 + - + +
262J THR* 6.2 1.8 - - + -
318J LEU* 5.6 0.7 - - - -
248T VAL* 4.0 30.5 - - + -
249T ILE 3.4 10.1 - - - +
250T GLU* 3.7 27.4 - - + +
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Residues in contact with ILE 249 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248J VAL* 1.3 74.6 - - - +
250J GLU* 1.3 62.8 + - - +
257J GLN* 4.0 24.2 - - + +
258J ARG 3.4 9.2 - - - +
259J ILE* 4.2 11.9 - - + -
314J ALA* 3.6 27.1 - - + +
315J SER* 3.4 41.5 - - - +
318J LEU* 4.5 15.0 - - + -
248T VAL* 3.4 5.1 - - - -
249T ILE* 2.8 55.3 + - + +
250T GLU* 6.0 0.4 - - - -
257T GLN* 4.3 5.2 - - - +
315T SER* 4.8 0.7 - - - +
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Residues in contact with GLU 250 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248J VAL* 4.1 6.3 - - + +
249J ILE* 1.3 75.4 - - - +
251J GLU* 1.3 64.5 + - + +
257J GLN* 3.4 6.7 - - - +
258J ARG* 2.2 78.8 + - + +
260J VAL* 3.7 16.0 - - + +
303J ARG* 3.6 8.0 + - - -
246T ARG* 5.1 11.9 + - - -
247T ALA 4.5 7.0 - - - +
248T VAL* 3.8 25.7 - - + +
249T ILE* 6.1 0.2 - - - -
318T LEU* 6.6 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