Contacts of the helix formed by residues 245 - 250 (chain J) in PDB entry 5XVO
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 PHE 245 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5J THR* 5.1 7.9 - - + -
7J VAL* 4.7 9.2 - - + -
41J LEU* 3.7 24.5 - - + -
43J GLU* 4.4 12.8 - - - -
178J TYR* 3.5 22.9 - + - -
182J LEU* 4.7 10.3 - - + -
241J LYS* 3.7 20.8 + - + -
242J ARG* 3.2 22.1 + - + +
243J LYS 3.2 1.4 - - - -
244J LEU* 1.3 73.5 - - - +
246J ALA* 1.3 62.1 + - - +
247J LEU 3.0 6.9 + - - -
248J PHE* 3.1 38.0 + + - +
249J MET* 3.4 2.1 + - + -
103M ILE* 3.3 35.2 - - + +
105M PHE* 4.7 21.8 - + - -
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Residues in contact with ALA 246 (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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228J ILE* 4.1 11.0 - - + -
242J ARG 4.3 0.6 + - - -
243J LYS* 3.2 19.0 + - - +
245J PHE* 1.3 77.7 - - - +
247J LEU* 1.3 54.2 + - - +
249J MET* 3.7 22.6 - - + +
250J ASN* 2.8 54.5 + - - +
252J TYR* 4.3 1.1 - - - -
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Residues in contact with LEU 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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179J GLY 4.8 2.5 - - - +
182J LEU* 4.3 17.0 - - + -
183J LEU* 4.8 9.2 - - + -
186J ILE* 6.4 0.4 - - + -
224J LEU* 4.0 28.5 - - + +
225J VAL* 4.1 21.1 - - + +
228J ILE* 4.2 14.6 - - + -
244J LEU* 3.1 26.9 + - + +
245J PHE 3.0 0.6 - - - -
246J ALA* 1.3 78.6 - - - +
248J PHE* 1.3 67.8 + - + +
250J ASN 4.1 2.3 - - - +
252J TYR* 3.6 25.3 - - + +
261J LEU* 3.4 40.8 + - + +
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Residues in contact with PHE 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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5J THR* 3.7 29.8 - - + +
38J ASP* 4.8 1.3 - - - +
39J VAL* 4.4 21.8 - - + -
63J LEU* 5.6 2.2 - - + -
65J LEU* 6.1 1.3 - - + -
182J LEU* 4.2 31.9 - - + -
186J ILE* 3.7 33.0 - - + -
245J PHE* 3.1 41.1 + + + +
247J LEU* 1.3 85.3 - - + +
249J MET* 1.3 58.8 + - - +
250J ASN 3.6 0.6 - - - +
260J PHE* 4.0 1.9 - - - +
261J LEU* 5.4 2.6 + - + +
262J THR* 4.5 16.4 - - + +
102M ARG* 2.6 38.4 + - + +
103M ILE* 4.9 4.5 - - + -
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Residues in contact with MET 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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242J ARG 5.7 1.6 - - - +
245J PHE* 3.4 2.5 + - + -
246J ALA* 3.1 32.3 + - + +
248J PHE* 1.3 78.6 - - - +
250J ASN* 1.3 70.2 + - - +
251J THR* 4.6 1.6 - - - +
260J PHE* 3.4 16.1 - - - -
102M ARG* 4.3 15.6 + - + +
103M ILE* 3.3 35.9 - - + +
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Residues in contact with ASN 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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228J ILE* 5.6 1.6 - - - +
246J ALA* 2.8 39.5 + - - +
247J LEU 4.1 4.3 - - - +
248J PHE 3.6 0.2 - - - -
249J MET* 1.3 87.2 - - - +
251J THR* 1.3 65.4 + - - +
252J TYR* 3.7 30.8 + - + +
260J PHE* 3.4 17.3 - - - -
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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