Contacts of the strand formed by residues 244 - 248 (chain J) in PDB entry 5GJQ
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 244 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209J CYS* 3.6 1.7 - - - +
210J THR* 2.7 31.6 - - - +
212J ILE* 4.3 4.9 - - - -
238J ALA* 2.9 42.4 + - - +
241J HIS 4.1 1.6 - - - -
242J ALA* 3.9 1.2 - - - +
243J PRO* 1.3 74.0 - - - +
245J ILE* 1.3 63.4 + - - +
246J ILE* 4.5 0.2 - - - +
288J ASN 3.3 4.5 + - - -
289J ILE* 3.3 30.9 - - - +
290J LYS 4.6 0.2 - - - -
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Residues in contact with ILE 245 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165J ILE* 3.9 35.2 - - + -
200J ALA 4.7 1.6 - - - +
203J VAL* 4.3 1.6 - - + -
204J ALA* 3.8 28.9 - - + +
207J THR* 4.2 6.1 - - + -
209J CYS* 4.1 8.5 - - + +
210J THR 2.5 8.3 + - - +
211J PHE* 3.1 28.4 - - + -
212J ILE* 2.6 33.3 + - - +
244J SER* 1.3 75.4 - - - +
246J ILE* 1.3 62.2 + - - +
290J LYS* 3.4 25.8 - - + +
292J ILE* 4.0 16.8 - - + -
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Residues in contact with ILE 246 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212J ILE* 3.9 17.3 - - + -
214J VAL* 4.2 16.6 - - + -
234J LEU* 4.1 15.7 - - + -
235J PHE* 3.9 33.4 - - + -
238J ALA* 4.1 14.8 - - + -
244J SER 3.8 0.6 + - - +
245J ILE* 1.3 77.1 - - - +
247J PHE* 1.3 61.2 + - - +
248J MET* 3.8 20.4 - - + -
276J LEU* 4.5 7.2 - - + -
289J ILE* 4.3 15.7 - - + -
290J LYS 3.0 5.7 + - - -
291J VAL* 2.9 15.8 - - + +
292J ILE 2.6 33.8 + - - +
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Residues in contact with PHE 247 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188J LEU* 4.5 0.9 - - + -
196J LYS* 4.3 2.0 - - + -
197J THR* 3.7 37.2 - - + -
200J ALA* 3.2 18.2 - - + -
211J PHE* 3.1 33.4 - + + -
212J ILE 2.8 11.2 + - - +
213J ARG* 4.3 17.0 - - - -
214J VAL 3.5 21.1 + - - -
245J ILE 3.9 0.2 + - - -
246J ILE* 1.3 75.3 - - - +
248J MET* 1.3 90.0 + - - +
249J ASP* 4.4 4.9 - - - -
292J ILE* 2.6 50.0 - - + -
294J ALA* 3.5 25.4 - - + -
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Residues in contact with MET 248 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213J ARG* 5.5 3.4 - - - +
214J VAL* 4.1 16.2 - - + +
215J SER* 6.2 0.4 - - - +
246J ILE* 3.8 11.7 - - + +
247J PHE* 1.3 93.2 - - - +
249J ASP* 1.3 60.8 + - - +
269J VAL* 4.3 15.3 - - + -
272J THR* 5.3 4.7 - - + -
273J MET* 3.5 26.0 - - + -
276J LEU* 3.6 24.0 - - + -
291J VAL* 3.1 42.2 - - + -
292J ILE 3.2 3.0 + - - +
293J MET* 3.6 19.3 - - - +
294J ALA* 3.5 24.6 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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