Contacts of the strand formed by residues 279 - 284 (chain J) in PDB entry 3IT8
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 PRO 279 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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188J VAL* 5.9 1.2 - - - +
200J LEU* 3.4 34.0 - - + +
216J TRP* 3.7 32.0 - - + -
217J ILE 3.3 15.9 - - - +
218J GLU* 4.0 1.9 - - - +
237J TRP* 4.3 11.0 - - + +
269J VAL* 4.7 7.4 - - + -
271J THR* 4.8 1.6 - - + +
275J MET* 3.3 29.4 - - + -
278J GLN* 1.3 93.5 - - + +
280J VAL* 1.3 58.7 + - - +
294J THR* 5.8 1.0 - - - -
296J SER* 5.3 0.2 + - - -
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Residues in contact with VAL 280 (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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188J VAL* 6.3 0.7 - - - -
215J LYS 3.6 0.5 - - - +
216J TRP* 3.5 8.5 - - - -
217J ILE* 2.8 37.3 + - + +
219J SER* 4.6 10.8 - - - -
222J PHE* 3.5 30.7 - - + -
226J TYR* 4.4 2.2 - - + -
279J PRO* 1.3 75.4 - - - +
281J CYS* 1.3 59.2 + - - +
282J VAL* 3.7 1.5 + - + -
292J VAL* 3.2 21.5 - - + -
293J TYR 2.8 24.9 - - - +
294J THR* 3.1 29.6 - - + +
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Residues in contact with CYS 281 (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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188J VAL* 3.7 16.3 - - + +
202J CYS* 2.0 50.0 - - - -
214J THR* 3.4 21.1 - - - -
215J LYS 3.9 2.7 - - - -
216J TRP* 3.8 19.8 - - + -
280J VAL* 1.3 71.5 - - - +
282J VAL* 1.3 59.0 + - - +
283J VAL* 3.9 5.6 - - - -
292J VAL* 3.5 1.4 - - - -
293J TYR* 2.7 43.6 + - + +
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Residues in contact with VAL 282 (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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214J THR* 3.4 5.6 + - - -
215J LYS* 2.8 47.3 + - + +
217J ILE* 3.9 24.0 - - + -
222J PHE* 4.0 17.0 - - + -
228J TYR* 4.0 19.7 - - + -
280J VAL* 4.4 4.0 - - + +
281J CYS* 1.3 75.9 - - - +
283J VAL* 1.3 62.5 + - - +
284J PHE* 3.7 31.8 - - + -
290J ALA* 4.7 3.4 - - + -
291J GLN 3.3 13.0 - - - +
292J VAL* 4.3 7.4 - - + -
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Residues in contact with VAL 283 (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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184J PRO* 5.3 0.7 - - + -
186J VAL* 4.2 4.9 - - + -
202J CYS* 4.1 2.2 - - - -
204J VAL* 4.0 36.6 - - + -
212J VAL* 4.6 5.4 - - + -
213J ILE 3.8 4.7 - - - +
214J THR* 4.2 4.3 - - - +
281J CYS* 3.9 20.4 - - - -
282J VAL* 1.3 73.5 - - - +
284J PHE* 1.3 68.1 + - - +
285J HIS* 4.6 5.8 - - + -
288J LEU* 3.7 19.2 - - + +
290J ALA* 3.4 3.9 - - - -
291J GLN 2.9 30.4 + - - -
293J TYR* 4.0 24.7 - - + -
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Residues in contact with PHE 284 (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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100J THR* 3.2 20.5 - - - +
102J LEU* 4.2 10.1 - - + -
103J LEU* 3.5 38.4 - - + -
212J VAL* 3.6 3.6 - - - +
213J ILE* 2.8 41.5 + - + +
215J LYS* 3.4 35.0 - - + -
228J TYR* 3.6 34.1 - + - -
282J VAL* 3.7 25.4 - - + -
283J VAL* 1.3 70.9 - - - +
285J HIS* 1.3 62.6 + - - +
289J GLU 3.8 6.5 - - - +
290J ALA* 3.6 24.9 - - + -
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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