Contacts of the strand formed by residues 283 - 290 (chain B) in PDB entry 3D87
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 283 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255B VAL* 2.6 30.3 - - - +
256B GLN* 3.8 3.3 + - - +
281B ASN 4.9 0.7 + - - -
282B ALA* 1.3 78.3 - - - +
284B ILE* 1.3 61.8 + - - +
285B SER* 3.7 3.5 + - - -
302B SER* 5.3 5.2 - - - -
303B VAL 2.9 22.5 + - - -
304B PRO* 3.0 23.5 - - - +
305B CYS* 3.6 7.0 - - - +
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Residues in contact with ILE 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B LEU* 3.4 8.2 - - + +
221B LEU* 3.1 44.2 - - + -
230B VAL* 4.3 0.4 - - + -
232B VAL* 4.4 9.6 - - + -
253B VAL* 3.3 34.1 - - + -
254B GLN 3.5 9.6 - - - +
255B VAL* 3.8 11.2 - - + -
276B VAL* 3.8 19.3 - - + -
283B SER* 1.3 74.6 - - - +
285B SER* 1.3 66.3 + - - +
286B VAL* 4.4 4.7 - - + -
302B SER* 3.4 0.6 - - - -
303B VAL* 2.8 34.0 + - + +
305B CYS* 3.4 20.9 - - - -
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Residues in contact with SER 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253B VAL* 3.6 0.5 - - - -
254B GLN* 2.9 50.9 + - - +
255B VAL 4.4 0.7 + - - -
256B GLN* 4.5 3.6 + - - -
283B SER 4.0 5.2 + - - -
284B ILE* 1.3 77.9 - - - +
286B VAL* 1.3 65.7 + - - +
300B TRP* 3.3 29.3 - - - -
301B ALA 2.8 10.3 - - - -
302B SER* 3.9 11.4 - - - +
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Residues in contact with VAL 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B PRO* 3.5 17.5 - - + +
219B LEU* 3.4 31.4 - - + -
232B VAL* 4.2 2.2 - - + -
234B TRP* 3.7 42.8 - - + -
251B PHE* 4.1 7.9 - - + -
252B CYS 3.1 9.9 - - - +
253B VAL* 4.1 14.1 - - + -
284B ILE* 4.4 1.1 - - + -
285B SER* 1.3 78.6 - - - +
287B ARG* 1.3 62.8 + - - +
300B TRP* 3.1 6.2 - - - -
301B ALA* 2.7 36.8 + - + +
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Residues in contact with ARG 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216B PRO* 3.7 6.3 - - - -
251B PHE* 3.3 2.6 - - - -
252B CYS* 2.8 36.3 + - + +
266B ARG* 3.1 16.2 - - - +
268B PHE* 6.0 1.0 - - - -
286B VAL* 1.3 76.2 - - - +
288B ALA* 1.3 61.3 + - - +
297B TRP* 3.3 51.8 - - + +
298B SER* 3.5 20.9 + - - +
299B GLU 3.7 7.0 - - - +
300B TRP* 3.3 50.4 - - + +
5001B PO4 2.7 43.8 + - - -
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Residues in contact with ALA 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213B PRO* 3.9 7.9 - - + +
214B ASP 5.0 0.7 - - - +
216B PRO* 3.8 9.4 - - + +
237B PRO* 5.7 0.7 - - + -
249B LEU* 3.8 20.2 - - + -
250B THR 3.1 5.4 - - - +
251B PHE* 3.4 29.8 - - + -
287B ARG* 1.3 72.8 - - - +
289B GLN* 1.3 58.2 + - - +
297B TRP* 3.3 8.2 - - - -
298B SER* 2.7 39.8 + - - +
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Residues in contact with GLN 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213B PRO* 4.4 1.3 - - - -
249B LEU* 3.0 13.5 - - - +
250B THR* 2.7 36.0 + - + +
288B ALA* 1.3 74.3 - - - +
290B ASP* 1.3 80.3 + - - +
293B TYR 4.1 4.4 - - - +
294B SER* 3.8 17.3 + - - +
295B SER 2.8 33.6 + - - +
296B SER 4.1 10.2 - - - +
297B TRP* 3.4 50.8 + - + +
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Residues in contact with ASP 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A ARG* 3.0 26.5 + - - -
114B TYR* 3.1 31.0 + - - +
211B ILE* 5.3 0.2 - - + -
213B PRO* 4.7 3.8 - - - +
240B TRP* 3.7 14.1 - - + -
248B SER 3.7 7.9 + - - +
249B LEU* 4.1 4.8 - - - +
250B THR* 3.2 7.4 - - - +
289B GLN* 1.3 85.6 - - - +
291B ARG* 1.3 68.0 + - - +
292B TYR* 3.1 8.2 + - - +
293B TYR* 3.0 38.5 + - - +
295B SER* 3.9 13.9 - - - +
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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