Contacts of the strand formed by residues 264 - 271 (chain B) in PDB entry 4J15
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 LYS 264 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A ARG* 4.2 14.4 - - - +
213B LYS* 2.9 29.5 + - - +
214B GLY* 4.0 9.8 - - - +
215B PHE* 3.3 37.2 - - + -
216B VAL* 2.6 37.1 + - - +
262B PHE 2.7 10.6 + - - +
263B GLU* 1.3 94.5 - - + +
265B VAL* 1.3 55.2 + - - +
292B GLU 3.7 4.5 - - - -
293B MET* 3.8 28.2 - - + +
294B ALA 5.6 0.9 - - - -
305B GLU* 5.1 3.8 + - - -
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Residues in contact with VAL 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B PHE* 3.4 8.5 - - - -
216B VAL* 3.1 7.4 - - + +
218B ILE* 3.8 38.4 - - + -
254B LYS* 4.0 19.1 - - + +
257B CYS* 3.8 7.4 - - + -
258B ILE* 4.4 4.0 - - + -
262B PHE* 3.7 28.5 - - + -
263B GLU 5.2 0.2 - - - +
264B LYS* 1.3 79.7 - - - +
266B PHE* 1.3 61.1 + - - +
291B ILE* 3.6 0.2 - - - -
292B GLU* 3.1 52.3 + - + +
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Residues in contact with PHE 266 (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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206B PHE* 3.9 14.4 - + + -
207B ARG* 3.7 27.4 - - + -
210B LEU* 3.8 29.2 - - + -
211B ILE* 3.7 33.9 - - + -
215B PHE* 3.4 33.2 - - + -
216B VAL 3.0 8.7 + - - -
217B GLU* 3.4 45.2 - - + +
218B ILE* 2.8 29.2 + - - +
254B LYS* 5.7 0.9 - - - -
265B VAL* 1.3 74.9 - - - +
267B SER* 1.3 63.0 + - - +
268B ILE* 4.5 3.6 - - + -
290B ASP 3.1 17.5 - - - +
291B ILE* 4.5 0.4 - - + -
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Residues in contact with SER 267 (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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217B GLU* 5.2 0.9 - - - -
218B ILE* 3.6 22.0 - - - -
220B THR* 4.0 19.5 + - - +
222B LYS* 6.0 1.8 - - - -
250B PRO* 3.9 17.0 - - - +
254B LYS* 4.7 2.9 - - - +
266B PHE* 1.3 77.4 - - - +
268B ILE* 1.3 64.9 + - - +
288B GLY 3.4 3.3 - - - +
289B LEU* 3.6 0.7 - - - -
290B ASP* 2.9 44.2 + - - +
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Residues in contact with ILE 268 (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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207A ARG* 5.5 1.1 + - - +
219A GLN* 4.4 10.5 - - - +
268A ILE 5.1 5.9 - - - +
203B CYS* 4.6 7.4 - - - +
206B PHE* 3.8 32.8 - - + -
207B ARG* 3.3 46.7 - - + +
217B GLU* 4.6 10.6 + - - +
218B ILE 4.9 1.1 + - - +
219B GLN* 4.9 10.7 + - - -
222B LYS* 4.9 4.9 + - - -
266B PHE* 4.5 5.6 - - + -
267B SER* 1.3 80.6 - - - +
269B GLY* 1.3 60.8 + - - +
287B VAL* 4.1 10.3 - - + -
288B GLY 3.2 3.6 - - - +
289B LEU* 3.8 26.7 - - + -
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Residues in contact with GLY 269 (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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219A GLN* 5.3 3.8 - - - -
268A ILE 6.0 0.9 - - - -
270A PRO* 5.6 1.6 - - - -
222B LYS* 4.2 9.6 - - - -
267B SER 4.3 0.2 - - - -
268B ILE* 1.3 78.2 - - - +
270B PRO* 1.3 76.6 - - - +
271B VAL* 3.6 3.9 - - - +
287B VAL* 4.4 7.6 - - - +
288B GLY 2.9 30.0 + - - +
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Residues in contact with PRO 270 (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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219A GLN* 6.0 1.3 - - - +
220A THR 5.7 0.2 - - - +
222A LYS* 3.5 33.7 - - + +
269A GLY* 5.8 0.4 - - - -
270A PRO* 4.0 5.4 - - + -
222B LYS* 3.9 35.4 + - + +
250B PRO* 5.7 2.3 - - - +
269B GLY* 1.3 87.7 - - - +
271B VAL* 1.3 60.8 + - - +
272B PHE* 4.1 15.1 - - + -
285B GLU* 3.6 27.4 - - + +
286B PHE 3.4 8.1 - - - +
287B VAL* 4.7 5.1 - - + -
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Residues in contact with VAL 271 (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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249B SER* 4.7 11.9 - - - +
250B PRO* 4.9 15.9 - - + -
269B GLY 3.6 10.8 - - - +
270B PRO* 1.3 79.2 - - - +
272B PHE* 1.3 76.9 + - - +
284B THR 3.4 0.3 - - - +
285B GLU* 3.3 8.1 - - - -
286B PHE* 2.8 57.9 + - + +
288B GLY* 3.6 21.3 - - - -
290B ASP* 4.8 8.1 - - - +
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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