Contacts of the strand formed by residues 264 - 271 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213A LYS 3.1 27.2 + - - +
214A GLY* 4.0 11.8 - - - +
215A PHE* 3.3 38.4 - - + -
216A VAL* 2.8 28.1 + - - +
262A PHE 3.0 9.5 + - - +
263A GLU* 1.3 92.1 - - + +
265A VAL* 1.3 64.9 + - - +
292A GLU 3.8 0.9 - - - -
293A MET* 3.9 28.7 - - + +
294A ALA 5.4 1.6 - - - +
305A GLU* 5.3 3.4 + - - -
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Residues in contact with VAL 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215A PHE* 3.3 7.8 - - - -
216A VAL* 3.3 12.3 - - + +
218A ILE* 3.9 23.3 - - + -
254A LYS* 4.1 25.1 - - + +
257A CYS* 4.2 4.3 - - + -
258A ILE* 4.5 4.5 - - + -
262A PHE* 3.8 28.3 - - + -
263A GLU 5.0 0.7 - - - +
264A LYS* 1.3 80.8 - - - +
266A PHE* 1.3 60.7 + - - +
291A ILE* 3.6 2.3 - - - -
292A GLU* 3.0 54.9 + - + +
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Residues in contact with PHE 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206A PHE* 4.0 13.7 - + + -
207A ARG* 3.7 22.4 - - + -
210A LEU* 3.7 44.4 - - + -
211A ILE* 3.9 27.8 - - + -
215A PHE* 3.7 16.8 - - + -
216A VAL 3.2 5.4 + - - -
217A GLU* 3.5 46.4 - - + -
218A ILE* 2.9 29.8 + - - +
254A LYS* 5.6 1.3 - - - -
265A VAL* 1.3 75.3 - - - +
267A SER* 1.3 66.8 + - - +
268A ILE* 4.3 2.7 - - + -
290A ASP 2.9 14.8 - - - +
291A ILE* 4.6 0.9 - - + -
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Residues in contact with SER 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206A PHE* 4.6 0.5 - - - -
217A GLU* 5.1 1.3 - - - -
218A ILE* 3.7 26.0 - - - -
220A THR* 4.4 20.3 + - - +
250A PRO* 4.7 6.2 - - - +
254A LYS* 4.8 4.0 - - - +
266A PHE* 1.3 77.3 - - - +
268A ILE* 1.3 68.7 + - - +
269A GLY 5.2 0.2 + - - -
288A GLY 3.5 2.4 + - - +
289A LEU* 3.5 0.2 - - - -
290A ASP* 2.9 48.1 + - - +
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Residues in contact with ILE 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203A CYS* 4.6 6.3 - - + +
206A PHE* 3.8 17.0 - - + -
207A ARG* 3.3 58.8 - - + +
217A GLU* 4.6 7.9 + - - +
218A ILE 4.9 0.6 + - - -
219A GLN* 4.8 11.6 + - - +
222A LYS* 5.4 1.3 + - - -
266A PHE* 4.3 6.1 - - + -
267A SER* 1.3 82.1 - - - +
269A GLY* 1.3 60.7 + - - +
287A VAL* 4.2 1.3 - - + -
288A GLY 3.3 3.6 - - - -
289A LEU* 3.2 32.3 - - + -
219B GLN* 4.1 19.2 + - - +
268B ILE 5.1 6.2 - - - +
269B GLY* 6.0 1.0 - - - -
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Residues in contact with GLY 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222A LYS* 4.5 10.8 - - - -
267A SER* 4.3 1.0 + - - -
268A ILE* 1.3 77.8 - - - +
270A PRO* 1.3 78.8 - - - +
271A VAL* 3.5 5.2 - - - +
287A VAL* 3.6 9.4 - - - +
288A GLY 3.1 27.7 + - - -
219B GLN* 5.4 2.9 - - - -
268B ILE 6.1 0.9 - - - -
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Residues in contact with PRO 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222A LYS* 3.4 36.7 + - + +
250A PRO* 5.5 1.4 - - - +
269A GLY* 1.3 84.9 - - - +
271A VAL* 1.3 62.3 + - - +
272A PHE* 3.7 19.7 - - + -
285A GLU* 3.5 24.2 - - + +
286A PHE 3.4 8.5 - - - +
287A VAL* 4.8 4.5 - - + -
219B GLN* 6.1 1.1 - - - +
222B LYS* 3.6 34.1 - - + +
268B ILE 6.1 0.4 - - - +
269B GLY* 5.6 1.1 - - - -
270B PRO* 4.0 7.6 - - + -
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Residues in contact with VAL 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249A SER* 5.0 3.6 - - - +
250A PRO* 4.0 33.0 - - + -
269A GLY 3.5 11.2 - - - +
270A PRO* 1.3 79.2 - - - +
272A PHE* 1.3 73.3 + - - +
284A THR 3.7 0.7 - - - +
285A GLU* 3.3 4.3 - - - -
286A PHE* 2.8 66.3 + - + +
288A GLY* 4.0 16.6 - - - +
290A ASP* 4.8 3.6 - - - +
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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
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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