Contacts of the strand formed by residues 264 - 270 (chain B) in PDB entry 4HXG
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 VAL 264 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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232B TYR* 2.7 38.3 + - + -
244B ASP 3.0 18.7 + - - +
245B LYS* 3.7 15.5 - - - -
246B ILE* 3.7 20.2 - - + -
257B LEU* 3.6 31.0 - - + -
262B ARG 4.9 0.9 - - - +
263B GLU* 1.3 75.2 - - - +
265B ALA* 1.3 58.2 + - - +
266B GLN 3.9 16.8 - - - +
267B ALA* 4.2 2.0 - - + -
276B PHE* 4.1 10.3 - - + -
277B THR 3.4 15.7 - - - +
278B LEU* 4.0 1.1 - - + -
279B PHE* 4.3 0.2 - - - -
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Residues in contact with ALA 265 (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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232B TYR* 4.2 8.9 + - - -
263B GLU 3.6 2.8 + - - -
264B VAL* 1.3 74.7 - - - +
266B GLN* 1.3 58.8 + - + +
277B THR* 2.9 32.9 + - - +
278B LEU 4.5 0.2 - - - +
279B PHE* 3.7 31.2 - - + -
284B VAL* 4.1 14.4 - - + -
303B ILE 5.9 0.2 - - - +
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Residues in contact with GLN 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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232B TYR* 5.4 2.5 - - - -
264B VAL* 3.6 3.1 - - - +
265B ALA* 1.3 79.4 - - + +
267B ALA* 1.3 66.8 + - - +
268B LYS* 4.1 18.5 - - - -
276B PHE* 3.2 3.6 - - - +
277B THR* 2.9 36.4 + - - +
303B ILE 4.9 3.2 + - - -
304B MET 3.7 9.7 + - - -
305B GLY* 3.7 28.9 - - - -
306B PHE* 3.6 20.1 + - + -
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Residues in contact with ALA 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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222B ILE* 3.8 22.4 - - + +
223B ASP* 4.6 3.5 - - - +
230B LEU* 3.9 14.7 - - + +
232B TYR* 5.3 1.0 - - + -
246B ILE* 3.7 31.0 - - + -
264B VAL* 4.2 0.9 - - + -
266B GLN* 1.3 82.1 - - - +
268B LYS* 1.3 68.3 + - - +
274B VAL* 4.7 0.4 - - + -
275B TYR 3.3 8.5 - - - +
276B PHE* 4.0 8.5 - - + -
306B PHE* 4.0 0.7 - - - -
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Residues in contact with LYS 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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20B PRO 4.3 6.3 + - - -
21B ARG* 4.4 17.0 - - - +
223B ASP* 3.4 11.9 - - - +
230B LEU* 3.9 4.7 - - - -
266B GLN* 4.1 16.6 - - + +
267B ALA* 1.3 79.5 - - - +
269B ILE* 1.3 61.7 + - - +
270B ARG* 4.4 17.2 - - + +
274B VAL* 3.2 7.6 - - - +
275B TYR* 2.8 34.1 + - + -
306B PHE* 2.9 46.8 + - + +
307B ASP* 3.6 29.4 + - - +
308B ALA 5.3 0.7 - - - +
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Residues in contact with ILE 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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223B ASP* 2.9 34.3 + - + +
224B SER* 3.9 24.1 - - - +
225B ASP* 3.1 32.4 - - - +
228B ARG* 4.2 14.8 - - + +
230B LEU* 4.0 13.9 - - + +
248B ILE* 3.7 28.0 - - + -
268B LYS* 1.3 76.4 - - - +
270B ARG* 1.3 74.8 + - - +
272B GLY* 4.8 2.0 - - - +
273B LYS 3.4 15.0 - - - +
274B VAL* 3.7 9.6 - - + -
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Residues in contact with ARG 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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21B ARG* 6.0 3.2 - - - +
22B THR 5.4 2.8 + - - -
23B ARG* 5.4 7.1 - - - +
223B ASP* 3.5 27.0 + - - -
224B SER 5.0 3.2 + - - -
225B ASP* 4.5 1.6 - - - +
268B LYS* 4.4 12.9 - - + +
269B ILE* 1.3 88.7 + - - +
271B ASN* 1.3 74.8 + - + +
272B GLY 3.4 0.7 - - - -
273B LYS* 2.9 22.2 + - - +
275B TYR* 4.5 19.3 - - + -
307B ASP* 3.1 25.6 + - - -
308B ALA* 2.6 35.2 + - + +
309B ASP* 4.9 12.8 + - - +
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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