Contacts of the strand formed by residues 273 - 280 (chain A) 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 LYS 273 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268A LYS 3.9 0.2 - - - +
269A ILE* 3.3 3.8 - - - +
270A ARG 2.9 33.6 + - - +
271A ASN* 3.0 12.8 + - + +
272A GLY* 1.3 79.9 - - - +
274A VAL* 1.3 61.4 + - - +
275A TYR* 4.1 16.8 + - + +
288A LEU* 4.0 17.3 - - + -
289A TRP 3.4 11.2 - - - +
290A ASP* 4.4 18.2 - - + -
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Residues in contact with VAL 274 (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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230A LEU* 4.2 15.0 - - + -
246A ILE* 3.6 30.7 - - + -
248A ILE* 4.1 17.3 - - + -
256A ILE* 4.3 4.9 - - + -
268A LYS 3.4 7.6 - - - +
269A ILE* 3.6 34.3 - - + -
272A GLY 4.1 0.2 + - - -
273A LYS* 1.3 73.2 - - - +
275A TYR* 1.3 69.0 + - - +
276A PHE* 3.7 6.6 - - + -
288A LEU* 3.6 1.8 - - - -
289A TRP* 2.8 48.4 + - + -
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Residues in contact with TYR 275 (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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267A ALA* 3.3 0.7 - - - -
268A LYS* 2.7 47.5 + - + +
270A ARG* 4.6 13.7 - - + -
273A LYS* 4.4 22.6 - - + +
274A VAL* 1.3 74.6 - - - +
276A PHE* 1.3 63.7 + - - +
286A LEU* 4.8 2.5 - - + -
287A TYR 3.6 9.6 - - - +
288A LEU* 4.1 34.2 - - + +
296A ILE* 5.3 0.7 - - + -
306A PHE* 3.6 21.7 - - + -
308A ALA* 3.8 24.6 - - + +
311A ARG 6.0 0.2 - - - -
312A LEU* 3.7 42.2 - - + +
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Residues in contact with PHE 276 (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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246A ILE* 3.9 32.3 - - + -
256A ILE* 5.5 3.1 - - + -
257A LEU* 6.0 5.6 - - + -
260A ILE* 5.6 2.9 - - + -
264A VAL* 4.2 4.3 - - + -
266A GLN 3.1 13.9 - - - +
267A ALA* 4.0 1.6 - - + -
274A VAL* 3.7 12.8 - - + -
275A TYR* 1.3 75.3 - - - +
277A THR* 1.3 64.2 + - - +
278A LEU* 3.6 40.2 - - + -
286A LEU* 3.4 5.4 - - - +
287A TYR* 2.7 67.4 + + + +
288A LEU 4.3 1.1 - - - -
289A TRP* 4.2 21.1 - - + -
293A VAL* 4.2 19.7 - - + -
306A PHE* 3.9 3.3 - - - -
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Residues in contact with THR 277 (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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264A VAL* 3.3 10.2 - - - +
265A ALA* 3.0 28.2 + - - +
266A GLN* 2.9 30.7 + - - +
276A PHE* 1.3 75.7 - - - +
278A LEU* 1.3 62.8 + - - +
284A VAL* 3.7 12.6 - - + +
285A ASN 2.8 18.6 - - - +
286A LEU* 3.8 10.1 - - - -
303A ILE* 3.9 23.8 + - + +
306A PHE* 3.6 19.7 - - + -
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Residues in contact with LEU 278 (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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257A LEU* 5.9 4.0 - - + -
260A ILE* 4.9 21.1 - - + -
262A ARG* 4.5 18.4 - - + +
263A GLU 3.3 10.1 - - - +
264A VAL* 3.7 26.2 - - + -
265A ALA 5.0 0.2 - - - -
276A PHE* 3.6 26.5 - - + -
277A THR* 1.3 73.7 - - - +
279A PHE* 1.3 65.3 + - - +
280A GLU* 3.5 18.9 + - + +
284A VAL* 3.2 8.9 - - - -
285A ASN 2.9 27.7 + - - -
287A TYR* 3.5 30.1 - - + -
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Residues in contact with PHE 279 (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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232A TYR* 5.8 0.2 - - - -
262A ARG* 3.5 15.6 - - - +
263A GLU* 3.0 37.6 + - + +
264A VAL 4.2 3.1 - - - -
265A ALA* 3.4 33.9 - - + -
278A LEU* 1.3 71.4 - - - +
280A GLU* 1.3 63.8 + - - +
283A SER 3.6 3.6 - - - -
284A VAL* 4.0 14.4 - - + -
302A TRP* 4.6 12.1 - + - -
391A MET* 3.8 23.1 - - + -
419A ASN* 3.0 30.7 - - + +
420A GLY* 3.2 28.6 - - - +
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Residues in contact with GLU 280 (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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260A ILE* 5.9 1.6 - - - +
262A ARG* 4.4 14.9 + - + +
278A LEU* 3.5 14.0 + - + +
279A PHE* 1.3 80.2 - - - +
281A GLU* 1.3 77.6 + - - +
282A GLY 3.2 1.8 - - - -
283A SER* 2.7 40.5 + - - -
285A ASN* 2.7 32.4 + - - +
287A TYR* 2.8 37.1 + - - -
298A LYS* 4.3 10.5 + - - +
391A MET* 4.7 0.2 - - - -
420A GLY* 3.7 3.1 - - - -
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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