Contacts of the strand formed by residues 278 - 288 (chain A) in PDB entry 4Z4D
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 278 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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266A LYS* 5.6 10.8 - - + -
267A VAL 3.5 3.8 - - - +
268A GLU* 3.9 19.7 - - + -
276A LYS 3.6 8.7 + - - +
277A ARG* 1.3 77.1 - - - +
279A TYR* 1.3 72.9 + - - +
347A VAL* 4.2 32.3 - - + +
17B C 5.8 7.4 - - - +
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Residues in contact with TYR 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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266A LYS* 3.1 8.2 - - - +
267A VAL* 2.8 38.9 + - + +
269A ILE* 3.6 17.9 - - + -
277A ARG* 3.3 44.8 + - + -
278A LYS* 1.3 81.3 - - - +
280A ARG* 1.3 60.5 + - - +
330A VAL* 3.7 35.0 - - + -
331A GLY* 4.6 11.7 - - - -
337A THR* 4.8 7.9 - - + -
339A LEU* 4.0 15.9 - - + -
20B U 3.0 30.4 + - - -
21B U 4.0 6.8 + - - -
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Residues in contact with ARG 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A GLY* 2.6 52.3 + - - +
265A LEU 3.5 3.6 - - - +
266A LYS* 3.8 38.9 - - + +
279A TYR* 1.3 74.1 - - - +
281A VAL* 1.3 66.5 + - - +
282A CYS* 3.6 1.1 + - - +
330A VAL* 3.2 5.2 - - - -
331A GLY* 3.1 29.0 + - - +
350A GLN* 4.6 3.8 + - - -
16B U 4.3 15.0 - - - -
17B C 3.3 31.6 + - - -
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Residues in contact with VAL 281 (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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262A ILE* 3.7 32.8 - - + +
263A LYS* 4.1 3.1 - - - +
264A GLY* 2.7 29.8 + - - -
265A LEU 2.8 22.1 + - - +
267A VAL* 3.7 26.0 - - + -
280A ARG* 1.3 74.5 - - - +
282A CYS* 1.3 62.4 + - - +
283A ASN 3.5 24.9 - - - +
328A LEU* 4.0 19.3 - - + -
329A GLN 3.5 6.5 - - - +
330A VAL* 4.0 8.5 - - + -
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Residues in contact with CYS 282 (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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263A LYS* 3.6 25.0 + - - +
280A ARG 3.6 1.3 + - - +
281A VAL* 1.3 74.4 - - - +
283A ASN* 1.3 67.2 + - - +
329A GLN* 2.8 42.9 + - - -
330A VAL* 4.1 2.2 - - - -
331A GLY 4.0 15.5 - - - +
333A GLU* 3.7 39.0 - - + +
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Residues in contact with ASN 283 (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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259A THR* 3.8 14.6 - - - +
263A LYS* 4.2 13.9 + - - +
281A VAL* 3.5 12.1 - - - +
282A CYS* 1.3 82.7 + - - +
284A VAL* 1.3 87.1 + - - +
328A LEU 3.7 0.5 - - - -
329A GLN* 2.8 49.4 + - + +
333A GLU* 6.3 0.2 - - + -
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Residues in contact with VAL 284 (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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255A ARG* 4.3 7.0 + - + -
258A PHE* 3.7 32.3 - - + -
259A THR* 3.4 28.5 + - + +
262A ILE* 3.8 19.1 - - + -
283A ASN* 1.3 95.3 + - - +
285A THR* 1.3 77.0 + - - +
286A ARG* 3.7 1.0 + - - -
326A PRO* 3.6 22.0 - - + -
327A CYS 3.5 7.2 - - - +
328A LEU* 4.0 5.4 - - + -
329A GLN* 5.5 0.7 - - - -
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Residues in contact with THR 285 (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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255A ARG* 3.5 8.4 - - - -
284A VAL* 1.3 75.5 - - - +
286A ARG* 1.3 62.1 + - - +
287A ARG 2.7 21.9 + - - -
292A GLN* 3.3 25.3 - - - +
326A PRO* 3.3 14.2 - - - +
327A CYS* 2.9 44.0 + - + +
329A GLN* 4.9 2.7 - - + +
338A TYR* 3.6 35.0 - - + -
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Residues in contact with ARG 286 (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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255A ARG* 4.0 36.2 + - - +
284A VAL 3.7 1.2 + - - -
285A THR* 1.3 74.5 - - - +
287A ARG* 1.3 111.1 + - + +
288A PRO* 4.1 2.3 - - - +
292A GLN* 4.5 1.4 + - - -
326A PRO* 5.2 1.7 - - - +
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Residues in contact with ARG 287 (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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285A THR* 2.7 26.0 + - - -
286A ARG* 1.3 127.9 - - + +
288A PRO* 1.3 73.0 - - + +
291A HIS* 3.8 21.1 + - + -
292A GLN* 3.6 34.2 + - - +
293A THR* 5.0 2.2 - - - +
326A PRO* 3.7 5.3 - - - +
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Residues in contact with PRO 288 (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 PRO* 5.0 13.7 - - + -
286A ARG 4.4 2.5 - - - +
287A ARG* 1.3 90.3 - - + +
289A ALA* 1.3 57.4 + - - +
290A SER* 3.0 14.4 - - - +
291A HIS* 2.9 17.4 + - + +
292A GLN* 2.6 33.7 + - - +
323A PRO 3.5 10.8 - - - +
324A HIS* 3.5 25.8 - - - +
325A LEU 3.5 11.0 - - - +
326A PRO* 4.1 0.6 - - + -
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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