Contacts of the strand formed by residues 279 - 285 (chain A) in PDB entry 4MSL
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 PHE 279 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275A LEU* 3.7 9.1 - - - +
276A GLY 2.8 34.8 + - - +
277A GLY* 4.2 1.7 - - - +
278A ARG* 1.3 98.1 - - - +
280A LEU* 1.3 60.5 + - - +
281A PHE* 3.4 22.2 - + + -
296A VAL* 3.9 9.4 - - + -
297A SER 3.8 1.6 - - - -
298A THR* 3.6 18.8 - - + -
324A ASN 4.4 4.7 - - - -
325A ASP 5.2 0.2 - - - -
326A ASP 4.1 4.7 - - - -
327A MET* 3.8 28.5 - - - -
328A VAL* 3.5 21.3 - - + -
347A ASP 4.2 0.4 - - - -
348A ASP 3.5 22.0 - - - -
349A ARG 3.3 27.4 - - - -
350A GLY* 3.4 12.3 - - - -
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Residues in contact with LEU 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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235A PHE* 4.0 25.4 - - + -
253A LEU* 4.7 2.2 - - + -
266A ILE* 4.1 5.8 - - + -
273A PHE* 4.1 20.9 - - + -
274A GLY 3.9 9.0 - - - +
275A LEU* 4.1 18.6 - - + -
278A ARG 3.8 0.2 + - - -
279A PHE* 1.3 71.9 - - - +
281A PHE* 1.3 68.5 + - - +
296A VAL* 3.6 1.6 - - - -
297A SER* 2.8 42.7 + - - +
300A GLN* 4.2 5.2 - - - -
301A GLY 4.0 18.6 - - - +
304A TRP* 3.3 35.0 - - + -
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Residues in contact with PHE 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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273A PHE* 3.2 7.6 - - - +
274A GLY 2.9 39.4 + - - +
276A GLY* 4.2 11.4 - - - -
279A PHE* 3.4 26.9 - + + -
280A LEU* 1.3 75.7 - - - +
282A ALA* 1.3 60.2 + - - +
294A ILE* 3.8 22.0 - - + -
295A HIS 3.5 1.8 - - - -
296A VAL* 3.9 22.4 - - + -
304A TRP* 4.4 0.9 - - - -
320A ILE* 3.8 22.9 - - + -
328A VAL* 3.5 35.7 - - + -
330A MET* 4.1 6.7 - - + -
350A GLY* 4.5 0.4 - - - -
353A TYR* 3.6 20.6 - - - -
809A 2ET 3.9 17.7 - - + -
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Residues in contact with ALA 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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253A LEU* 4.5 3.1 - - + -
270A ILE* 4.4 22.2 - - + -
272A SER 3.4 8.1 - - - +
273A PHE* 4.2 6.3 - - + +
281A PHE* 1.3 76.0 - - - +
283A SER* 1.3 61.0 + - - +
284A VAL* 3.8 7.2 + - + +
293A ARG 3.6 0.7 - - - +
294A ILE* 3.5 6.2 - - - -
295A HIS* 2.8 33.5 + - + -
304A TRP* 3.7 24.2 - - + -
809A 2ET 5.2 0.2 - - - -
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Residues in contact with SER 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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270A ILE* 3.8 3.6 - - - +
271A TYR* 2.9 32.8 + - - +
272A SER* 2.7 42.6 + - - +
282A ALA* 1.3 73.1 - - - +
284A VAL* 1.3 61.0 + - - +
292A ARG* 4.1 9.6 - - - -
293A ARG 3.5 6.7 - - - -
294A ILE* 4.3 7.4 - - - +
318A TYR* 4.7 0.9 - - - -
809A 2ET 2.9 35.8 + - - +
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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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268A VAL 3.8 11.7 - - - +
269A LYS* 3.4 17.5 - - + +
270A ILE* 4.3 15.5 - - + -
271A TYR* 5.2 0.2 - - - -
282A ALA* 4.0 7.9 - - + +
283A SER* 1.3 78.6 - - - +
285A MET* 1.3 73.6 + - - +
292A ARG* 3.0 5.7 - - - -
293A ARG* 2.9 34.2 + - - +
295A HIS* 3.4 38.4 - - + +
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Residues in contact with MET 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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248A LEU 4.5 3.6 - - - +
249A GLY* 3.5 29.8 - - - +
269A LYS* 3.2 24.1 + - + +
271A TYR* 3.3 39.0 - - + +
283A SER 4.5 0.2 + - - -
284A VAL* 1.3 83.4 - - - +
286A ALA* 1.3 65.4 + - - +
287A ASP* 3.7 2.9 + - - +
289A ASP 3.6 16.4 - - - +
290A THR* 3.8 20.6 - - - +
291A THR 3.2 24.5 - - - +
292A ARG* 3.9 4.7 - - + -
314A GLN* 4.9 10.3 - - - +
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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