Contacts of the strand formed by residues 376 - 381 (chain A) in PDB entry 3A3K
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 376 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129A SER 5.1 1.6 - - - -
132A LYS* 3.6 20.4 - - + -
133A LEU* 3.6 44.0 - - + -
136A PHE* 3.8 37.4 - + + -
243A VAL* 4.6 5.4 - - + -
280A ILE* 4.2 4.7 - - + -
281A THR 3.4 21.3 - - - +
282A TYR* 3.6 25.1 - + - -
283A LYS* 3.8 4.0 - - - +
374A THR* 3.5 37.7 - - + -
375A ASP* 1.3 72.0 - - - +
377A SER* 1.3 62.5 + - - +
393A ASN* 3.5 5.4 - - - +
394A TYR* 2.9 35.2 + + + +
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Residues in contact with SER 377 (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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136A PHE* 4.8 2.2 - - - -
279A ILE 3.6 2.4 - - - +
280A ILE* 3.7 4.2 - - - +
281A THR* 3.0 44.1 + - - +
282A TYR 4.2 0.4 + - - -
283A LYS* 3.4 23.0 - - - +
284A GLU 4.4 1.6 + - - -
376A PHE* 1.3 75.0 - - - +
378A LEU* 1.3 59.8 + - - +
379A TRP* 4.0 3.5 - - - -
390A VAL* 3.7 22.6 - - - +
392A LEU 3.4 4.0 - - - -
393A ASN* 3.0 19.2 + - - -
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Residues in contact with LEU 378 (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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136A PHE* 4.3 12.4 - - + -
140A LEU* 4.2 15.3 - - + -
239A PHE* 3.8 26.0 - - + -
278A LYS* 3.8 27.1 - - + -
279A ILE 3.5 13.0 - - - +
280A ILE* 3.9 13.7 - - + -
377A SER* 1.3 72.3 - - - +
379A TRP* 1.3 62.4 + - - +
390A VAL* 3.5 1.7 - - - -
391A VAL* 2.9 30.7 + - + +
392A LEU* 2.9 45.4 + - + -
409A LEU* 4.4 12.8 - - + -
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Residues in contact with TRP 379 (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* 3.6 24.5 - - + -
249A LYS 5.8 0.4 - - - -
257A GLN* 4.0 30.7 - - + -
278A LYS* 3.3 5.2 - - - +
279A ILE* 2.8 51.1 + - + +
281A THR* 3.2 35.2 + - + +
284A GLU* 6.5 0.4 - - + -
313A LEU* 6.1 3.1 - - + -
377A SER* 4.0 6.7 - - - -
378A LEU* 1.3 79.2 - - - +
380A ASP* 1.3 62.6 + - - +
388A PHE* 3.9 18.3 - - + -
389A ARG* 3.2 30.5 - - - +
390A VAL* 3.6 24.2 - - + +
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Residues in contact with ASP 380 (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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277A ALA 4.3 2.2 - - - +
278A LYS* 2.9 45.4 + - + +
378A LEU 4.1 1.0 + - - -
379A TRP* 1.3 74.6 - - - +
381A MET* 1.3 60.2 + - - +
388A PHE* 3.4 13.6 - - - -
389A ARG* 3.0 51.7 + - - -
391A VAL* 3.3 19.1 - - + +
408A LYS 4.6 0.5 - - - +
409A LEU* 3.8 4.7 - - - -
410A TYR* 2.9 25.2 + - + +
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Residues in contact with MET 381 (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 TRP* 3.7 15.0 - - + +
271A ARG* 3.5 22.0 - - + +
274A PHE* 3.9 9.6 - - + +
275A GLN* 3.4 39.0 - - + +
277A ALA 4.8 0.8 + - - +
380A ASP* 1.3 76.7 - - - +
382A ASP* 1.3 77.7 + - - +
383A PRO* 3.3 13.7 - - + +
386A GLY* 3.4 29.2 - - - +
387A ALA 3.3 5.6 - - - -
388A PHE* 3.7 23.4 - - + -
389A ARG* 3.5 5.2 + - - -
410A TYR* 3.7 21.3 - - + +
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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