Contacts of the strand formed by residues 276 - 286 (chain A) in PDB entry 3LW6
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 TYR 276 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129A VAL* 3.6 47.0 - - + +
132A GLN* 2.6 40.8 + - - +
133A PHE* 5.3 0.5 + - - -
274A VAL* 3.5 26.5 - - + -
275A LYS* 1.3 75.1 - - - +
277A LYS* 1.3 81.0 + - - +
278A ILE* 3.9 19.2 - - + +
296A ILE* 4.3 3.1 - - + -
297A LEU 3.2 13.2 - - - +
298A LEU* 4.0 9.0 - - + -
299A ASP* 4.4 3.3 - - - +
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Residues in contact with LYS 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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276A TYR* 1.3 85.4 - - - +
278A ILE* 1.3 61.3 + - - +
279A LEU* 3.6 20.2 + - + -
296A ILE* 3.7 1.6 - - - -
297A LEU* 2.8 51.9 + - + +
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Residues in contact with ILE 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A VAL* 3.9 21.8 - - + -
133A PHE* 3.6 33.2 - - + -
276A TYR* 3.9 22.1 - - + +
277A LYS* 1.3 72.1 - - - +
279A LEU* 1.3 62.9 + - - +
280A LYS 3.6 22.4 - - - +
281A VAL* 3.8 19.3 - - + -
294A LEU* 4.3 9.0 - - + -
295A ASN 3.5 8.7 - - - +
296A ILE* 4.2 8.1 - - + -
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Residues in contact with LEU 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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116A VAL* 4.1 15.0 - - + -
277A LYS* 4.1 25.4 - - + -
278A ILE* 1.3 74.0 - - - +
280A LYS* 1.3 70.0 + - + +
295A ASN* 2.9 16.1 + - + +
297A LEU* 4.0 37.5 - - + -
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Residues in contact with LYS 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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278A ILE* 3.4 6.9 + - - +
279A LEU* 1.3 85.5 + - + +
281A VAL* 1.3 70.4 + - - +
282A HIS* 3.3 39.0 - - + +
293A ILE 3.8 0.3 - - - +
294A LEU 3.8 0.2 - - - -
295A ASN* 2.9 39.8 + - + +
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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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133A PHE* 3.9 19.7 - - + -
278A ILE* 3.8 19.5 - - + -
280A LYS* 1.3 83.2 - - - +
282A HIS* 1.3 68.2 + - - +
283A GLU* 4.1 7.1 + - + +
292A THR* 3.8 26.0 - - + -
293A ILE 3.3 3.1 - - - -
294A LEU* 3.8 11.7 - - + -
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Residues in contact with HIS 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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280A LYS* 3.3 36.2 - - + +
281A VAL* 1.3 75.6 + - - +
283A GLU* 1.3 66.3 + - - +
284A MET* 3.8 5.0 + - + -
292A THR* 3.5 5.4 - - - +
293A ILE* 2.8 58.6 + - + +
295A ASN* 3.9 27.7 + - - -
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Residues in contact with GLU 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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281A VAL* 4.1 8.9 + - + +
282A HIS* 1.3 75.6 - - - +
284A MET* 1.3 59.6 + - - +
285A LEU 4.4 0.2 + - - -
291A VAL 3.9 3.8 - - - -
292A THR* 4.9 5.6 - - + +
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Residues in contact with MET 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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87A PHE* 5.0 13.0 - - + -
90A LEU* 5.2 2.9 - - - -
282A HIS* 3.8 5.1 + - + -
283A GLU* 1.3 75.3 - - - +
285A LEU* 1.3 68.7 + - - +
286A ILE* 3.8 35.0 - - + -
290A PRO* 3.3 5.2 - - - +
291A VAL* 2.8 40.3 + - + +
293A ILE* 3.8 33.2 - - + -
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Residues in contact with LEU 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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283A GLU 4.4 0.2 + - - -
284A MET* 1.3 79.3 - - - +
286A ILE* 1.3 65.0 + - - +
287A ASP 4.1 1.1 + - - -
288A GLN* 3.8 33.0 - - - +
289A VAL 3.2 3.6 - - - +
290A PRO* 3.4 36.3 - - + -
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Residues in contact with ILE 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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87A PHE* 5.4 0.9 - - + -
90A LEU* 4.5 12.3 - - + +
91A LEU* 4.2 32.5 - - + +
94A VAL* 3.9 38.2 - - + +
95A PRO* 5.1 7.9 - - + -
284A MET* 3.8 28.3 - - + -
285A LEU* 1.3 79.2 - - - +
287A ASP* 1.3 82.9 + - - +
289A VAL* 2.9 28.3 + - - +
291A VAL* 5.0 5.6 - - + -
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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