Contacts of the strand formed by residues 380 - 386 (chain A) in PDB entry 1LWT
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 SER 380 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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340A LYS* 3.9 20.3 - - - +
341A THR 3.5 9.9 + - - -
342A ILE* 4.2 6.1 - - - -
364A ASN 4.6 0.2 - - - -
365A ALA* 3.1 5.9 - - - +
366A GLU* 2.7 58.5 + - - +
378A LYS 2.8 7.5 + - - -
379A ILE* 1.3 72.6 - - - +
381A TYR* 1.3 70.4 + - - +
382A ALA* 5.8 0.2 - - - +
14B G 6.6 0.2 - - - -
15B C 5.6 8.5 + - - -
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Residues in contact with TYR 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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66A GLU* 3.3 36.9 + - - -
340A LYS* 3.3 6.3 - - - +
341A THR* 2.8 54.2 + - + +
342A ILE 3.6 24.5 - - - -
344A THR* 4.1 25.8 + - - +
347A ARG* 4.1 26.2 + - + -
363A VAL* 4.0 15.3 - - + -
364A ASN 3.8 2.5 - - - -
365A ALA* 3.9 7.2 - - + -
379A ILE* 3.5 39.3 - - + +
380A SER* 1.3 84.9 + - - +
382A ALA* 1.3 60.7 + - - +
383A ILE 3.6 2.4 + - - +
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Residues in contact with ALA 382 (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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338A THR* 4.6 8.8 - - + +
339A ILE 3.9 4.5 - - - -
340A LYS* 4.0 23.6 - - - +
362A SER 3.9 1.6 - - - +
363A VAL* 4.0 0.4 - - - +
364A ASN* 3.1 45.5 + - + +
381A TYR* 1.3 73.4 - - - +
383A ILE* 1.3 63.3 + - - +
384A TYR* 3.3 6.6 + - - +
20C C 6.1 1.6 - - + -
21C T 5.2 6.7 - - + +
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Residues in contact with ILE 383 (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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338A THR* 3.4 5.8 - - - +
339A ILE* 2.7 49.4 + - + +
341A THR* 4.7 10.5 - - + -
347A ARG* 5.2 5.4 - - + -
350A LEU* 3.6 35.2 - - + -
351A VAL* 4.9 5.2 - - + -
361A VAL* 3.9 19.3 - - + -
362A SER 3.8 4.5 - - - -
363A VAL* 4.0 19.4 - - + +
381A TYR 3.6 4.9 - - - +
382A ALA* 1.3 70.3 - - - +
384A TYR* 1.3 59.5 + - - +
385A MSE 3.6 29.6 - - + -
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Residues in contact with TYR 384 (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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336A LYS* 3.2 29.3 - - + +
337A ALA 4.1 1.6 - - - -
338A THR* 3.8 20.2 - - + +
360A VAL* 5.0 2.7 - - + -
361A VAL* 3.1 7.2 - - - +
362A SER* 2.6 53.9 + - - +
382A ALA 4.3 4.0 - - - +
383A ILE* 1.3 72.3 - - - +
385A MSE 1.3 82.8 + - - +
386A SER* 4.4 3.8 - - - -
18C T 2.4 64.1 + + + +
19C T 3.9 23.1 - - + -
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Residues in contact with MSE 385 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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319A LEU* 3.5 32.5 - - + -
336A LYS* 3.5 6.1 - - - +
337A ALA* 2.9 43.4 + - + +
339A ILE* 4.4 10.5 - - - -
350A LEU* 4.4 6.5 - - + -
354A ALA* 3.3 29.6 - - + -
359A LEU* 3.8 26.0 - - + -
360A VAL 3.1 8.1 - - - +
361A VAL* 4.4 8.3 - - + -
383A ILE* 3.6 25.6 - - + -
384A TYR* 1.3 86.0 - - - +
386A SER* 1.3 66.5 + - - +
391A LEU* 5.1 0.9 - - + -
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Residues in contact with SER 386 (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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336A LYS* 3.2 36.3 + - - -
359A LEU* 3.6 7.4 - - - +
360A VAL* 2.8 43.1 + - - +
384A TYR* 4.4 5.1 - - - -
385A MSE 1.3 79.4 - - - +
387A GLY* 1.3 59.9 + - - +
391A LEU* 3.6 16.8 - - - +
18C T 4.3 8.5 + - - -
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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