Contacts of the strand formed by residues 349 - 354 (chain A) in PDB entry 1L2L
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 349 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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320A PRO* 4.1 19.7 - - + -
321A ALA* 2.6 34.3 + - + +
323A PRO* 3.6 11.5 - - + +
326A VAL* 3.7 11.4 - - - +
344A PHE* 3.7 17.1 - + - +
345A HIS* 4.0 0.3 - - - -
346A THR* 3.2 27.3 + - - +
347A TYR 3.5 4.1 - - - -
348A GLY* 1.3 82.5 - - - +
350A TYR* 1.3 69.2 + - - +
351A LEU* 3.6 33.9 - - + -
398A GLN 5.4 0.2 - - - -
402A VAL* 3.8 29.4 - - + -
426A PHE* 3.4 20.4 - + + -
427A ILE 3.3 14.1 - - - +
429A THR* 3.9 4.6 - - - +
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Residues in contact with TYR 350 (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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343A HIS* 3.6 20.2 - + + -
344A PHE 3.1 8.3 - - - +
345A HIS* 3.6 18.4 - - + -
346A THR 3.9 11.0 - - - -
349A TYR* 1.3 84.9 - - - +
351A LEU* 1.3 69.6 + - - +
365A LEU* 3.8 21.1 - - + -
368A SER* 3.2 24.2 - - - -
369A ALA* 3.3 34.4 - - + -
372A ALA* 3.6 8.7 - - - +
425A THR 4.5 0.4 - - - -
426A PHE* 3.7 0.2 - - - -
427A ILE* 3.1 34.9 + - + +
429A THR* 4.1 14.2 + - - -
445A ILE* 3.4 31.0 - - + +
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Residues in contact with LEU 351 (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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323A PRO* 4.8 3.8 - - + +
326A VAL* 4.4 13.0 - - + -
327A ILE* 3.9 31.6 - - + -
330A LEU* 4.9 7.1 - - + +
343A HIS* 3.5 2.1 + - - -
344A PHE* 2.6 48.9 + - + +
349A TYR* 3.6 25.1 - - + +
350A TYR* 1.3 81.4 - - - +
352A ALA* 1.3 58.6 + - - +
365A LEU* 4.7 1.8 - - - -
406A LEU* 3.7 27.4 - - + -
424A LEU* 4.3 13.0 - - + -
425A THR 3.3 5.4 - - - +
426A PHE* 3.7 17.5 - - + -
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Residues in contact with ALA 352 (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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330A LEU* 6.0 0.4 - - - -
341A ARG* 5.8 2.5 - - - +
342A ILE 3.0 11.4 - - - +
343A HIS* 4.6 3.4 - - + -
351A LEU* 1.3 76.6 - - - +
353A LEU* 1.3 63.0 + - - +
354A THR* 4.4 5.2 - - + -
361A VAL* 4.1 11.0 - - + -
365A LEU* 3.9 16.2 - - + -
423A GLN 3.3 3.5 - - - +
424A LEU* 3.5 6.1 - - - +
425A THR* 3.0 51.3 + - + -
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Residues in contact with LEU 353 (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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327A ILE* 4.9 7.0 - - + +
330A LEU* 3.7 41.5 - - + +
331A LEU* 4.5 18.6 - - + -
334A ILE* 4.9 7.6 - - + -
340A LYS 3.7 1.0 - - - +
341A ARG* 3.5 2.6 - - - -
342A ILE* 2.9 41.1 + - + +
352A ALA* 1.3 72.1 - - - +
354A THR* 1.3 60.3 + - - +
419A ILE* 3.6 29.4 - - + -
422A TYR* 3.8 19.6 - - + -
423A GLN 3.3 8.7 - - - +
424A LEU* 3.8 22.4 - - + -
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Residues in contact with THR 354 (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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340A LYS 3.3 4.7 - - - -
341A ARG* 3.7 18.8 - - + +
352A ALA* 4.4 3.6 - - + -
353A LEU* 1.3 85.7 - - - +
355A ARG* 1.3 64.2 + - - +
356A GLU* 2.7 48.0 + - - +
361A VAL* 3.8 27.7 - - + +
422A TYR* 3.7 6.1 - - - -
423A GLN* 2.8 41.1 + - - +
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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