Contacts of the strand formed by residues 347 - 351 (chain B) in PDB entry 5LG1
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 GLN 347 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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360A LYS* 3.7 29.7 - - - +
345B GLU 4.6 5.3 + - - +
346B PRO* 1.3 74.1 - - - +
348B VAL* 1.3 61.3 + - - +
349B TYR* 2.4 40.5 + - + +
368B LEU 3.4 1.7 - - - +
369B VAL* 3.2 5.5 - - - -
370B LYS* 2.9 63.2 + - + +
371B GLY* 5.6 4.8 - - - -
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Residues in contact with VAL 348 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A GLU* 4.0 1.4 - - - +
346B PRO 4.0 6.7 + - - +
347B GLN* 1.3 76.1 - - - +
349B TYR* 1.3 74.9 + - - +
367B CYS* 3.6 27.8 - - - -
368B LEU 3.3 3.1 - - - +
369B VAL* 4.1 9.4 - - + -
425B CYS* 4.3 3.4 - - - +
427B VAL* 3.6 33.9 - - + -
437B THR* 4.0 16.2 - - + -
439B LYS* 3.7 47.3 - - + +
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Residues in contact with TYR 349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354A SER* 3.8 21.1 - - - -
356A GLU* 3.8 27.1 + - + -
357A GLU* 3.6 46.4 - - + +
360A LYS* 3.9 14.4 + - - +
347B GLN* 2.4 48.4 + - + +
348B VAL* 1.3 82.1 - - - +
350B THR* 1.3 62.5 + - - +
351B LEU* 4.0 4.9 + - + +
366B THR 4.0 0.2 - - - +
367B CYS* 3.4 2.1 - - - -
368B LEU* 2.6 68.9 + - + +
370B LYS* 4.1 4.9 - - + -
439B LYS* 5.2 0.2 - - - -
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Residues in contact with THR 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354A SER* 4.1 10.0 + - - -
356A GLU* 5.6 0.8 + - - -
348B VAL 4.4 0.2 - - - -
349B TYR* 1.3 75.4 - - - +
351B LEU* 1.3 68.6 + - - +
352B PRO* 4.1 5.0 - - - +
366B THR 3.4 5.6 - - - +
367B CYS* 4.4 3.6 - - + -
381B TRP* 5.0 2.7 - - + -
423B PHE 5.8 0.2 - - - +
425B CYS* 4.1 17.0 - - + +
439B LYS* 3.7 37.0 - - + +
440B SER 3.1 20.8 + - - +
441B LEU* 3.9 24.5 - - + +
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Residues in contact with LEU 351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351A LEU* 4.2 15.3 - - + -
352A PRO 4.2 9.4 - - - +
353A PRO* 5.9 0.4 - - + -
354A SER* 3.6 33.7 - - - +
366A THR* 3.7 29.2 - - + +
349B TYR* 4.4 10.5 - - + +
350B THR* 1.3 85.1 - - - +
352B PRO* 1.3 73.9 - - + +
365B LEU 4.1 0.3 - - - -
366B THR* 2.7 58.1 + - + +
368B LEU* 4.8 8.1 - - + -
407B TYR* 4.6 4.3 - - + -
441B LEU* 3.6 6.0 - - - +
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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