Contacts of the strand formed by residues 341 - 346 (chain B) in PDB entry 3GUT
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 341 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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339B GLY 3.2 18.6 - - - +
340B PRO* 1.3 75.0 - - - +
342B LEU* 1.3 78.1 + - - +
343B GLN* 3.3 29.1 + - + -
384B ILE* 3.9 2.4 - - - -
385B CYS* 3.3 53.0 + - + +
386B ASN* 3.8 12.3 + - - -
529B LEU* 3.6 17.3 - - - +
530B GLU* 5.7 7.0 - - + +
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Residues in contact with LEU 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341B TYR* 1.3 87.8 - - - +
343B GLN* 1.3 89.8 + - - +
382B VAL* 4.1 19.5 - - + -
383B LYS 3.9 6.7 - - - +
384B ILE* 4.0 19.7 - - + -
393B VAL* 4.8 7.9 - - + -
514B PHE* 4.5 10.3 - - + +
515B THR* 5.4 0.2 - - - -
516B ALA* 3.7 34.1 - - + +
529B LEU* 5.0 2.5 - - + -
530B GLU 4.1 20.1 + - - +
532B VAL* 3.3 32.7 - - + +
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Residues in contact with GLN 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341B TYR* 3.3 32.1 + - + -
342B LEU* 1.3 89.6 - - - +
344B ILE* 1.3 70.0 + - - +
345B LEU* 3.5 18.8 + - + +
382B VAL* 3.4 0.2 - - - -
383B LYS* 2.8 41.6 + - - +
385B CYS* 3.7 11.3 - - - -
532B VAL* 5.1 1.8 - - - -
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Residues in contact with ILE 344 (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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342B LEU* 4.4 0.2 - - - +
343B GLN* 1.3 83.2 + - - +
345B LEU* 1.3 64.0 + - - +
346B GLU 3.8 3.6 - - - +
347B GLN* 3.7 46.4 - - + +
348B PRO* 5.9 0.2 - - + -
381B GLN 3.8 3.6 - - - +
382B VAL* 3.7 19.7 - - + -
514B PHE* 3.9 19.3 - - + -
532B VAL* 4.3 16.3 - - + +
533B VAL 3.8 24.0 - - - +
534B SER* 3.9 17.5 - - - -
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Residues in contact with LEU 345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343B GLN* 3.5 20.8 + - - +
344B ILE* 1.3 82.0 - - - +
346B GLU* 1.3 59.2 + - - +
347B GLN 4.3 0.3 + - - -
381B GLN* 2.6 41.1 + - + +
383B LYS* 3.7 39.0 - - + -
431B VAL* 3.9 21.1 - - + -
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Residues in contact with GLU 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344B ILE* 4.0 4.1 - - - +
345B LEU* 1.3 78.5 - - - +
347B GLN* 1.3 71.8 + - - +
348B PRO* 4.6 0.2 - - - +
369B GLY* 3.3 5.4 - - - -
370B ALA* 3.8 3.4 - - + +
371B SER* 2.9 29.8 + - - +
378B SER* 2.3 43.3 + - - -
379B TYR 3.2 17.7 - - - +
380B PRO* 3.2 19.6 - - - +
381B GLN* 2.9 21.7 + - + +
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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