Contacts of the helix formed by residues 377 - 382 (chain A) in PDB entry 1FSU
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 TRP 377 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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294A VAL* 3.9 32.3 - - + -
332A VAL* 4.1 9.4 - - + -
334A SER* 4.9 1.6 - - - -
336A LEU* 4.1 23.2 + - + -
337A LEU* 3.5 28.5 - - + -
353A TRP* 6.2 0.9 - + - -
356A THR* 3.9 13.3 - - + +
359A LYS* 6.3 1.1 - - + -
360A LEU* 3.9 39.9 - - + +
375A ASP* 3.3 18.7 + - - +
376A VAL* 1.3 74.9 - - - +
378A LYS* 1.3 63.3 + - + +
380A ILE* 3.2 11.4 + - + -
381A SER* 2.8 52.2 + - - -
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Residues in contact with LYS 378 (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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375A ASP* 5.3 1.8 + - - -
376A VAL 3.4 0.2 - - - -
377A TRP* 1.3 82.6 - - - +
379A THR* 1.3 57.5 + - - +
381A SER* 4.8 0.7 - - - -
382A GLU* 2.9 59.5 + - - +
383A GLY 3.4 0.9 + - - -
384A SER* 3.0 32.3 + - - +
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Residues in contact with THR 379 (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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344A ASN* 2.8 25.5 + - - +
346A GLU* 3.4 32.8 - - + -
348A ILE* 4.4 11.9 - - + -
376A VAL* 3.2 15.9 + - - +
377A TRP 3.1 0.2 - - - -
378A LYS* 1.3 79.9 - - - +
380A ILE* 1.3 53.0 + - - +
383A GLY* 2.9 17.0 + - - -
384A SER* 3.4 18.6 + - - +
385A PRO 3.6 3.1 + - - -
386A SER* 3.4 12.6 - - - +
387A PRO* 3.4 25.3 - - - +
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Residues in contact with ILE 380 (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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80A VAL* 3.4 34.2 - - + +
82A LEU* 4.1 4.5 - - + -
332A VAL* 3.9 26.9 - - + -
337A LEU* 4.1 10.1 - - + -
339A GLN* 4.7 2.6 - - - +
344A ASN* 3.9 7.9 + - - +
348A ILE* 3.7 21.5 - - + -
353A TRP* 3.7 36.6 - - + -
356A THR* 5.2 0.7 - - + -
376A VAL* 2.9 32.5 + - + +
377A TRP* 3.9 13.2 - - + +
379A THR* 1.3 79.4 - - - +
381A SER* 1.3 61.5 + - - +
383A GLY 4.2 1.2 + - - -
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Residues in contact with SER 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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336A LEU 3.9 4.5 + - - -
337A LEU* 3.6 13.6 - - - -
338A LYS* 2.9 25.7 + - - +
339A GLN* 3.0 35.0 + - - +
377A TRP* 2.8 48.1 + - - -
378A LYS* 4.8 0.4 - - - -
380A ILE* 1.3 75.9 - - - +
382A GLU* 1.3 63.6 + - - +
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Residues in contact with GLU 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 LYS* 3.9 32.8 + - + +
339A GLN* 3.2 21.5 + - - +
378A LYS* 2.9 45.7 + - + +
381A SER* 1.3 84.0 - - - +
383A GLY* 1.3 62.3 + - - +
384A SER* 3.5 4.5 + - - +
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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