Contacts of the strand formed by residues 369 - 376 (chain A) in PDB entry 2FYT
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 LEU 369 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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339A LYS* 4.0 10.6 + - - +
340A VAL* 3.7 10.5 - - + +
341A ASP 3.6 13.0 - - - +
342A VAL 4.2 1.6 - - - +
343A ILE* 4.1 17.2 - - + +
364A ALA 3.6 1.4 + - - -
365A LYS* 3.1 45.3 + - + +
366A ASN 5.4 0.9 - - - +
368A TYR* 1.3 76.3 - - - +
370A ALA* 1.3 73.0 + - - +
371A LYS* 3.5 1.4 + - - -
373A GLY* 3.6 20.6 - - - +
374A SER* 3.5 35.9 - - - +
375A VAL* 4.5 1.6 - - + +
442A HIS* 4.8 5.4 - - + -
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Residues in contact with ALA 370 (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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339A LYS* 3.9 24.0 - - + -
340A VAL 2.9 24.3 + - - +
341A ASP* 4.7 11.7 - - - +
368A TYR 3.1 3.0 + - - -
369A LEU* 1.3 77.1 - - - +
371A LYS* 1.3 72.4 + - - +
372A GLY 3.1 0.5 + - - -
373A GLY* 2.7 18.2 + - - +
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Residues in contact with LYS 371 (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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339A LYS* 5.7 1.2 - - - +
369A LEU 3.5 2.6 + - - -
370A ALA* 1.3 78.3 - - - +
372A GLY* 1.3 62.4 + - - +
373A GLY 3.4 0.2 + - - -
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Residues in contact with GLY 372 (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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370A ALA 3.1 0.6 + - - -
371A LYS* 1.3 76.5 - - - +
373A GLY* 1.3 64.8 + - - +
374A SER* 4.3 2.1 + - - -
478A LYS* 4.3 8.5 + - - -
479A ASN* 5.5 1.0 - - - +
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Residues in contact with GLY 373 (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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341A ASP* 3.3 17.7 - - - -
369A LEU* 3.6 16.3 - - - +
370A ALA* 2.7 18.2 + - - -
371A LYS 3.2 1.6 + - - -
372A GLY* 1.3 76.4 + - - +
374A SER* 1.3 64.2 + - - -
442A HIS* 4.1 2.9 + - - -
478A LYS* 3.1 17.5 + - - -
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Residues in contact with SER 374 (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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270A ILE* 5.7 0.9 - - - -
341A ASP 3.1 8.7 + - - -
342A VAL* 3.3 8.1 - - - +
343A ILE 2.9 24.3 + - - +
369A LEU* 3.5 6.9 - - - +
372A GLY 4.3 1.9 + - - -
373A GLY* 1.3 74.5 - - - -
375A VAL* 1.3 61.5 + - - +
376A TYR* 3.5 30.7 + - - -
442A HIS* 3.4 10.5 - - - -
478A LYS* 3.1 25.1 + - - +
479A ASN* 3.9 6.9 + - - -
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Residues in contact with VAL 375 (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 ILE* 3.3 29.2 - - + -
361A VAL* 3.9 19.3 - - + -
362A LEU* 6.3 0.4 - - + -
365A LYS* 4.2 20.9 - - + -
369A LEU* 4.7 0.7 - - + -
374A SER* 1.3 73.4 - - - +
376A TYR* 1.3 68.8 + - - +
377A PRO 4.1 1.3 - - - +
378A ASP* 3.3 22.3 - - - +
441A CYS* 3.6 37.9 - - + +
442A HIS* 3.2 21.6 + - + +
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Residues in contact with TYR 376 (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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260A TYR* 4.7 1.0 - - + -
263A PHE* 3.3 47.1 - + + -
270A ILE* 3.6 24.1 - - + +
342A VAL* 3.8 18.6 - - + -
343A ILE 2.8 10.9 + - - +
344A ILE* 3.5 6.5 - - + +
345A SER* 3.1 25.6 + - - +
347A TRP* 5.3 1.0 + - - -
374A SER* 3.5 32.0 + - - -
375A VAL* 1.3 85.2 - - - +
377A PRO* 1.4 67.7 - - + +
378A ASP* 3.8 20.0 - - - -
476A PHE* 4.1 7.2 - + + -
478A LYS* 2.6 39.6 + - + +
479A ASN* 3.9 4.2 + - - +
480A CYS* 4.5 1.3 - - - -
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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