Contacts of the strand formed by residues 331 - 335 (chain E) in PDB entry 1FPY
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 MET 331 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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330E VAL* 1.3 88.2 - - + +
332E LEU* 1.3 54.6 + - - +
333E ALA* 2.9 5.6 + - + +
340E SER* 3.4 26.2 + - - +
341E ALA* 4.6 2.5 - - - -
342E SER* 2.4 38.0 + - - -
392E MET* 6.2 0.2 - - + -
396E LEU 5.7 2.0 - - - +
397E TYR* 5.1 11.7 - - + +
400E PRO* 5.7 9.9 - - + -
405E LYS* 5.3 6.7 - - + +
407E ILE* 3.9 31.4 - - + -
408E PRO 4.0 0.4 - - - -
409E GLN* 3.5 35.2 - - - +
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Residues in contact with LEU 332 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302E ILE* 3.6 33.5 - - + +
305E ALA* 3.4 32.1 - - + -
306E LYS* 5.7 0.7 - - + -
330E VAL 3.4 2.0 + - - -
331E MET* 1.3 67.1 - - - +
333E ALA* 1.3 59.2 + - - +
342E SER* 3.4 14.8 - - - +
343E ILE* 4.5 6.3 - - + -
360E PHE* 4.5 8.5 - - + -
407E ILE* 5.0 1.9 - - - +
408E PRO* 2.9 41.5 + - + +
409E GLN* 3.1 36.3 - - - +
410E VAL* 3.4 21.3 - - + +
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Residues in contact with ALA 333 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302E ILE* 4.3 5.6 - - - -
331E MET* 2.9 8.3 + - + +
332E LEU* 1.3 74.8 - - - +
334E TYR* 1.3 64.1 + - + +
341E ALA* 3.5 11.4 - - + +
342E SER* 3.8 0.6 + - - -
343E ILE* 3.0 31.7 + - - +
390E GLU 5.8 0.7 - - - +
392E MET* 3.3 35.4 - - + +
407E ILE* 4.3 11.4 - - + -
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Residues in contact with TYR 334 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287E TYR* 4.5 8.7 - + - +
290E LEU* 5.1 1.1 - - + -
295E LEU* 3.5 32.4 - - + +
298E ILE* 3.9 28.0 - - + -
302E ILE* 4.7 1.6 - - + -
333E ALA* 1.3 79.3 - - + +
335E SER* 1.3 62.5 + - - +
341E ALA* 4.2 1.3 - - - -
343E ILE* 3.2 25.6 - - + +
345E ILE* 4.3 11.9 - - + -
387E HIS* 5.1 0.5 - - - -
388E PRO* 3.3 29.4 - - + -
389E GLY 2.5 22.3 + - - -
390E GLU 3.9 2.0 - - - -
391E PRO* 3.2 44.8 - - + +
392E MET* 2.9 25.6 + - - +
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Residues in contact with SER 335 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287E TYR* 3.8 11.7 - - - -
334E TYR* 1.3 76.9 - - - +
336E ALA* 1.3 59.5 + - - +
337E ARG 2.9 12.8 + - - -
338E ASN* 3.1 21.5 + - - -
341E ALA* 4.4 2.9 - - - -
343E ILE 3.3 3.6 + - - -
344E ARG* 3.2 10.9 - - - +
345E ILE* 2.7 30.8 + - - +
392E MET 2.8 29.3 + - - -
393E ASP* 3.2 7.4 + - - -
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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