Contacts of the strand formed by residues 435 - 440 (chain A) in PDB entry 2FY5
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 THR 435 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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418A GLN* 4.9 1.1 - - - +
422A GLN* 3.3 24.9 + - - +
433A VAL* 2.8 14.8 + - - +
434A PRO* 1.3 74.4 + - - +
436A TYR* 1.3 72.6 + - - +
451A ASN* 3.9 5.7 + - - -
452A ILE 3.8 0.8 - - - +
453A ARG* 3.7 25.9 - - - +
454A SER* 4.6 8.7 - - - -
455A ALA* 3.8 13.6 - - - +
535A PHE* 4.0 4.6 - - - -
537A LEU* 3.1 39.4 - - + +
539A THR* 4.4 7.9 - - + +
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Residues in contact with TYR 436 (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 TRP* 5.1 1.9 + - - -
84A MET* 4.7 26.6 - - + +
435A THR* 1.3 77.2 - - - +
437A GLU* 1.3 59.0 + - - +
438A SER* 3.4 30.8 + - - -
449A VAL* 3.6 26.5 - - - +
450A ASP 4.5 2.1 + - - -
451A ASN* 3.0 36.1 - - + -
452A ILE 4.0 0.2 - - - -
503A ASP* 5.4 0.2 - - - -
535A PHE* 3.5 42.6 - + + -
537A LEU 2.9 9.0 + - - +
538A SER* 4.1 15.7 - - - +
539A THR* 2.7 40.6 + - - -
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Residues in contact with GLU 437 (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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414A ASP* 2.5 32.4 - - - +
418A GLN* 2.9 34.5 - - - +
436A TYR* 1.3 76.2 - - - +
438A SER* 1.3 71.0 + - - +
439A ALA 3.2 1.4 + - - -
451A ASN* 2.9 9.4 + - - +
452A ILE* 3.1 47.3 + - + +
454A SER* 4.1 0.7 - - - +
489A GLN* 3.0 16.5 + - - -
493A THR* 4.7 0.2 + - - -
539A THR* 3.3 18.8 - - - +
540A SER* 4.7 2.9 - - - -
541A GLN* 5.4 0.7 - - - +
564A TYR* 3.5 2.4 + - - +
2000A SOP 3.9 10.7 - - - +
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Residues in contact with SER 438 (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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436A TYR* 3.4 23.9 + - - -
437A GLU* 1.3 77.0 - - - +
439A ALA* 1.3 59.2 + - - +
440A SER 4.0 0.2 - - - -
449A VAL* 4.7 8.1 - - - +
450A ASP 4.3 2.5 - - - -
539A THR 3.3 5.5 + - - -
540A SER* 3.5 19.4 - - - -
541A GLN 5.3 0.3 + - - -
2000A SOP 3.5 57.2 - - - +
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Residues in contact with ALA 439 (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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437A GLU 3.2 0.4 + - - -
438A SER* 1.3 71.4 - - - +
440A SER* 1.3 63.0 + - - +
441A ILE* 4.4 0.4 - - + +
449A VAL* 3.1 6.0 - - - +
450A ASP 2.9 42.6 + - - +
452A ILE* 3.4 34.3 - - + -
496A ALA* 3.8 15.5 - - + +
497A ILE* 4.1 9.2 - - + +
2000A SOP 3.8 4.0 - - - -
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Residues in contact with SER 440 (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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150A LEU* 6.0 0.3 - - - +
330A ILE* 5.4 2.9 - - - -
438A SER 4.0 1.0 - - - -
439A ALA* 1.3 72.0 - - - +
441A ILE* 1.3 61.2 + - - +
442A ARG* 3.3 31.7 + - - +
443A ARG* 5.5 2.8 + - - +
448A ARG 3.7 7.4 - - - -
449A VAL* 4.1 2.9 - - - -
497A ILE* 3.7 21.3 - - - +
2000A SOP 2.8 40.7 + - - +
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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