Contacts of the strand formed by residues 471 - 475 (chain X) in PDB entry 4IFL
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 471 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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421X ILE* 4.3 2.5 - - - -
467X VAL* 3.4 4.3 - - - -
468X LEU 3.0 32.8 + - - +
469X ASN* 3.1 12.9 + - + +
470X ARG* 1.3 83.1 - - - +
472X LEU* 1.3 59.6 + - - +
473X TYR* 3.4 16.1 - - + +
489X CYS* 3.7 26.5 - - - -
490X TYR 3.5 12.3 - - - +
491X TYR* 3.7 36.8 - - + -
539X VAL* 6.0 4.0 - - + -
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Residues in contact with LEU 472 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419X GLY* 3.9 9.0 - - - -
421X ILE* 4.0 13.3 - - + +
426X TYR* 3.8 38.1 - - + -
428X VAL* 3.9 10.5 - - + -
440X VAL* 4.6 0.4 - - + -
465X VAL* 3.4 29.4 - - + -
466X ALA 3.8 1.3 - - - -
467X VAL* 3.7 20.2 - - + -
471X LEU* 1.3 72.6 - - - +
473X TYR* 1.3 63.4 + - - +
489X CYS* 3.2 2.9 - - - -
490X TYR* 2.6 50.1 + - + +
497X TRP* 3.9 28.3 - - + -
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Residues in contact with TYR 473 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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464X GLY 4.3 0.2 - - - -
465X VAL* 3.1 14.5 - - - +
466X ALA* 2.8 36.6 + - + +
468X LEU* 3.8 20.4 + - + -
471X LEU* 3.4 37.7 - - + +
472X LEU* 1.3 75.8 - - - +
474X ALA* 1.3 59.7 + - - +
475X VAL* 4.3 12.8 - - + -
488X GLU 3.4 4.0 - - - +
489X CYS* 3.7 28.9 - - + -
497X TRP* 4.7 0.7 - - - -
500X ILE* 4.0 30.2 - - + +
519X ILE* 3.6 26.0 - - + -
537X TYR* 4.3 10.1 - + - -
539X VAL* 3.5 27.5 - - + +
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Residues in contact with ALA 474 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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428X VAL* 4.3 4.3 - - + -
456X MET* 3.5 32.5 - - - -
460X ARG* 3.9 10.0 - - - +
463X VAL* 3.9 11.2 - - + -
464X GLY 3.5 4.3 - - - -
465X VAL* 4.6 1.6 - - + -
473X TYR* 1.3 71.4 - - - +
475X VAL* 1.3 60.2 + - - +
487X ALA* 3.3 3.8 - - - +
488X GLU* 2.9 33.6 + - + -
497X TRP* 3.8 16.8 - - + -
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Residues in contact with VAL 475 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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462X GLY 4.8 0.3 - - - +
463X VAL* 3.6 1.8 - - - +
464X GLY* 2.8 43.1 + - - +
473X TYR* 4.3 14.6 - - + -
474X ALA* 1.3 82.1 - - - +
476X GLY* 1.3 68.3 + - - +
477X GLY 3.8 0.2 + - - -
486X SER 4.2 1.8 - - - -
487X ALA* 4.2 12.8 - - + -
500X ILE* 5.7 0.2 - - + -
503X MET* 3.6 30.5 - - + -
510X ALA* 5.9 1.6 - - + +
512X VAL* 4.1 30.6 - - + +
519X ILE* 4.5 3.1 - - + -
521X ALA* 4.6 0.7 - - + -
544X TRP* 4.0 18.6 - - + -
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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