Contacts of the strand formed by residues 424 - 428 (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 HIS 424 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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420X VAL* 3.2 5.7 - - - +
421X ILE 2.9 33.2 + - - +
422X ASP* 3.1 17.0 + - + +
423X GLY* 1.3 85.6 + - - +
425X ILE* 1.3 64.5 + - - +
426X TYR* 3.8 4.0 + + + -
442X ARG* 3.7 37.2 - - + -
443X TYR 3.2 11.4 - - - +
444X GLU* 3.7 37.7 + - + -
445X PRO* 4.1 1.5 - - + +
446X GLU* 6.1 4.3 - - + -
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Residues in contact with ILE 425 (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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368X CYS* 3.7 24.9 - - - -
370X VAL* 3.7 21.3 - - + -
375X TYR* 3.6 42.6 - - + -
377X VAL* 4.6 4.0 - - + -
393X LEU* 4.4 4.9 - - + -
418X VAL* 4.2 13.5 - - + -
419X GLY 3.6 4.5 - - - +
420X VAL* 4.5 1.8 - - + +
424X HIS* 1.3 71.7 - - - +
426X TYR* 1.3 72.9 + - - +
441X GLU 3.7 0.5 - - - +
442X ARG* 3.3 2.6 - - - -
443X TYR* 2.8 60.1 + - + +
445X PRO* 4.9 1.6 - - + -
450X TRP* 3.8 12.3 - - + -
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Residues in contact with TYR 426 (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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418X VAL* 3.1 28.9 - - - +
419X GLY 2.6 21.2 + - - +
421X ILE* 3.9 40.5 - - + +
424X HIS* 4.1 6.7 - + - -
425X ILE* 1.3 77.6 - - - +
427X ALA* 1.3 59.4 + - - +
428X VAL* 3.9 4.5 + - + +
440X VAL* 4.0 14.8 - - + -
441X GLU 3.4 3.8 - - - -
442X ARG* 3.5 43.3 + - + -
453X VAL* 4.3 7.4 - - + -
472X LEU* 3.8 31.0 - - + -
490X TYR* 3.7 24.2 + + - -
492X PRO* 3.9 20.3 - - - +
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Residues in contact with ALA 427 (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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377X VAL* 4.8 0.7 - - + -
409X MET* 3.5 32.1 - - - -
413X ARG* 3.9 13.2 - - - +
416X ILE* 3.9 8.1 - - + -
417X GLY 4.0 2.9 - - - -
418X VAL* 4.4 1.8 - - - -
425X ILE 3.8 1.6 + - - -
426X TYR* 1.3 70.1 - - - +
428X VAL* 1.3 61.3 + - - +
439X SER 4.1 0.7 - - - +
440X VAL* 3.2 8.3 - - - +
441X GLU* 2.8 35.1 + - + +
450X TRP* 3.6 16.4 - - + -
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Residues in contact with VAL 428 (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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416X ILE* 3.8 2.9 - - - +
417X GLY 2.9 36.7 + - - +
426X TYR 4.3 6.3 - - - +
427X ALA* 1.3 78.4 - - - +
429X GLY* 1.3 70.3 + - - +
430X GLY 3.4 0.9 + - - -
439X SER 4.2 1.6 - - - -
440X VAL* 4.3 10.1 - - + -
456X MET* 3.5 32.8 - - + -
463X VAL* 3.5 8.2 - - + +
465X VAL* 3.8 26.2 - - + -
472X LEU* 3.9 27.4 - - + -
473X TYR 6.5 0.2 - - - -
474X ALA* 4.3 5.8 - - + -
497X TRP* 4.9 1.8 - - + -
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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