Contacts of the strand formed by residues 373 - 377 (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 373 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369X VAL* 3.1 7.9 - - - -
370X VAL 3.0 34.6 + - - +
371X GLY* 3.9 9.4 - - - +
372X GLY* 1.3 81.1 - - - +
374X LEU* 1.4 60.4 + - - +
375X TYR* 3.6 14.2 - - + +
395X CYS* 3.7 27.1 - - - -
396X TYR 3.9 1.3 - - - +
397X ASN* 3.5 46.9 - - + +
609X THR* 5.3 0.2 - - - -
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Residues in contact with LEU 374 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329X TYR* 3.9 20.9 - - + -
331X ALA* 4.9 6.3 - - + -
342X LEU* 3.9 27.8 - - + -
367X GLY* 4.9 2.7 - - - -
368X CYS 3.6 7.2 - - - +
369X VAL* 4.1 7.6 - - + +
372X GLY 4.2 0.8 + - - -
373X LEU* 1.4 71.7 - - - +
375X TYR* 1.3 68.8 + - - +
376X ALA* 4.3 0.4 + - + -
395X CYS* 3.4 4.3 - - - -
396X TYR* 2.7 63.7 + - + +
398X PRO* 4.7 5.0 - - + +
403X TRP* 4.2 7.9 - - + -
606X VAL* 5.9 0.4 - - - -
607X ALA* 3.6 33.2 - - + +
609X THR* 5.1 3.3 - - + +
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Residues in contact with TYR 375 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366X ALA 3.7 0.5 - - - +
367X GLY* 3.1 26.7 - - - -
368X CYS* 2.8 24.2 + - - +
370X VAL* 3.9 29.4 + - + +
373X LEU* 3.6 32.5 - - + +
374X LEU* 1.3 77.4 - - - +
376X ALA* 1.3 59.4 + - - +
377X VAL* 4.1 1.7 - - + +
393X LEU* 3.7 29.4 - - + -
394X ASP 3.3 9.9 - - - -
395X CYS* 3.7 26.6 - - + -
406X CYS* 4.2 11.2 - - - -
425X ILE* 3.6 20.6 - - + -
443X TYR* 4.3 12.1 + + - -
445X PRO* 3.8 22.4 - - + +
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Residues in contact with ALA 376 (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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331X ALA* 5.1 3.4 - - + -
358X LEU* 4.1 3.6 - - + -
362X ARG* 3.2 21.9 + - - +
365X LEU* 3.6 23.6 - - + -
366X ALA 3.7 4.3 - - - -
367X GLY* 4.9 0.2 - - - -
374X LEU 4.3 0.4 + - - -
375X TYR* 1.3 71.8 - - - +
377X VAL* 1.3 60.3 + - - +
393X LEU* 3.5 1.7 - - - +
394X ASP 2.9 31.3 + - - +
403X TRP* 4.0 25.6 - - + -
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Residues in contact with VAL 377 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362X ARG* 3.4 1.1 - - - +
365X LEU* 3.4 1.3 - - - +
366X ALA 3.0 34.4 + - - +
368X CYS* 4.6 4.0 - - - -
375X TYR* 4.2 11.4 - - + +
376X ALA* 1.3 77.2 - - - +
378X GLY* 1.3 69.9 + - - +
392X ALA 3.6 3.4 - - - +
393X LEU* 3.8 18.2 - - + -
409X MET* 3.8 16.4 - - + -
416X ILE* 3.4 23.2 - - + +
418X VAL* 3.9 22.9 - - + -
425X ILE* 4.6 8.5 - - + -
450X TRP* 4.1 16.2 - - + -
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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