Contacts of the strand formed by residues 393 - 396 (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 393 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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375X TYR* 3.7 33.7 - - + -
376X ALA 3.5 1.3 - - - +
377X VAL* 3.8 22.7 - - + -
391X SER 3.7 1.6 + - - +
392X ALA* 1.3 75.9 - - - +
394X ASP* 1.3 68.8 + - - +
405X PRO* 4.0 0.2 - - - +
406X CYS* 2.9 39.2 + - + +
407X ALA 3.6 13.7 + - - +
408X PRO* 4.5 0.8 - - - +
425X ILE* 4.4 4.0 - - + -
443X TYR* 3.5 50.9 - - + -
450X TRP* 3.7 19.3 - - + +
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Residues in contact with ASP 394 (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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358X LEU* 5.5 0.7 - - + -
359X GLN* 4.7 9.3 - - - +
360X VAL* 6.2 0.3 - - - +
362X ARG* 2.7 30.8 + - - +
375X TYR* 3.3 9.1 - - - +
376X ALA 2.9 32.3 + - - +
392X ALA* 3.7 13.8 - - - +
393X LEU* 1.3 79.2 - - - +
395X CYS* 1.3 60.7 + - - +
403X TRP* 3.8 21.6 - - + -
404X SER 3.7 3.1 - - - +
405X PRO* 3.5 26.3 - - - +
406X CYS* 4.6 0.4 - - - -
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Residues in contact with CYS 395 (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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373X LEU* 3.7 41.1 - - - -
374X LEU 3.4 4.0 - - - -
375X TYR* 3.7 19.1 - - + -
394X ASP* 1.3 75.1 - - - +
396X TYR* 1.3 63.6 + - - +
397X ASN* 4.0 1.2 + - - -
402X GLN 3.6 2.1 - - - +
403X TRP* 3.2 5.6 - - - -
404X SER* 2.7 49.7 + - - +
406X CYS* 3.7 17.7 - - - -
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Residues in contact with TYR 396 (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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329X TYR* 4.1 14.4 - + - -
342X LEU* 3.5 25.4 - - + -
355X LEU* 3.5 13.5 - - - +
356X ALA* 4.3 1.6 - - + -
373X LEU* 3.9 2.4 - - - -
374X LEU* 2.7 51.1 + - + -
395X CYS* 1.3 76.6 - - - +
397X ASN* 1.3 58.3 + - - +
398X PRO* 3.4 32.8 + - + +
401X ASN* 2.5 57.3 + - - +
402X GLN 3.6 9.2 - - - -
403X TRP* 3.6 44.5 - + + -
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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