Contacts of the strand formed by residues 386 - 390 (chain C) in PDB entry 4E3C
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 386 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312C VAL* 5.0 1.6 - - + -
313C HIS 3.0 15.6 + - - +
314C ILE* 3.6 12.4 - - + +
315C LEU 3.4 15.1 + - - -
353C LEU* 3.5 37.0 - - + -
354C LEU 3.2 21.5 - - - +
355C GLN* 3.5 32.8 - - + +
361C LEU* 3.6 26.7 - - + -
370C CYS* 4.6 12.3 - - - -
385C ASP* 1.3 79.5 - - - +
387C VAL* 1.3 67.8 + - - +
388C PHE* 3.3 3.7 + - + +
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Residues in contact with VAL 387 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315C LEU* 4.1 15.7 - - + -
317C MET* 3.7 29.6 - - + -
354C LEU* 2.7 43.5 + - + +
355C GLN* 4.8 0.8 - - - +
356C GLU* 4.4 17.9 - - + +
385C ASP* 3.7 17.7 + - - +
386C LEU* 1.3 69.8 - - - +
388C PHE* 1.3 60.8 + - - +
389C LEU* 4.1 9.6 - - + +
446C ARG 5.2 0.9 - - - +
449C GLN* 4.3 20.2 - - + +
450C GLY* 4.1 16.2 - - - +
453C ALA* 5.1 3.6 - - + -
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Residues in contact with PHE 388 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314C ILE* 3.8 23.1 - - + -
315C LEU 2.9 32.5 + - - +
316C ASN* 3.3 30.5 - - + -
317C MET* 3.0 18.0 - - - +
318C VAL* 4.4 2.2 - - + -
340C ILE* 4.5 11.7 - - + -
344C THR* 5.3 2.0 - - - -
346C ILE* 3.4 28.5 - - + -
351C GLN* 3.8 22.2 - - + -
352C GLU 3.4 9.9 - - - +
353C LEU* 4.0 24.0 - - + +
386C LEU 3.3 3.4 + - - +
387C VAL* 1.3 75.0 - - - +
389C LEU* 1.3 90.2 + - - +
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Residues in contact with LEU 389 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317C MET* 3.8 18.6 - - + -
318C VAL* 5.4 1.3 - - - +
351C GLN 3.7 0.2 - - - -
352C GLU* 2.7 47.5 + - - +
354C LEU* 3.4 35.0 - - + -
387C VAL* 4.1 11.4 - - + +
388C PHE* 1.3 102.8 - - - +
390C PHE* 1.3 66.2 + - - +
394C LYS* 4.6 15.5 - - - +
450C GLY 5.8 1.6 - - - +
454C ALA* 4.9 7.2 - - + -
612C LEU* 4.6 19.7 - - + -
616C VAL* 5.6 4.5 - - + -
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Residues in contact with PHE 390 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318C VAL* 3.6 34.3 - - + -
346C ILE* 3.4 29.8 - - + -
350C ASP* 3.0 29.2 - - - +
352C GLU* 4.5 4.2 - - - +
389C LEU* 1.3 78.8 - - - +
391C ASP* 1.3 83.5 + - - +
392C ASN* 3.2 33.5 + - + -
394C LYS* 4.5 27.9 + - + -
616C VAL* 6.1 1.4 - - - +
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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