Contacts of the helix formed by residues 385 - 393 (chain C) in PDB entry 3F7F
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 SER 385 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6C ARG* 3.5 26.2 - - - +
8C ASP* 3.6 26.3 + - - +
384C LYS* 1.3 75.7 - - - +
386C LEU* 1.3 59.7 + - - +
387C VAL* 3.6 8.7 + - - +
388C ASP* 2.9 33.9 + - - +
389C LEU* 2.7 27.4 + - - +
454C LYS* 4.8 0.5 + - - -
495C TYR* 5.6 0.2 - - - -
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Residues in contact with LEU 386 (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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6C ARG 4.4 2.8 + - - -
384C LYS 4.0 0.2 + - - -
385C SER* 1.3 72.8 - - - +
387C VAL* 1.3 65.9 + - + +
388C ASP 3.1 0.2 + - - -
389C LEU* 3.1 9.8 + - + +
390C GLN* 2.9 55.5 + - + +
395C LEU* 6.3 0.9 - - + -
494C PHE* 4.1 21.3 - - + -
495C TYR* 3.6 21.7 + - + +
620C HIS* 5.9 2.0 - - + +
621C GLN* 3.8 44.4 - - + +
624C SER* 4.0 13.2 - - - +
625C ILE* 4.0 14.6 - - + -
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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
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385C SER* 3.2 8.3 + - - +
386C LEU* 1.3 78.2 - - + +
388C ASP* 1.3 64.3 + - - +
390C GLN* 4.1 7.8 - - - +
391C SER* 3.3 15.8 + - - -
414C ARG* 3.5 37.5 + - + +
617C GLU* 4.5 6.5 - - - +
620C HIS* 3.8 33.0 - - + +
668C TYR* 4.1 16.2 - - + +
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Residues in contact with ASP 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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6C ARG* 5.4 2.1 + - - -
8C ASP* 3.7 3.6 - - - +
384C LYS* 4.2 19.8 - - + +
385C SER* 2.9 31.7 + - - +
387C VAL* 1.3 76.8 - - - +
389C LEU* 1.3 61.0 + - - +
391C SER* 3.3 3.5 + - - -
392C GLU* 3.0 33.9 + - - +
414C ARG* 3.2 19.4 + - - +
415C TYR* 5.5 0.5 - - - -
454C LYS* 3.0 37.4 + - - +
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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
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382C VAL* 3.7 17.5 - - + -
384C LYS* 3.6 41.3 - - + +
385C SER 2.7 19.0 + - - +
386C LEU* 3.9 9.2 - - + +
388C ASP* 1.3 69.8 - - - +
390C GLN* 1.3 60.5 + - - +
392C GLU* 4.4 7.2 - - - +
393C HIS* 2.8 53.5 + - + +
395C LEU* 4.7 5.2 - - + -
494C PHE* 6.2 0.2 - - + -
495C TYR* 4.3 15.5 - - + -
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Residues in contact with GLN 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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386C LEU* 2.9 46.5 + - + +
387C VAL* 4.1 7.3 - - - +
389C LEU* 1.3 76.7 - - - +
391C SER* 1.3 62.8 + - - +
394C ASP* 3.1 5.2 + - - -
395C LEU* 2.9 55.6 + - + +
396C ASP* 3.8 25.2 + - + +
494C PHE* 5.4 4.8 - - + -
620C HIS* 4.9 6.6 - - - -
624C SER* 4.5 21.8 + - - -
628C ARG* 6.3 0.6 - - - +
669C ARG* 5.0 4.7 + - - -
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Residues in contact with SER 391 (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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387C VAL 3.3 6.2 + - - -
388C ASP 3.3 3.2 + - - -
389C LEU 3.2 0.4 - - - -
390C GLN* 1.3 81.8 - - - +
392C GLU* 1.3 63.9 + - - +
394C ASP* 3.6 7.5 + - - +
396C ASP* 5.3 3.6 - - - +
414C ARG* 2.7 46.2 + - - -
447C GLU* 5.3 3.1 + - - -
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Residues in contact with GLU 392 (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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384C LYS* 2.4 43.2 + - - +
388C ASP* 3.0 19.2 + - - +
389C LEU* 3.7 4.4 - - - +
391C SER* 1.3 79.7 - - - +
393C HIS* 1.3 81.6 + - + +
394C ASP* 3.4 3.8 + - - +
451C ARG* 5.2 15.2 - - + -
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Residues in contact with HIS 393 (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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389C LEU* 2.8 33.9 + - + +
392C GLU* 1.3 92.8 - - + +
394C ASP* 1.3 71.9 + - - +
395C LEU* 3.1 36.9 + - + +
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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