Contacts of the helix formed by residues 387 - 394 (chain C) in PDB entry 4L28
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 387 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179A ASP* 5.1 11.6 + - - -
336C ARG* 3.8 1.3 - - - -
382C MET 4.0 5.4 + - - -
383C THR* 3.7 21.1 - - - -
384C LYS 2.8 19.9 + - - +
386C LEU* 1.3 79.6 - - - +
388C ASP* 1.3 63.6 + - - +
389C ARG* 3.2 30.0 + - - +
390C TRP* 4.1 1.6 - - - -
391C MET* 3.2 17.2 + - - +
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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
----------------------------------------------------------
182A ARG* 3.7 36.6 + - - +
336C ARG* 2.6 37.1 + - - +
386C LEU 3.7 2.2 + - - -
387C SER* 1.3 73.3 + - - +
389C ARG* 1.3 59.1 + - - +
391C MET* 3.1 5.5 + - - +
392C LEU* 2.9 38.7 + - + +
397C LEU* 4.1 9.8 - - + +
402C LEU* 5.6 9.8 - - + +
501C HIS* 4.9 8.9 - - + -
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Residues in contact with ARG 389 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383C THR* 3.7 24.0 + - - -
387C SER* 3.2 17.5 + - - +
388C ASP* 1.3 79.3 - - - +
390C TRP* 1.3 71.5 + - - +
392C LEU* 3.7 12.2 - - + +
393C GLN* 2.7 63.9 + - - +
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Residues in contact with TRP 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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302C GLU* 3.6 23.6 - - + -
332C PHE* 3.8 28.3 - + - -
383C THR 3.7 17.5 - - - +
384C LYS* 3.3 63.2 - - + +
385C PHE* 3.6 15.7 - - - -
387C SER* 3.4 3.7 + - - +
388C ASP 3.2 0.2 - - - -
389C ARG* 1.3 98.8 - - - +
391C MET* 1.3 76.0 + - - +
393C GLN* 3.6 8.0 - - - +
394C LYS* 2.9 56.5 + - + +
396C PHE* 4.0 14.1 - + - -
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Residues in contact with MET 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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332C PHE* 3.8 24.0 - - + -
333C THR* 5.1 3.4 - - - +
336C ARG* 4.0 23.8 - - - +
385C PHE* 3.5 35.0 - - - +
387C SER 3.2 13.2 + - - +
388C ASP 3.1 8.2 + - - +
390C TRP* 1.3 92.1 - - - +
392C LEU* 1.3 57.9 + - - +
395C GLY 3.2 2.1 + - - -
396C PHE* 2.8 53.4 + - + +
397C LEU* 3.0 29.2 + - + -
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Residues in contact with LEU 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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388C ASP* 2.9 27.0 + - + +
389C ARG* 3.7 8.7 - - + +
391C MET* 1.3 77.8 - - - +
393C GLN* 1.3 59.5 + - - +
395C GLY* 3.0 18.5 + - - -
397C LEU* 3.2 40.6 - - + +
398C LYS 4.6 0.9 - - - +
399C GLU* 4.5 17.9 - - + +
402C LEU* 5.2 12.8 - - + -
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Residues in contact with GLN 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 ARG* 2.7 49.7 + - - +
390C TRP* 3.6 10.2 - - - +
392C LEU* 1.3 76.8 - - - +
394C LYS* 1.3 70.0 + - + +
395C GLY 3.2 1.2 + - - -
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Residues in contact with LYS 394 (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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302C GLU* 3.1 37.1 + - + +
390C TRP* 2.9 52.3 + - + +
393C GLN* 1.3 89.4 - - + +
395C GLY* 1.3 61.9 + - - +
396C PHE* 3.3 30.1 + - + -
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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