Contacts of the helix formed by residues 387 - 394 (chain A) in PDB entry 4L0D
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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382A MET 4.0 2.5 + - - -
383A THR* 3.8 25.8 - - - -
384A LYS 3.3 8.8 + - - +
385A PHE 3.3 0.4 - - - -
386A LEU* 1.3 78.0 - - - +
388A ASP* 1.3 64.0 + - - +
389A ARG* 3.1 35.4 + - - +
390A TRP* 3.2 9.4 + - - -
391A MET* 3.2 13.7 + - - +
179B ASP* 5.4 7.6 - - - -
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Residues in contact with ASP 388 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336A ARG* 2.6 31.8 + - - +
386A LEU 3.6 6.2 - - - +
387A SER* 1.3 73.4 + - - +
389A ARG* 1.3 58.3 + - - +
391A MET* 3.2 6.0 + - - +
392A LEU* 2.9 38.8 + - + +
397A LEU* 4.3 7.5 - - + +
182B ARG* 4.5 23.8 + - - +
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Residues in contact with ARG 389 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383A THR* 3.8 23.6 + - - -
387A SER* 3.1 16.2 + - - +
388A ASP* 1.3 78.5 - - - +
390A TRP* 1.3 74.2 + - - +
392A LEU* 3.8 11.1 - - + +
393A GLN* 2.9 53.2 + - - +
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Residues in contact with TRP 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302A GLU* 4.0 12.1 - - + -
332A PHE* 3.7 35.7 - + - -
383A THR 4.0 13.0 - - - +
384A LYS* 3.0 66.0 - - + +
385A PHE* 3.8 12.3 - - - -
387A SER* 3.2 9.3 + - - +
389A ARG* 1.3 99.3 - - - +
391A MET* 1.3 70.9 + - - +
392A LEU 3.2 0.2 - - - -
393A GLN* 3.7 9.9 - - - +
394A LYS* 3.0 57.9 + - + +
396A PHE* 4.0 14.6 - + - -
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Residues in contact with MET 391 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332A PHE* 3.9 19.3 - - + -
333A THR* 5.1 4.9 - - - +
336A ARG* 3.9 24.5 - - - +
385A PHE* 3.4 40.2 - - - +
387A SER 3.4 13.9 - - - +
388A ASP* 3.2 8.9 + - - +
390A TRP* 1.3 87.9 - - - +
392A LEU* 1.3 58.6 + - - +
394A LYS 3.8 0.3 + - - -
395A GLY 3.4 1.0 + - - -
396A PHE* 2.8 55.9 + - + +
397A LEU* 3.2 26.7 + - + -
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Residues in contact with LEU 392 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388A ASP* 2.9 28.3 + - + +
389A ARG* 3.8 10.1 - - + +
391A MET* 1.3 76.3 - - - +
393A GLN* 1.3 64.6 + - - +
395A GLY* 3.1 13.7 + - - -
397A LEU* 3.4 40.8 - - + +
398A LYS 4.7 0.2 - - - -
399A GLU* 4.4 19.3 - - + +
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Residues in contact with GLN 393 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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389A ARG* 2.9 47.4 + - - +
390A TRP* 3.7 10.3 - - - +
392A LEU* 1.3 79.6 - - - +
394A LYS* 1.3 77.9 + - + +
395A GLY* 3.3 0.6 + - - -
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Residues in contact with LYS 394 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302A GLU* 3.7 29.2 + - + +
384A LYS* 5.9 0.4 - - - +
390A TRP* 3.0 57.1 + - + +
393A GLN* 1.3 96.3 - - + +
395A GLY* 1.3 61.7 + - - +
396A PHE* 3.4 30.7 + - + -
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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