Contacts of the helix formed by residues 369 - 377 (chain H) in PDB entry 5LN3
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 ARG 369 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352H THR* 3.6 20.3 - - - +
355H PHE* 4.0 15.2 - - - -
356H LYS* 5.5 9.2 - - - +
366H ARG* 3.2 30.5 - - - +
368H ILE* 1.3 82.2 + - - +
370H PHE* 1.4 69.8 - - - +
371H GLU* 3.3 52.8 + - + +
372H LEU* 3.7 19.0 + - + +
373H LEU* 4.0 9.6 - - - +
406H GLU* 4.8 2.8 + - - +
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Residues in contact with PHE 370 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351H ARG* 5.2 3.8 - - + -
352H THR* 5.4 4.3 - - - -
355H PHE* 3.3 72.7 - + + -
366H ARG* 4.3 2.9 - - - +
368H ILE 4.3 0.2 - - - -
369H ARG* 1.4 80.4 - - - +
371H GLU* 1.4 54.7 + - - +
372H LEU 3.3 0.9 - - - -
373H LEU* 3.2 26.3 - - + +
374H ALA* 3.0 44.1 + - + -
377H CYS* 6.0 4.7 - - - -
385H ILE* 5.0 12.6 - - + -
388H VAL* 4.4 23.3 - - + -
389H CYS* 5.7 0.9 - - - -
409H PHE* 4.0 23.6 - + + -
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Residues in contact with GLU 371 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348H LEU* 5.6 3.3 - - + +
352H THR* 3.9 24.9 - - - +
369H ARG* 3.3 38.0 + - + +
370H PHE* 1.4 75.7 - - - +
372H LEU* 1.4 69.6 + - + +
374H ALA* 3.1 18.1 + - - +
375H ARG* 3.1 24.2 + - + +
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Residues in contact with LEU 372 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204E GLN 4.1 11.9 - - - +
205E VAL* 3.6 22.0 - - - +
206E MET 3.6 21.3 - - - +
207E GLU* 3.9 22.9 - - + -
369H ARG* 3.7 15.1 + - + +
370H PHE 3.3 0.4 - - - -
371H GLU* 1.4 82.6 - - + +
373H LEU* 1.3 69.7 + - + +
375H ARG* 3.5 23.1 + - - +
376H LEU* 3.5 18.5 + - + +
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Residues in contact with LEU 373 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207E GLU* 5.2 13.2 - - + -
369H ARG 4.0 9.9 - - - +
370H PHE* 3.2 28.5 - - + +
372H LEU* 1.3 84.1 - - + +
374H ALA* 1.4 56.0 + - - +
376H LEU* 3.0 28.5 + - + +
377H CYS* 3.0 24.3 + - - -
406H GLU* 3.8 24.5 - - - +
409H PHE* 3.7 36.6 - - + -
410H LEU* 4.8 13.7 - - + -
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Residues in contact with ALA 374 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348H LEU* 4.8 6.5 - - + +
351H ARG* 3.2 39.8 + - + -
352H THR* 5.7 0.9 - - - +
370H PHE* 3.0 27.8 + - + +
371H GLU* 3.1 16.1 + - - +
373H LEU* 1.4 79.6 - - - +
375H ARG* 1.4 60.2 + - + +
377H CYS* 3.2 22.0 + - - +
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Residues in contact with ARG 375 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32E LYS* 3.1 22.2 + - - +
33E LEU* 6.0 0.9 - - - +
172E SER* 3.4 28.8 + - - +
173E ALA* 3.2 42.5 + - - +
175E GLU* 3.7 13.3 + - - +
176E GLY* 3.2 24.0 - - - +
177E ALA 5.2 0.2 - - - +
205E VAL* 5.8 1.4 - - - +
348H LEU* 3.7 38.7 - - + +
371H GLU* 3.1 20.9 + - + +
372H LEU* 3.9 20.7 - - - +
373H LEU 3.3 0.2 - - - -
374H ALA* 1.4 73.7 - - - +
376H LEU* 1.4 63.9 + - + +
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Residues in contact with LEU 376 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33E LEU* 5.0 12.0 - - - +
53E ARG* 3.8 28.9 - - - +
172E SER* 4.3 14.6 - - - +
207E GLU* 5.7 11.9 - - + +
372H LEU* 3.5 15.4 + - + +
373H LEU* 3.0 15.5 + - + +
375H ARG* 1.4 79.1 - - + +
377H CYS* 1.3 64.4 + - - +
378H PRO* 4.0 3.1 - - - +
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Residues in contact with CYS 377 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32E LYS* 4.1 5.9 + - - -
33E LEU* 5.3 3.0 - - - +
351H ARG* 4.1 0.6 + - - +
370H PHE* 6.0 4.5 - - - -
373H LEU* 3.0 32.5 + - - -
374H ALA* 3.2 20.4 + - - +
375H ARG 3.7 5.0 - - - +
376H LEU* 1.3 78.8 - - - +
378H PRO* 1.4 79.0 - - + +
379H ASN 3.6 0.9 + - - -
385H ILE* 6.5 1.1 - - + -
388H VAL* 6.6 0.4 - - - -
413H VAL* 3.7 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