Contacts of the helix formed by residues 417 - 427 (chain A) in PDB entry 3CS0
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 ASN 417 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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256A GLU 4.7 2.2 + - - -
257A TYR* 3.3 19.2 - - + +
378A ASN* 3.2 21.5 - - + +
382A ASP* 3.1 31.6 + - - +
384A GLY 4.5 2.0 - - - -
385A VAL* 3.7 12.1 - - - -
415A VAL* 3.4 6.2 - - - +
416A LYS* 1.3 82.3 - - - +
418A ILE* 1.3 65.0 + - - +
419A ALA* 3.0 37.8 + - - +
420A GLU* 3.3 10.8 + - - +
421A LEU 3.3 15.6 + - - -
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Residues in contact with ILE 418 (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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257A TYR 4.0 4.3 - - - +
258A GLY* 4.0 8.3 - - - +
259A GLN* 4.2 7.6 - - + -
362A VAL* 3.5 38.1 - - + -
367A ILE* 3.4 27.1 - - + -
376A MSE 4.4 0.4 - - - -
377A SER* 3.9 20.2 - - - +
378A ASN* 3.0 12.8 + - - +
385A VAL* 3.6 20.6 - - + +
417A ASN* 1.3 74.9 - - - +
419A ALA* 1.3 61.9 + - - +
421A LEU* 3.6 3.1 - - - +
422A ARG* 3.0 45.2 + - - +
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Residues in contact with ALA 419 (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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128A VAL* 4.9 8.1 - - + +
254A MSE 5.1 0.2 - - - +
255A VAL 4.9 7.4 - - - +
256A GLU 5.5 0.4 - - - -
257A TYR* 3.3 20.2 + - - +
258A GLY* 4.0 8.3 - - - +
417A ASN* 3.0 13.8 + - - +
418A ILE* 1.3 77.7 - - - +
420A GLU* 1.3 65.0 + - + +
422A ARG* 3.1 9.6 + - - +
423A LYS* 3.1 20.6 + - - +
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Residues in contact with GLU 420 (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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414A ALA* 2.8 22.6 - - - +
415A VAL* 4.3 1.8 - - - -
416A LYS* 2.8 54.8 + - - +
417A ASN* 3.3 18.7 + - - +
419A ALA* 1.3 73.8 - - + +
421A LEU* 1.3 57.5 + - - +
423A LYS* 2.7 34.4 + - - +
424A VAL* 3.2 10.4 + - - +
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Residues in contact with LEU 421 (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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367A ILE* 3.1 38.8 - - + -
368A PHE* 4.3 11.4 - - + -
376A MSE 5.4 2.0 - - + -
385A VAL* 4.3 9.9 - - + -
407A ILE* 4.1 18.8 - - + -
410A ALA* 4.3 6.5 - - + -
415A VAL* 3.5 37.8 - - + +
417A ASN 3.3 5.1 + - - +
418A ILE* 3.6 10.3 - - - +
419A ALA 3.3 0.2 - - - -
420A GLU* 1.3 79.0 - - - +
422A ARG* 1.3 60.5 + - - +
423A LYS 3.2 1.0 + - - -
424A VAL* 3.4 4.2 + - + +
425A LEU* 3.3 30.4 + - + +
432A LEU* 5.7 1.3 - - + -
434A LEU* 4.2 13.7 - - + -
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Residues in contact with ARG 422 (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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127A MSE 4.1 31.8 - - + +
128A VAL* 3.5 22.6 + - - +
129A GLY* 4.0 6.9 - - - -
130A LYS* 4.7 7.7 - - - +
258A GLY 3.4 24.2 + - - -
362A VAL* 4.9 3.8 - - - +
366A SER* 2.6 42.3 + - - -
367A ILE* 3.5 26.5 - - + +
418A ILE* 3.0 30.2 + - - +
419A ALA* 3.1 7.6 + - - +
421A LEU* 1.3 75.3 - - - +
423A LYS* 1.3 57.6 + - - +
425A LEU* 3.9 9.0 - - + +
426A ASP* 2.8 37.9 + - - +
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Residues in contact with LYS 423 (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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140A GLN* 3.6 25.3 - - - +
142A GLN* 5.6 2.4 + - - +
413A GLN* 5.6 5.2 - - - +
419A ALA 3.1 8.4 + - - +
420A GLU* 2.7 23.0 + - - +
422A ARG* 1.3 76.9 - - - +
424A VAL* 1.3 63.6 + - + +
426A ASP* 3.0 26.9 + - + +
427A SER* 3.5 5.4 + - - -
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Residues in contact with VAL 424 (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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410A ALA* 3.6 40.8 - - + +
411A ASN* 4.1 20.0 - - + +
413A GLN* 3.5 41.3 - - + +
414A ALA 5.7 0.7 - - - +
415A VAL* 5.0 4.9 - - + -
420A GLU 3.2 10.4 + - - +
421A LEU 3.7 6.7 - - - +
423A LYS* 1.3 76.0 - - + +
425A LEU* 1.3 59.9 + - - +
427A SER* 2.5 26.1 + - - +
429A PRO* 3.5 6.0 - - + +
432A LEU* 4.3 9.2 - - + -
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Residues in contact with LEU 425 (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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367A ILE* 2.9 31.9 - - + +
368A PHE* 3.7 19.3 - - + -
421A LEU* 3.3 29.2 + - + +
422A ARG* 4.1 7.0 - - + +
423A LYS 3.2 0.4 - - - -
424A VAL* 1.3 77.0 - - - +
426A ASP* 1.3 65.4 + - - +
428A LYS* 3.0 22.5 + - - +
429A PRO* 4.2 7.1 - - + +
432A LEU* 3.4 40.8 - - + -
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Residues in contact with ASP 426 (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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126A LYS* 2.9 68.6 + - - +
127A MSE 4.3 4.1 + - - +
142A GLN* 3.8 9.5 + - - +
422A ARG* 2.8 31.2 + - - +
423A LYS* 3.0 25.9 + - + +
425A LEU* 1.3 78.3 - - - +
427A SER* 1.3 59.3 + - - +
428A LYS* 3.0 4.4 + - - +
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Residues in contact with SER 427 (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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413A GLN* 5.2 4.4 + - - -
423A LYS 3.5 3.9 + - - -
424A VAL* 2.5 26.4 + - - +
426A ASP* 1.3 74.7 - - - +
428A LYS* 1.3 70.6 + - - +
429A PRO* 3.7 9.9 - - - +
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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