Contacts of the strand formed by residues 411 - 414 (chain A) in PDB entry 2CAN
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 ILE 411 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236A ALA 3.8 16.2 - - - +
237A GLY* 3.9 8.1 - - - +
372A ARG* 3.6 22.7 - - - +
379A ALA* 3.9 20.9 - - + -
380A ILE 3.5 11.7 - - - +
381A VAL* 4.6 9.2 - - + -
406A PRO* 2.9 27.7 - - - +
407A THR* 3.0 29.6 + - + +
408A HIS* 4.2 14.2 - - + +
410A ASP* 1.3 94.7 - - - +
412A ILE* 1.3 65.1 + - - +
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Residues in contact with ILE 412 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379A ALA* 3.2 4.1 - - - -
380A ILE* 3.0 45.5 + - + +
382A ILE* 3.7 20.4 - - + -
390A ALA* 3.7 20.4 - - + +
393A VAL* 3.7 37.5 - - + -
394A CYS* 4.0 22.2 - - - -
397A LEU* 4.9 0.9 - - + -
404A ALA* 4.1 5.2 - - + -
405A LYS 4.1 3.4 - - - +
406A PRO* 4.6 0.2 - - + -
411A ILE* 1.3 79.9 - - - +
413A ARG* 1.3 71.0 + - - +
414A PHE* 3.9 22.6 + - + -
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Residues in contact with ARG 413 (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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81A PHE 3.6 8.5 - - - +
82A LEU* 4.5 15.9 - - + +
85A TYR* 3.7 29.0 - - - +
234A GLY 3.9 5.8 + - - -
235A GLU* 3.0 41.3 + - - +
238A VAL* 4.1 9.3 - - + +
266A GLN* 3.0 25.9 - - - +
377A LEU* 4.4 11.2 - - + -
378A ASN 3.4 16.2 - - - +
379A ALA* 4.1 3.6 - - + -
404A ALA* 3.7 12.1 - - - +
405A LYS 3.5 15.6 + - - +
407A THR* 3.4 31.1 - - + +
411A ILE 4.2 0.6 - - - -
412A ILE* 1.3 74.9 - - - +
414A PHE* 1.3 68.1 + - - +
415A ALA* 3.9 20.6 - - + -
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Residues in contact with PHE 414 (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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81A PHE* 3.8 28.7 - + + -
356A LEU* 4.3 10.6 - - + +
360A LEU* 4.1 26.7 - - + -
376A LEU 3.4 3.6 - - - +
378A ASN* 2.8 37.0 + - + +
379A ALA* 5.0 1.1 - - - -
380A ILE* 3.5 39.9 - - + -
393A VAL* 6.2 0.7 - - + -
397A LEU* 3.9 25.4 - - + -
402A LEU* 4.3 2.2 - - + -
404A ALA* 4.3 2.7 - - + -
412A ILE* 3.9 22.9 - - + -
413A ARG* 1.3 75.9 - - - +
415A ALA* 1.3 59.1 + - - +
416A PRO* 3.7 7.7 - - - +
432A ILE* 3.9 27.4 - - + -
436A ILE* 6.0 1.3 - - + -
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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