Contacts of the strand formed by residues 409 - 417 (chain A) in PDB entry 2C11
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 THR 409 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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323A PHE* 4.0 15.8 + - - -
325A VAL* 3.8 36.9 - - + +
408A ALA* 1.3 73.6 - - - +
410A TYR* 1.3 67.9 + - - +
411A VAL* 4.1 6.0 + - + +
430A CYS* 3.3 3.8 - - - -
431A VAL* 2.8 40.3 + - + +
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Residues in contact with TYR 410 (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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398A LEU* 4.2 10.1 - - + -
400A ARG* 3.1 66.8 + - + +
404A CYS* 3.4 23.3 + - + +
405A PRO 2.5 23.1 + - - -
406A TYR 3.8 9.4 - - - -
408A ALA* 3.4 29.1 + - + -
409A THR* 1.3 76.7 - - - +
411A VAL* 1.3 66.2 + - - +
412A ASP* 4.9 1.6 - - - +
427A ASP* 3.5 39.0 - - + +
429A PHE 3.6 2.7 - - - -
430A CYS* 4.1 9.9 - - + -
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Residues in contact with VAL 411 (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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325A VAL* 4.4 15.9 - - + -
327A GLY 4.8 6.7 - - - +
339A PHE* 4.2 26.0 - - + -
409A THR* 4.4 9.4 - - + +
410A TYR* 1.3 80.1 - - - +
412A ASP* 1.3 73.8 + - - +
427A ASP* 2.9 1.5 - - - -
428A ALA 2.4 35.5 + - - -
429A PHE* 2.9 33.3 + - + +
431A VAL* 5.1 4.0 - - + -
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Residues in contact with ASP 412 (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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65A ARG* 4.9 6.1 + - - -
410A TYR 4.9 1.4 - - - +
411A VAL* 1.3 97.4 - - - +
413A TRP* 1.3 64.3 + - - +
414A HIS* 5.8 0.2 - - - -
424A THR* 3.6 21.2 - - + +
425A ILE 3.2 5.8 - - - -
426A ARG* 3.7 21.3 + - - +
427A ASP* 3.4 14.9 + - - +
428A ALA* 4.3 0.7 - - - -
429A PHE* 3.8 8.0 - - - -
1743A CU 3.7 18.2 - - - -
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Residues in contact with TRP 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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62A ASP* 3.0 39.4 + - + +
100A GLU* 5.7 4.3 - - + -
341A LEU* 3.2 32.3 - - + +
343A ALA* 4.1 12.6 - - + -
392A GLY* 3.6 33.0 - - - -
393A LYS* 4.1 7.0 - - - -
395A THR* 3.9 14.4 - - + -
412A ASP* 1.3 78.9 - - - +
414A HIS* 1.3 76.5 + - - +
415A PHE* 3.9 38.4 - + + -
417A LEU* 4.7 3.6 - - + -
423A LYS 3.8 0.5 - - - +
424A THR* 3.1 3.6 - - - -
425A ILE* 2.7 36.6 + - + +
428A ALA* 3.7 17.5 - - + -
429A PHE* 3.7 15.3 - + - -
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Residues in contact with HIS 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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62A ASP* 5.5 0.9 - - - +
63A LEU 3.9 18.7 + - - +
64A SER* 3.5 29.2 - - - -
65A ARG* 3.3 44.1 + - + +
68A LEU* 4.1 5.0 - - + +
412A ASP* 4.5 0.4 - - + -
413A TRP* 1.3 90.5 + - - +
415A PHE* 1.3 65.3 + - - +
422A PRO* 5.5 0.9 - - + -
423A LYS 3.3 6.5 - - - +
424A THR* 2.9 34.2 + - + +
1743A CU 2.4 30.9 - - - -
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Residues in contact with PHE 415 (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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68A LEU* 3.7 11.6 - - - +
393A LYS 6.1 1.1 - - - -
413A TRP* 3.9 34.8 - + + -
414A HIS* 1.3 80.8 - - - +
416A LEU* 1.3 59.9 + - - +
417A LEU* 3.8 30.9 + - + -
421A ALA 4.3 0.7 - - - +
422A PRO* 3.1 2.4 - - - +
423A LYS* 2.9 93.1 + - + +
424A THR 4.1 2.0 - - - -
425A ILE* 3.5 29.6 - - + -
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Residues in contact with LEU 416 (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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68A LEU* 3.6 40.2 - - + +
72A MET* 3.6 40.8 - - + -
96A VAL* 5.8 0.2 - - - +
98A SER* 3.3 4.0 - - - -
99A VAL* 3.0 38.0 + - + +
415A PHE* 1.3 73.2 - - - +
417A LEU* 1.3 62.1 + - - +
419A SER* 3.6 18.1 - - - +
421A ALA 3.2 45.3 - - - +
422A PRO* 3.2 5.4 - - + -
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Residues in contact with LEU 417 (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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97A PHE* 3.8 2.9 - - + +
98A SER* 3.3 28.5 - - - -
99A VAL 6.0 0.4 - - - +
343A ALA* 4.3 15.9 - - + -
344A PHE* 4.3 12.1 - - + -
393A LYS* 3.8 56.3 - - + +
413A TRP* 4.7 2.7 - - + -
415A PHE* 3.7 35.5 + - + -
416A LEU* 1.3 78.7 - - - +
418A GLU* 1.3 59.1 + - - +
419A SER* 2.7 24.5 + - - -
423A LYS* 3.4 10.2 + - - -
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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