Contacts of the strand formed by residues 411 - 417 (chain A) in PDB entry 3CPE
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 HIS 411 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400A LEU* 5.0 4.3 - - + -
401A ASP 3.6 4.7 - - - +
402A CYS* 3.7 6.0 - - - -
403A SER* 3.1 36.6 + - - -
404A GLU 5.2 0.2 - - - -
406A ARG* 3.8 12.5 - - + -
410A TYR* 1.3 70.8 - - - +
412A ALA* 1.3 59.2 + - - +
413A LEU 4.2 0.2 - - - -
429A LEU* 3.3 10.2 - - + +
430A HIS* 3.3 4.3 - - - -
431A SER* 2.7 45.6 + - - +
434A ILE* 2.8 35.0 + - + -
436A HIS* 4.4 8.0 + - + -
439A LEU* 3.9 40.2 - - + +
462A THR* 4.5 13.7 - - + -
569A PO4 5.3 0.9 - - - -
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Residues in contact with ALA 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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400A LEU* 3.3 4.1 - - - +
401A ASP 2.9 28.9 + - - +
411A HIS* 1.3 73.5 - - - +
413A LEU* 1.3 57.9 + - - +
414A HIS* 4.9 0.7 - - - +
429A LEU 3.4 2.9 - - - -
430A HIS* 4.7 0.7 - - + -
542A ASP* 3.2 38.4 - - + +
543A LEU* 4.0 17.5 - - + -
546A SER* 2.7 28.8 + - - -
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Residues in contact with LEU 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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384A PHE* 4.7 2.7 - - + -
398A ALA* 4.0 17.0 - - + -
399A THR 3.2 17.3 - - - +
400A LEU* 3.9 24.0 - - + +
411A HIS 4.2 0.4 - - - -
412A ALA* 1.3 72.6 - - - +
414A HIS* 1.3 65.6 + - - +
415A ILE* 4.2 22.0 - - + -
427A GLY 3.8 0.2 - - - +
428A VAL* 3.1 9.8 - - - +
429A LEU* 2.8 58.8 + - + +
443A VAL* 4.0 31.4 - - + -
446A TYR* 4.7 11.4 - - + -
447A LEU* 4.4 2.9 - - + -
455A VAL* 4.2 2.9 - - + -
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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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397A ILE 3.6 0.7 - - - +
398A ALA* 3.1 8.0 - - - +
399A THR* 2.9 39.4 + - - +
412A ALA 4.9 0.9 - - - -
413A LEU* 1.3 76.0 - - - +
415A ILE* 1.3 62.7 + - - +
416A ILE* 4.0 15.9 - - + +
425A GLN* 3.0 31.3 + - + -
427A GLY 3.5 2.0 - - - -
428A VAL* 3.7 13.4 - - + +
519A THR* 3.6 17.5 - - + -
543A LEU* 2.7 32.7 + - + +
546A SER* 3.5 27.1 - - - -
547A LEU* 3.5 21.9 - - + +
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Residues in contact with ILE 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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384A PHE* 3.8 30.1 - - + -
396A TYR* 3.9 22.9 - - + -
397A ILE 3.3 4.9 - - - +
398A ALA* 4.2 12.3 - - + -
413A LEU* 4.2 10.5 - - + -
414A HIS* 1.3 78.0 - - - +
416A ILE* 1.3 60.4 + - - +
425A GLN* 3.5 4.2 - - - -
426A VAL* 2.8 48.6 + - + -
427A GLY 2.7 18.3 + - - +
446A TYR* 4.0 17.9 - - + +
447A LEU* 4.8 3.1 - - + +
450A TYR* 3.9 22.2 - - + -
453A CYS* 4.1 5.2 - - - -
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Residues in contact with ILE 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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396A TYR* 3.3 4.9 - - - -
397A ILE 2.7 40.8 + - - +
399A THR* 5.4 0.7 - - - +
414A HIS* 4.0 19.7 - - + +
415A ILE* 1.3 81.2 - - - +
417A ASP* 1.3 65.9 + - - +
418A VAL* 3.2 5.6 + - + +
423A TRP* 3.8 13.9 - - + -
424A GLU 3.3 7.4 - - - +
425A GLN* 3.9 19.7 - - + -
512A LEU* 3.8 23.8 - - + -
547A LEU* 4.0 15.7 - - + -
550A PHE* 3.7 41.5 - - + -
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Residues in contact with ASP 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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394A ARG* 3.0 34.5 + - - -
395A LYS 3.5 4.2 - - - +
396A TYR* 3.6 18.9 + - + -
415A ILE 4.2 0.4 - - - -
416A ILE* 1.3 68.1 - - - +
418A VAL* 1.3 58.9 + - - +
419A THR* 2.7 28.7 + - - -
420A ASP 4.6 0.9 + - - -
422A VAL 4.2 2.6 - - - +
423A TRP* 3.3 8.3 - - - -
424A GLU* 2.5 45.8 + - + +
426A VAL* 3.6 20.1 - - + +
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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