Contacts of the strand formed by residues 441 - 446 (chain A) in PDB entry 2EZ9
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 VAL 441 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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389A ILE* 3.4 13.5 - - + +
391A SER 5.3 0.7 - - - +
429A ALA* 3.8 37.0 - - + +
432A ALA* 3.8 28.3 - - + +
433A LYS* 3.8 27.8 - - - +
436A TYR 4.7 1.3 - - - +
439A ARG 3.5 12.3 + - - +
440A GLN* 1.3 81.9 - - - +
442A PHE* 1.3 68.2 + - - +
466A PRO 4.4 1.8 + - - +
467A VAL* 3.7 5.2 - - + -
468A ILE* 2.9 29.5 + - - +
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Residues in contact with PHE 442 (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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380A VAL* 3.9 26.2 - - + -
383A ILE* 4.0 17.9 - - + -
384A ALA* 4.1 7.4 - - + -
388A ALA* 4.1 7.2 - - + -
389A ILE 2.9 11.5 + - - +
390A TYR* 3.5 39.5 - + + -
391A SER* 2.8 30.4 + - - -
440A GLN* 3.2 40.4 - - + -
441A VAL* 1.3 82.1 - - - +
443A ASN* 1.3 58.9 - - - +
444A LEU* 4.0 14.4 - - + -
467A VAL* 4.4 0.2 - - - -
468A ILE* 3.3 39.3 - - + +
470A VAL* 4.6 2.2 - - + -
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Residues in contact with ASN 443 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391A SER 3.3 3.8 - - - -
425A GLY* 3.1 30.3 - - - +
426A ILE* 3.4 22.2 - - - +
429A ALA* 3.9 17.5 - - + -
442A PHE* 1.3 71.4 - - - +
444A LEU* 1.3 60.9 + - - +
445A ALA* 3.7 16.8 - - - +
450A ALA* 5.9 0.6 - - - +
457A LEU* 5.1 0.2 - - - +
467A VAL* 3.9 1.5 - - + +
468A ILE 2.8 8.5 + - - +
469A ASN* 2.9 33.7 + - - +
470A VAL 2.8 33.0 + - - +
471A VAL* 5.6 4.4 - - - +
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Residues in contact with LEU 444 (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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377A LEU* 4.0 22.2 - - + -
380A VAL* 4.2 14.1 - - + -
390A TYR* 4.1 20.6 - - + -
391A SER 2.9 12.6 + - - +
392A ILE* 3.5 12.5 - - + -
393A ASP 2.9 25.5 + - - -
397A ILE* 3.8 23.6 - - + +
401A ALA* 4.6 1.8 - - + -
405A LEU* 4.1 13.5 - - + -
442A PHE* 4.0 18.2 - - + -
443A ASN* 1.3 78.6 + - - +
445A ALA* 1.3 59.1 + - - +
470A VAL* 3.7 27.4 - - + -
472A PHE* 4.4 4.9 - - + -
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Residues in contact with ALA 445 (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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393A ASP* 3.6 24.2 - - + +
397A ILE* 4.6 2.2 - - - -
426A ILE* 5.8 0.7 - - + +
443A ASN* 3.7 17.7 - - - +
444A LEU* 1.3 75.5 - - - +
446A GLY* 1.3 69.2 + - - +
450A ALA* 4.1 15.3 - - + -
470A VAL 3.0 9.6 + - - +
471A VAL* 3.2 6.3 - - + -
472A PHE* 2.8 30.1 + - - -
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Residues in contact with GLY 446 (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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393A ASP* 4.4 3.2 - - - +
394A VAL 5.6 0.2 + - - -
397A ILE* 4.4 12.1 - - - +
445A ALA* 1.3 77.0 - - - +
447A ASP* 1.3 61.1 + - - -
448A GLY 3.3 2.7 - - - -
449A GLY 3.4 0.9 + - - -
450A ALA* 2.9 27.7 + - - +
471A VAL* 4.3 1.1 - - - -
472A PHE* 3.8 11.7 - - - -
1611A TDK 3.5 29.5 + - - -
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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