Contacts of the strand formed by residues 438 - 444 (chain A) in PDB entry 1EX0
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 ASP 438 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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348A LEU 2.9 10.3 + - - +
349A GLN* 3.4 2.6 + - + -
350A MET* 2.9 27.7 + - - +
436A ASN 4.0 0.2 - - - +
437A SER* 1.3 73.4 - - - +
439A LEU* 1.3 62.5 + - - +
440A ILE* 4.1 10.9 - - + +
455A VAL* 3.8 24.9 - - + +
456A ASP 3.4 7.6 - - - +
457A ALA* 3.4 13.6 - - - +
504A LYS* 2.8 35.0 + - - -
508A THR* 6.0 1.0 - - - +
1320A CA 2.9 23.6 - - - -
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Residues in contact with LEU 439 (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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350A MET* 3.3 19.5 - - + -
352A ILE* 3.8 13.5 - - + -
369A VAL* 4.0 15.9 - - + -
438A ASP* 1.3 73.2 - - - +
440A ILE* 1.3 63.6 + - - +
441A TYR* 4.1 8.5 + - + +
455A VAL* 3.3 5.7 - - - +
456A ASP* 2.9 47.2 + - + +
459A HIS* 3.7 36.1 - - + -
460A ILE* 3.5 28.7 - - + -
622A GLN* 3.7 23.6 - - - +
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Residues in contact with ILE 440 (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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349A GLN* 3.8 47.6 - - + +
350A MET 2.7 11.9 + - - +
351A ASP* 3.5 13.3 - - - +
352A ILE* 2.7 33.4 + - - +
438A ASP* 4.1 11.9 - - + +
439A LEU* 1.3 80.6 - - - +
441A TYR* 1.3 61.3 - - - +
442A ILE* 3.7 21.7 + - + +
452A VAL* 3.9 22.0 - - + -
454A ASN 3.8 3.6 - - - +
455A VAL* 4.2 13.7 - - + -
506A LEU* 4.0 11.2 - - + -
508A THR* 4.3 6.7 - - - +
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Residues in contact with TYR 441 (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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352A ILE* 3.5 41.1 - - + -
354A LEU* 4.3 18.2 - - + -
439A LEU* 4.1 13.2 - - + +
440A ILE* 1.3 73.2 - - - +
442A ILE* 1.3 53.9 + - - +
452A VAL* 3.7 2.1 - - - -
453A GLU* 2.7 35.8 + - + -
454A ASN* 3.0 41.9 + - - +
456A ASP* 4.2 24.5 + - + -
607A PHE* 4.8 4.0 - + - -
609A THR* 5.0 3.1 - - + -
618A VAL* 5.1 0.2 - - + -
620A ALA* 3.6 34.1 + - + +
621A LYS* 4.4 5.6 + - - -
622A GLN* 3.1 30.3 + - - +
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Residues in contact with ILE 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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351A ASP* 3.7 34.1 - - + +
352A ILE 3.1 5.3 + - - +
353A PHE* 3.3 26.0 - - + -
354A LEU* 2.9 26.9 + - - +
440A ILE* 3.8 19.3 - - + +
441A TYR* 1.3 76.8 - - - +
443A THR* 1.3 75.6 + - - +
444A ALA 3.6 0.2 + - - -
450A HIS* 3.6 21.8 - - + -
451A VAL 3.3 10.8 - - - +
452A VAL* 4.2 12.8 - - + -
506A LEU* 5.4 6.7 - - + -
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Residues in contact with THR 443 (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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354A LEU* 3.4 14.6 - - - +
355A GLU 4.0 7.0 - - - +
356A GLU* 4.0 8.7 - - + -
442A ILE* 1.3 74.7 - - - +
444A ALA* 1.3 70.0 + - - +
445A LYS* 3.7 9.3 + - + +
450A HIS* 3.2 6.9 - - - -
451A VAL* 2.8 54.9 + - + +
453A GLU* 2.6 25.6 + - - +
611A ARG* 3.0 26.2 + - - +
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Residues in contact with ALA 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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353A PHE* 4.6 4.9 - - + -
354A LEU 2.9 18.3 + - - +
355A GLU* 4.3 0.5 - - - -
361A ASN* 4.6 6.1 + - - +
364A LEU* 3.8 27.1 - - + -
442A ILE* 3.6 2.2 + - - +
443A THR* 1.3 73.5 - - - +
445A LYS* 1.3 64.7 + - - +
446A LYS* 3.3 16.8 + - - -
449A THR 4.6 0.2 - - - +
450A HIS* 3.6 24.2 - - + +
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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