Contacts of the strand formed by residues 438 - 444 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348B LEU 2.8 13.4 + - - +
349B GLN* 3.5 2.1 + - + -
350B MET* 2.9 27.9 + - - +
436B ASN 3.9 0.2 - - - +
437B SER* 1.3 75.2 - - - +
439B LEU* 1.3 64.2 + - - +
440B ILE* 4.3 8.8 - - + +
455B VAL* 3.9 20.0 - - + +
456B ASP 3.5 6.5 - - - +
457B ALA* 3.4 17.8 - - - +
460B ILE* 4.5 0.4 - - - -
504B LYS* 2.8 36.2 + - - -
508B THR* 5.5 2.1 + - - -
1321B CA 2.7 27.9 - - - -
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Residues in contact with LEU 439 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350B MET* 3.4 11.7 - - + +
352B ILE* 3.8 18.2 - - + -
369B VAL* 4.1 16.8 - - + -
438B ASP* 1.3 73.9 - - - +
440B ILE* 1.3 59.3 + - - +
441B TYR* 3.8 11.6 - - + +
454B ASN 4.1 0.2 - - - +
455B VAL* 3.3 7.4 - - - +
456B ASP* 2.8 49.9 + - + +
459B HIS* 3.8 34.8 - - + -
460B ILE* 3.8 23.3 - - + -
622B GLN* 3.4 25.1 - - + +
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Residues in contact with ILE 440 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349B GLN* 3.9 44.0 - - + +
350B MET 2.8 10.2 + - - +
351B ASP* 3.3 16.3 - - - +
352B ILE* 2.7 32.4 + - - +
438B ASP* 4.3 7.9 - - + +
439B LEU* 1.3 82.1 - - - +
441B TYR* 1.3 58.6 + - - +
442B ILE* 3.7 20.2 + - + +
452B VAL* 3.9 23.6 - - + -
454B ASN 3.8 3.4 - - - +
455B VAL* 3.9 18.8 - - + -
506B LEU* 4.0 14.1 - - + -
508B THR* 4.5 3.6 - - + -
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Residues in contact with TYR 441 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352B ILE* 3.4 39.3 - - + -
354B LEU* 3.6 16.4 - - + -
439B LEU* 3.8 22.0 - - + +
440B ILE* 1.3 74.1 - - - +
442B ILE* 1.3 57.1 + - - +
452B VAL* 3.9 0.7 - - - -
453B GLU* 2.8 36.0 + - + +
454B ASN* 3.0 29.5 + - + +
455B VAL 5.2 0.2 - - - -
456B ASP* 4.3 15.7 + - + -
607B PHE* 4.9 6.1 - + - -
609B THR* 5.3 1.6 - - + -
618B VAL* 5.4 2.9 - - + -
620B ALA* 3.5 39.1 - - + +
621B LYS* 4.4 5.2 + - - -
622B GLN* 2.8 33.3 + - + +
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Residues in contact with ILE 442 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351B ASP* 3.7 30.7 - - + +
352B ILE 2.9 8.0 + - - +
353B PHE* 3.2 28.5 - - + +
354B LEU* 2.8 28.3 + - - +
440B ILE* 3.7 22.9 - - + +
441B TYR* 1.3 77.6 - - - +
443B THR* 1.3 65.1 + - - +
444B ALA 3.5 0.3 + - - -
450B HIS* 3.8 30.5 - - + -
451B VAL 3.5 11.9 - - - +
452B VAL* 4.6 8.1 - - + +
506B LEU* 4.8 9.9 - - + -
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Residues in contact with THR 443 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354B LEU* 3.6 16.1 - - - +
355B GLU 4.1 1.5 + - - +
356B GLU* 3.9 30.3 - - + +
442B ILE* 1.3 71.8 - - - +
444B ALA* 1.3 60.8 + - - +
445B LYS* 3.7 22.9 + - + +
450B HIS* 3.1 6.8 - - - -
451B VAL* 2.8 40.9 + - + -
453B GLU* 2.6 34.5 + - - +
618B VAL* 4.9 2.9 - - - +
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Residues in contact with ALA 444 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353B PHE* 4.6 9.4 - - + -
354B LEU 3.0 18.8 + - - +
355B GLU* 4.6 1.7 - - - +
356B GLU* 4.4 6.4 + - - +
361B ASN* 4.8 4.7 + - - +
364B LEU* 3.7 30.1 - - + -
442B ILE 3.5 1.8 + - - -
443B THR* 1.3 73.6 - - - +
445B LYS* 1.3 65.2 + - - +
446B LYS 4.1 0.3 + - - -
450B HIS* 3.8 23.6 - - + +
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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