Contacts of the strand formed by residues 539 - 544 (chain X) in PDB entry 2DE0
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 TYR 539 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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513X HIS* 5.1 1.6 - + - -
516X ARG* 5.5 4.9 + - - -
520X GLU* 4.4 25.4 + - + -
534X ASN* 3.7 1.9 - - - +
535X HIS* 2.8 35.9 + - + +
537X ASP* 2.7 30.8 + - - +
538X GLY* 1.3 81.6 - - - +
540X SER* 1.3 51.4 + - - +
552X LEU* 4.3 24.5 - - + -
553X TYR* 3.3 21.1 - - - +
554X PRO* 3.9 21.4 - - + +
555X SER* 3.4 9.4 + - - -
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Residues in contact with SER 540 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507X GLN* 5.4 3.1 + - - -
531X VAL* 4.6 3.0 - - - +
533X GLY 3.4 14.3 + - - -
534X ASN* 3.7 13.7 + - - +
535X HIS* 4.4 0.7 - - - +
539X TYR* 1.3 71.2 - - - +
541X LYS* 1.3 60.5 + - - +
552X LEU* 3.2 8.6 - - - -
553X TYR* 2.8 73.1 + - - -
555X SER* 3.4 21.1 + - - -
558X VAL* 5.9 0.3 - - - +
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Residues in contact with LYS 541 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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531X VAL* 3.8 3.3 - - - +
532X ALA* 2.9 45.6 + - + +
533X GLY* 2.9 15.9 + - - +
535X HIS* 4.1 24.1 + - + +
540X SER* 1.3 73.9 - - - +
542X GLY* 1.3 61.4 + - - +
550X THR* 3.5 26.2 - - + +
551X GLY* 3.5 15.3 - - - +
552X LEU* 4.2 8.3 - - + -
553X TYR* 3.8 2.9 - - - -
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Residues in contact with GLY 542 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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521X ILE* 4.1 6.6 - - - +
529X ILE* 4.8 0.2 - - - -
530X GLY 3.0 14.8 - - - -
531X VAL* 4.1 0.2 - - - -
532X ALA* 3.8 6.7 - - - -
541X LYS* 1.3 79.9 - - - +
543X VAL* 1.3 63.3 + - - -
549X ARG 4.0 0.2 - - - +
550X THR* 3.3 7.3 - - - +
551X GLY 3.0 31.9 + - - +
553X TYR* 3.7 8.3 - - - -
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Residues in contact with VAL 543 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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521X ILE* 4.4 0.4 - - - -
529X ILE* 3.2 7.3 - - - +
530X GLY* 2.6 51.9 + - - +
532X ALA* 6.4 1.1 - - + -
542X GLY* 1.3 75.2 - - - -
544X ASN* 1.3 65.0 + - - +
545X ARG* 3.1 24.2 + - + +
548X GLY* 4.6 6.1 - - - -
549X ARG 3.2 19.7 - - - +
550X THR* 3.2 21.1 - - + +
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Residues in contact with ASN 544 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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521X ILE* 4.0 14.2 - - + +
522X PRO 2.7 26.0 + - - +
523X MET* 3.9 1.0 - - - +
527X ASP* 3.1 31.5 + - - +
528X ILE 3.8 1.2 - - - +
529X ILE* 3.9 15.5 - - + -
543X VAL* 1.3 71.2 - - - +
545X ARG* 1.3 50.6 + - - +
546X LYS* 3.3 14.6 + - - +
547X LEU* 2.6 53.2 + - + +
548X GLY* 2.8 15.4 + - - -
549X ARG* 2.7 14.2 + - + +
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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