Contacts of the strand formed by residues 542 - 549 (chain A) in PDB entry 4OE5
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 THR 542 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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180A LEU* 4.5 0.2 - - + -
197A TYR* 3.3 43.3 + - + +
198A ARG 2.9 18.0 + - - -
200A LEU* 4.0 2.2 - - - -
226A MET* 3.8 23.7 - - + +
310A ARG* 2.9 21.1 + - - -
539A LEU* 3.4 30.9 - - + +
540A ARG 3.4 0.6 + - - -
541A TRP* 1.3 82.2 - - - +
543A SER* 1.3 59.1 + - - +
532B PRO 4.5 4.0 - - - +
533B GLY* 3.5 5.9 - - - +
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Residues in contact with SER 543 (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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198A ARG* 2.8 67.7 + - - +
199A GLY 5.1 1.6 - - - -
200A LEU* 4.0 12.5 - - - +
310A ARG* 4.1 15.2 + - - +
542A THR* 1.3 74.7 + - - +
544A PRO* 1.3 64.3 + - - +
499B ASN* 5.7 1.6 - - - -
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Residues in contact with PRO 544 (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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195A THR* 3.7 13.2 - - + -
196A VAL 3.4 7.0 - - - +
197A TYR* 3.9 9.0 - - + -
198A ARG* 3.4 9.7 + - - -
542A THR* 3.8 1.1 - - - +
543A SER* 1.3 88.2 + - - +
545A GLN* 1.3 58.2 + - - +
528B THR* 3.6 36.0 - - - +
531B LYS* 3.6 20.2 - - + -
532B PRO 3.3 25.8 - - - +
533B GLY 3.5 14.6 - - - +
534B GLY* 3.7 4.9 - - - +
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Residues in contact with GLN 545 (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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194A SER 3.8 0.3 - - - +
195A THR* 3.2 3.1 - - - -
196A VAL* 2.7 51.5 + - + +
198A ARG* 3.5 23.5 - - + +
543A SER 3.5 0.4 + - - -
544A PRO* 1.3 72.4 - - - +
546A VAL* 1.3 70.0 + - - +
547A ILE* 3.7 25.0 + - + +
494B THR* 5.1 3.6 + - - +
497B LEU 4.1 4.2 + - - -
498B ARG* 3.2 33.4 + - - +
501B ALA 2.9 20.4 + - - +
502B GLY 3.3 15.9 - - - +
504B PHE* 3.8 15.2 - - + +
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Residues in contact with VAL 546 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A ASN* 3.3 29.6 - - - +
194A SER 3.4 4.5 - - - +
195A THR* 4.2 17.5 - - + +
544A PRO 4.4 0.2 + - - -
545A GLN* 1.3 74.3 - - - +
547A ILE* 1.3 60.1 + - - +
548A LYS* 3.8 21.0 - - + +
502B GLY 2.9 6.5 + - - +
503B ASN* 3.5 13.7 - - + +
504B PHE* 2.9 27.2 + - - +
527B GLY* 3.9 10.3 - - - +
528B THR* 3.7 26.0 - - - +
531B LYS* 5.1 4.0 - - + -
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Residues in contact with ILE 547 (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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192A THR 4.0 0.3 - - - +
193A ASN* 3.4 4.2 - - - -
194A SER* 2.8 43.7 + - - +
196A VAL* 3.8 23.1 - - + -
545A GLN* 3.7 28.0 - - + +
546A VAL* 1.3 76.3 - - - +
548A LYS* 1.3 66.6 + - - +
549A GLU* 5.6 0.4 - - + -
494B THR* 3.8 24.5 - - + -
504B PHE* 3.2 15.9 - - + +
506B ILE* 3.6 29.6 - - + -
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Residues in contact with LYS 548 (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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192A THR 3.3 5.8 - - - +
193A ASN* 3.6 31.4 - - + +
546A VAL* 3.8 16.1 - - + +
547A ILE* 1.3 82.1 - - - +
549A GLU* 1.3 54.4 + - - +
550A THR 4.4 0.2 + - - -
504B PHE 2.9 7.7 + - - +
505B TYR* 3.2 42.5 + - + +
506B ILE* 2.8 30.2 + - - +
508B ASP* 5.5 0.7 - - - +
524B ARG 4.9 7.7 + - - -
526B SER 4.2 16.2 + - - -
527B GLY* 5.8 0.4 - - - -
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Residues in contact with GLU 549 (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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191A SER* 3.2 5.4 - - - -
192A THR* 2.9 41.8 + - - +
547A ILE* 4.3 1.1 + - + -
548A LYS* 1.3 74.8 - - - +
550A THR* 1.3 70.9 + - - +
551A HIS* 3.2 34.4 + - + +
490B VAL* 5.3 3.8 - - - +
506B ILE* 3.4 45.1 - - + +
507B ASN* 4.8 4.2 + - - -
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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