Contacts of the strand formed by residues 541 - 547 (chain B) in PDB entry 3P1X
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 541 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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529B VAL* 4.0 25.9 + - + +
532B LEU* 3.5 13.3 - - - +
539B LEU* 4.0 19.0 - - + +
540B LYS* 1.3 74.9 - - - +
542B GLU* 1.3 67.0 + - - +
543B LEU 4.1 0.5 + - - -
557B MSE 3.0 26.6 - - + +
558B GLU 3.4 3.4 - - - -
559B VAL* 3.7 33.0 - - + -
577B LYS* 3.8 44.6 - - + +
580B ALA* 4.3 6.1 - - + -
581B ALA* 3.3 22.4 - - + +
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Residues in contact with GLU 542 (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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540B LYS* 4.5 20.7 - - + +
541B TYR* 1.3 78.3 - - - +
543B LEU* 1.3 64.3 + - - +
544B ILE* 3.2 18.7 + - + +
557B MSE 3.5 4.1 - - - -
558B GLU* 2.8 44.5 + - + +
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Residues in contact with LEU 543 (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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541B TYR 4.1 1.2 + - - -
542B GLU* 1.3 73.0 + - - +
544B ILE* 1.3 61.3 + - - +
545B SER 3.2 28.9 - - - +
546B GLU* 3.8 24.2 - - + +
555B PHE* 4.2 12.6 - - + -
556B VAL 3.4 15.0 - - - +
557B MSE 3.6 19.0 - - - +
573B LYS* 4.0 24.7 - - + +
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Residues in contact with ILE 544 (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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544A ILE* 3.8 22.5 - - + +
558A GLU* 5.9 4.0 - - - +
565A LYS* 6.6 0.4 - - - -
542B GLU* 3.5 19.7 - - + +
543B LEU* 1.3 77.9 - - - +
545B SER* 1.3 63.2 + - - +
556B VAL* 2.8 14.9 + - + +
558B GLU* 3.3 44.6 - - + +
567B GLN* 3.9 20.2 - - - +
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Residues in contact with SER 545 (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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543A LEU 4.4 1.9 + - - -
544A ILE* 3.2 19.4 + - - +
543B LEU* 3.2 12.8 - - - +
544B ILE* 1.3 84.0 - - - +
546B GLU* 1.3 62.1 + - - +
547B THR* 4.0 14.0 + - - +
554B ARG 4.1 2.4 + - - -
555B PHE* 3.3 1.7 - - - -
556B VAL* 2.9 47.3 + - - +
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Residues in contact with GLU 546 (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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544A ILE 2.9 9.3 + - - +
545A SER* 3.2 11.3 + - - +
546A GLU 3.0 24.1 + - - +
547A THR* 3.7 26.3 - - + +
543B LEU* 3.8 20.8 - - + +
545B SER* 1.3 76.2 + - - +
547B THR* 1.3 61.1 + - - +
553B LYS* 2.8 31.9 + - - +
554B ARG 3.3 5.6 - - - -
555B PHE* 3.5 25.9 - - + -
573B LYS* 4.8 4.0 + - - -
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Residues in contact with THR 547 (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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543A LEU* 3.7 37.9 - - + +
544A ILE 4.2 4.3 - - - -
546A GLU* 4.6 9.6 - - - +
545B SER* 4.0 11.1 + - - +
546B GLU* 1.3 82.4 - - - +
548B GLY* 1.3 67.8 + - - +
553B LYS* 3.5 8.2 - - - +
554B ARG* 3.0 42.0 + - - +
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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