Contacts of the strand formed by residues 543 - 547 (chain A) in PDB entry 1IT8
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 GLU 543 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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447A GLN* 3.4 13.2 - - - +
448A PHE* 3.6 20.6 - - + -
483A ARG* 3.7 9.8 + - - +
489A LEU 3.2 24.0 - - - +
490A THR* 4.0 0.5 - - - -
491A LEU* 3.2 37.7 + - + +
508A MET* 4.2 15.9 - - - +
538A ILE* 5.9 0.3 - - - +
541A TYR 4.0 0.2 + - - -
542A ASP* 1.3 79.5 + - - +
544A VAL* 1.3 63.5 - - - +
556A THR* 4.3 1.2 + - - -
557A GLY 3.5 8.4 - - - +
558A GLN* 4.3 3.6 + - - +
578A ARG* 2.7 45.8 + - - -
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Residues in contact with VAL 544 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491A LEU* 5.5 0.4 - - - -
508A MET 3.8 3.8 - - - +
510A VAL* 3.5 33.2 - - + -
538A ILE* 3.7 33.0 - - + -
542A ASP 4.3 2.7 - - - +
543A GLU* 1.3 80.6 + - - +
545A LEU* 1.3 65.1 + - - +
546A VAL* 3.8 1.1 + - + +
556A THR* 3.4 10.5 + - - -
557A GLY 2.7 35.7 + - - +
559A ALA* 4.0 24.9 - - + +
575A VAL* 3.9 18.4 - - + -
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Residues in contact with LEU 545 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491A LEU* 4.7 6.7 - - + -
496A ALA* 3.5 42.6 - - + +
499A LEU* 4.4 4.7 - - + -
500A HIS* 3.9 32.1 - - + +
503A LEU* 5.8 0.4 - - + -
507A ARG 4.0 7.4 - - - +
508A MET* 2.7 46.9 + - + +
509A ARG* 3.3 13.1 - - + +
510A VAL* 3.1 25.4 + - - -
544A VAL* 1.3 74.9 - - - +
546A VAL* 1.3 63.3 + - - +
547A VAL* 3.6 0.7 + - - -
553A LEU* 4.2 11.2 - - + -
555A ALA 4.2 2.2 - - - -
556A THR* 4.7 1.1 - - - +
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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
----------------------------------------------------------
510A VAL* 3.4 16.8 - - + -
512A VAL* 4.1 15.0 - - + -
520A ALA* 3.9 18.8 - - + -
526A VAL* 3.9 29.8 - - + -
544A VAL* 4.2 4.3 - - + +
545A LEU* 1.3 68.1 - - - +
547A VAL* 1.3 67.0 + - - +
553A LEU* 3.5 5.0 - - - +
554A LEU* 2.8 27.5 + - + -
555A ALA* 2.9 32.9 + - + +
556A THR* 4.7 1.3 - - - +
575A VAL* 4.2 16.4 - - + -
577A VAL* 4.8 3.1 - - + -
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Residues in contact with VAL 547 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500A HIS* 3.7 5.4 - - + +
505A TYR* 4.8 1.3 - - + -
509A ARG* 4.0 20.9 - - + -
510A VAL 3.0 17.6 + - - +
511A VAL* 4.0 14.4 - - + -
512A VAL* 2.9 29.3 + - - +
545A LEU 4.3 3.1 - - - +
546A VAL* 1.3 77.2 - - - +
548A ASN* 1.3 65.5 + - - +
551A ASP* 3.0 20.9 - - - +
552A GLU 2.8 47.3 - - - +
553A LEU 3.6 2.2 - - - +
554A LEU* 3.7 8.3 - - - -
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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