Contacts of the strand formed by residues 540 - 543 (chain E) in PDB entry 3HR4
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 540 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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538E ARG* 3.7 3.9 + - - +
539E VAL* 1.3 72.8 - - - +
541E ILE* 1.3 70.8 + - - +
542E LEU* 4.6 4.5 - - + -
568E LYS* 3.6 28.9 - - + +
570E VAL* 4.8 6.5 - - + -
575E TYR* 4.0 23.6 - - + -
582E GLU* 4.7 1.9 + - - -
583E GLU* 2.8 27.0 + - - -
585E LEU 3.3 6.6 + - - +
586E LEU* 3.1 36.1 - - + +
587E LEU 3.1 12.0 + - - -
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Residues in contact with ILE 541 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539E VAL* 3.9 12.1 - - + +
540E THR* 1.3 78.8 - - - +
542E LEU* 1.3 62.0 + - - +
554E ALA* 4.1 23.1 - - + +
557E LEU* 4.0 27.1 - - + -
558E GLY* 3.7 34.8 - - - +
561E PHE* 4.9 3.4 - - + -
567E PRO* 4.3 9.4 - - + -
568E LYS 2.8 10.0 + - - +
569E VAL* 3.2 17.6 - - + +
570E VAL 2.6 32.7 + - - +
587E LEU* 3.3 22.4 - - + +
589E VAL* 4.9 1.6 - - + -
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Residues in contact with LEU 542 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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540E THR* 4.2 1.5 - - + -
541E ILE* 1.3 77.3 - - - +
543E PHE* 1.3 61.0 + - - +
570E VAL* 3.0 23.6 - - + +
571E CYS 3.6 11.2 - - - +
572E MET* 4.0 5.8 - - + -
575E TYR* 3.4 54.5 - - + -
586E LEU* 4.2 16.4 - - + -
587E LEU 2.9 8.5 + - - +
588E VAL* 3.2 26.2 - - + +
589E VAL* 3.1 25.3 + - - +
605E LEU* 3.9 18.4 - - + -
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Residues in contact with PHE 543 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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542E LEU* 1.3 77.5 - - - +
544E ALA* 1.3 59.1 + - - +
545E THR* 4.4 9.2 - - + -
550E SER 4.0 5.2 - - - +
551E GLU* 3.0 55.9 - - + -
554E ALA* 3.9 15.5 - - + -
555E TRP* 4.0 9.0 - + - -
569E VAL* 3.8 26.0 - - + -
570E VAL* 3.1 26.4 + - - -
571E CYS* 3.2 44.6 - - + -
572E MET* 3.1 23.5 + - - +
589E VAL 3.2 11.4 - - - +
601E ASN* 5.5 0.2 - - - -
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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