Contacts of the strand formed by residues 536 - 540 (chain E) in PDB entry 3HN3
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 ILE 536 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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499E ILE* 3.2 18.4 - - + +
501E LEU* 3.7 23.1 - - + -
525E PHE* 4.1 20.9 - - + +
528E TRP* 3.8 28.0 - - + -
529E TYR* 4.1 10.1 - - + +
534E LYS 3.5 13.9 - - - +
535E PRO* 1.3 74.5 - - - +
537E ILE* 1.3 72.0 + - - +
580E TYR* 3.0 35.5 + - + +
581E VAL* 3.2 11.8 - - + +
582E VAL* 2.8 30.8 + - - -
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Residues in contact with ILE 537 (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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336E PHE* 5.5 0.2 - - + -
345E PHE* 3.6 33.0 - - + -
404E ILE* 4.1 8.5 - - + -
445E MET* 4.1 22.7 - - + -
498E VAL* 4.0 9.9 - - + -
499E ILE 2.8 6.7 + - - +
500E CYS* 3.4 11.9 - - - -
501E LEU* 2.9 26.3 + - - -
536E ILE* 1.3 80.8 - - - +
538E GLN* 1.3 71.7 + - - +
539E SER* 3.2 12.0 + - - +
582E VAL* 3.7 15.9 - - + -
583E GLY* 3.5 19.5 - - - +
584E GLU 4.4 1.1 - - - +
585E LEU* 4.5 11.9 - - + -
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Residues in contact with GLN 538 (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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501E LEU* 3.6 7.3 + - - +
503E SER* 2.9 29.2 + - - +
521E LEU* 3.7 2.3 - - - +
524E GLN* 2.9 26.9 + - - +
525E PHE* 3.6 11.3 - - + -
536E ILE* 4.2 2.5 + - - +
537E ILE* 1.3 68.5 - - - +
539E SER* 1.3 55.5 + - - +
540E GLU 2.9 25.1 + - - +
541E TYR* 4.2 16.4 - - + -
569E TYR* 3.8 14.6 - - + -
573E LEU* 3.9 25.8 - - + -
581E VAL* 4.9 1.4 - - - +
583E GLY 3.0 10.2 + - - +
584E GLU* 3.3 3.6 - - - -
585E LEU 2.8 31.5 + - - +
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Residues in contact with SER 539 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349E ASN* 2.7 33.6 + - - +
382E ARG* 4.4 4.9 - - - -
404E ILE* 6.4 0.4 - - - -
482E VAL* 3.3 16.1 - - - +
500E CYS* 3.5 16.7 - - - -
501E LEU 2.9 20.5 + - - -
502E ASN* 2.8 20.0 + - - -
537E ILE* 3.2 10.7 + - - -
538E GLN* 1.3 74.0 - - - +
540E GLU* 1.3 55.5 + - - +
585E LEU* 3.2 15.9 - - - +
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Residues in contact with GLU 540 (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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349E ASN* 4.3 1.6 - - - +
382E ARG* 2.9 22.5 + - - +
385E HIS* 3.8 10.6 + - - -
450E ASN* 3.5 7.8 + - - +
451E GLU* 4.1 4.2 - - - +
501E LEU 3.7 0.2 + - - -
502E ASN* 3.0 37.5 + - + +
503E SER 3.2 11.0 + - - +
504E TYR* 2.6 37.2 + - + +
538E GLN* 2.9 23.0 + - - -
539E SER* 1.3 83.5 - - - +
541E TYR* 1.3 63.5 + - - +
585E LEU 3.5 4.9 - - - -
587E TRP* 3.7 20.4 - - + -
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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