Contacts of the strand formed by residues 535 - 542 (chain E) in PDB entry 3CB4
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 HIS 535 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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531E ALA* 3.3 2.4 - - - -
532E ILE* 2.9 41.4 + - + +
533E GLY* 5.3 0.2 - - - -
534E THR* 1.3 89.8 + - - +
536E ILE* 1.3 65.5 + - - +
537E ILE* 3.5 8.2 + - + +
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Residues in contact with ILE 536 (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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529E GLN* 3.1 35.0 - - + +
530E ALA 3.8 7.6 - - - +
531E ALA* 4.0 6.5 - - + -
534E THR 3.5 8.6 + - - +
535E HIS* 1.3 70.8 - - - +
537E ILE* 1.3 61.3 + - - +
538E ALA 4.0 10.8 - - - +
539E ARG* 3.7 48.0 - - + +
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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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483E VAL* 4.4 7.6 - - + -
504E SER 3.7 22.9 - - - +
505E GLN* 2.9 43.2 + - + +
508E GLY* 4.0 16.2 - - - -
530E ALA* 2.9 23.6 + - + +
531E ALA* 4.1 2.7 - - - -
532E ILE* 3.9 35.2 - - + -
535E HIS* 3.5 15.7 + - + +
536E ILE* 1.3 77.5 - - - +
538E ALA* 1.3 59.5 + - - +
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Residues in contact with ALA 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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505E GLN* 4.6 1.3 - - - +
508E GLY 4.0 3.1 - - - -
509E ARG* 3.9 31.0 - - + +
512E VAL* 3.5 20.1 - - + +
529E GLN* 3.3 3.3 - - - +
530E ALA* 2.7 37.0 + - + +
536E ILE* 3.7 3.2 - - - +
537E ILE* 1.3 82.7 - - - +
539E ARG* 1.3 59.9 + - - +
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Residues in contact with ARG 539 (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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512E VAL* 4.3 2.2 - - - -
527E ALA* 5.1 13.5 - - + +
528E ILE 3.4 16.4 - - - +
529E GLN* 3.1 36.5 - - + +
536E ILE* 3.7 31.7 - - + +
538E ALA* 1.3 75.0 - - - +
540E SER* 1.3 67.8 + - - +
541E THR* 5.7 4.3 - - - -
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Residues in contact with SER 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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512E VAL* 3.4 21.9 - - - +
513E GLU* 4.7 3.4 - - - -
516E LYS* 3.2 33.3 - - - +
526E ILE 3.9 0.7 - - - +
527E ALA* 3.8 1.0 - - - -
528E ILE* 2.9 35.8 + - - +
539E ARG* 1.3 79.3 - - - +
541E THR* 1.3 64.9 + - - +
542E VAL 4.2 0.2 - - - -
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Residues in contact with THR 541 (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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516E LYS* 5.5 0.8 - - - +
525E ASP* 4.4 11.3 - - - +
526E ILE 3.5 10.7 + - - -
527E ALA* 4.5 9.9 - - - +
539E ARG* 5.7 5.2 - - - -
540E SER* 1.3 82.0 + - - +
542E VAL* 1.3 64.1 + - - +
543E LYS* 3.1 41.1 + - - +
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Residues in contact with VAL 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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516E LYS* 4.6 16.4 - - + +
519E ILE* 3.8 18.8 - - + +
520E PRO 3.5 26.5 - - - +
521E ARG* 3.6 24.2 - - + +
522E GLN 5.0 0.7 - - - +
524E PHE 4.2 2.4 - - - +
525E ASP* 3.6 2.6 - - - -
526E ILE* 3.0 36.2 + - + +
528E ILE* 3.9 27.4 - - + -
541E THR* 1.3 69.2 - - - +
543E LYS* 1.3 66.1 + - - +
544E GLN 3.5 1.2 + - - -
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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