Contacts of the strand formed by residues 535 - 542 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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531C ALA* 3.3 2.0 - - - -
532C ILE 2.8 41.5 + - - +
533C GLY* 5.7 0.2 - - - -
534C THR* 1.3 86.6 + - - +
536C ILE* 1.3 63.5 + - - +
537C ILE* 3.7 2.7 + - + +
167E VAL* 3.6 29.0 - - + +
168E GLY 3.9 16.8 + - - -
170E GLN* 4.4 9.4 - - + +
171E ASP* 3.2 34.2 + - - -
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Residues in contact with ILE 536 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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486C LEU* 6.0 0.4 - - + -
529C GLN* 3.2 33.9 - - + +
530C ALA 3.5 13.9 - - - +
531C ALA* 4.2 7.0 - - + -
534C THR 4.2 8.1 - - - +
535C HIS* 1.3 71.6 - - - +
537C ILE* 1.3 61.9 + - - +
538C ALA 3.7 17.5 - - - +
539C ARG* 3.5 25.4 - - + +
27E ILE* 3.6 17.4 - - + +
166E GLY 4.7 4.0 - - - +
170E GLN* 3.4 44.3 + - - +
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Residues in contact with ILE 537 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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483C VAL* 4.5 4.0 - - + -
504C SER 3.4 27.6 - - - +
505C GLN* 2.7 28.7 - - - +
508C GLY* 4.2 12.1 - - - -
530C ALA* 3.1 20.0 + - + +
531C ALA* 4.2 2.7 - - - +
532C ILE* 4.2 19.1 - - + -
535C HIS 3.7 9.6 + - - +
536C ILE* 1.3 75.8 - - - +
538C ALA* 1.3 62.1 + - + +
26E GLN* 4.1 4.2 - - - +
27E ILE* 3.6 16.4 - - - +
165E THR 3.3 28.0 - - - +
166E GLY* 3.9 18.4 - - - -
167E VAL* 4.2 10.3 - - + +
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Residues in contact with ALA 538 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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505C GLN* 4.9 0.2 - - - +
508C GLY 4.2 3.1 - - - -
509C ARG* 3.8 39.7 - - + +
512C VAL* 3.9 13.0 - - + -
529C GLN* 3.2 6.1 - - - +
530C ALA* 2.9 28.5 + - + +
536C ILE* 3.7 3.0 - - - +
537C ILE* 1.3 83.8 - - + +
539C ARG* 1.3 60.9 + - - +
26E GLN* 3.6 11.2 - - - +
27E ILE* 4.3 0.9 - - - +
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Residues in contact with ARG 539 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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512C VAL* 4.3 2.9 - - - -
527C ALA* 5.3 6.5 - - + -
528C ILE 3.3 13.5 - - - +
529C GLN* 2.8 46.5 + - + +
536C ILE* 3.5 28.2 - - + +
538C ALA* 1.3 75.3 - - - +
540C SER* 1.3 69.4 + - - +
541C THR* 5.3 11.7 - - - -
26E GLN 3.0 9.7 + - - +
27E ILE* 3.5 25.9 + - - +
28E CYS* 2.8 27.6 - - - +
29E GLY 3.6 1.2 - - - +
30E GLY* 4.4 1.4 - - - -
62E ASP 6.0 0.2 + - - -
63E TYR* 4.5 12.7 - - - +
64E LYS* 4.7 14.6 + - - +
170E GLN* 3.7 13.9 - - - +
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Residues in contact with SER 540 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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512C VAL* 3.6 19.6 - - - +
513C GLU* 5.0 1.3 - - - -
516C LYS* 3.0 36.0 - - - +
526C ILE 3.9 0.5 - - - +
528C ILE* 2.9 36.4 + - - +
539C ARG* 1.3 77.4 - - - +
541C THR* 1.3 64.4 + - - +
542C VAL 4.0 1.2 + - - -
28E CYS 5.7 0.2 - - - -
29E GLY 3.6 14.9 + - - -
30E GLY* 4.6 5.8 - - - -
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Residues in contact with THR 541 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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516C LYS* 5.4 1.0 - - - +
525C ASP* 4.4 12.6 + - - +
526C ILE 3.2 12.8 + - - -
527C ALA* 4.3 11.6 + - - +
539C ARG* 5.3 9.9 - - - -
540C SER* 1.3 78.9 + - - +
542C VAL* 1.3 62.2 + - - +
543C LYS* 3.2 42.3 + - - +
29E GLY 4.7 3.4 + - - +
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Residues in contact with VAL 542 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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516C LYS* 4.0 24.0 - - + +
519C ILE* 3.6 28.7 - - + +
520C PRO 3.7 14.6 - - - +
521C ARG* 3.8 20.6 - - + +
522C GLN 5.5 0.2 + - - -
524C PHE 4.2 1.9 - - - +
525C ASP* 3.6 1.0 - - - -
526C ILE* 2.8 40.3 + - + +
528C ILE* 3.8 28.3 - - + -
540C SER 5.1 0.2 - - - +
541C THR* 1.3 67.8 - - - +
543C LYS* 1.3 65.1 + - - +
544C GLN 3.6 0.7 + - - -
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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