Contacts of the strand formed by residues 535 - 542 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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531A ALA* 4.0 0.9 - - - -
532A ILE* 2.8 37.3 + - + +
534A THR* 1.3 88.7 + - + +
536A ILE* 1.3 63.1 + - - +
537A ILE* 3.6 4.5 + - + +
166C GLY 5.1 2.7 - - - +
167C VAL* 4.0 28.4 - - + +
168C GLY* 3.8 25.9 + - - -
170C GLN* 4.0 12.1 - - + -
171C ASP* 4.3 21.4 + - - -
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Residues in contact with ILE 536 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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529A GLN* 3.2 30.1 - - - +
530A ALA 3.7 10.5 - - - +
531A ALA* 3.9 5.2 - - + -
534A THR 4.1 9.0 - - - +
535A HIS* 1.3 71.6 - - - +
537A ILE* 1.3 62.5 + - - +
538A ALA 3.9 18.2 - - - +
539A ARG* 3.3 38.1 - - + +
27C ILE* 3.4 29.4 - - + +
166C GLY 4.8 8.3 - - - +
170C GLN* 3.3 31.4 + - - +
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Residues in contact with ILE 537 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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483A VAL* 4.0 22.7 - - + -
504A SER 3.5 23.1 - - - +
505A GLN* 3.0 36.8 - - - +
508A GLY* 3.9 16.8 - - - -
530A ALA* 3.0 19.5 + - + +
531A ALA* 3.9 4.0 - - - -
532A ILE* 4.2 20.4 - - + -
535A HIS* 4.5 5.6 - - + +
536A ILE* 1.3 76.2 - - - +
538A ALA* 1.3 62.0 + - + +
26C GLN* 3.9 7.4 - - - +
27C ILE* 3.5 15.6 - - - +
165C THR* 3.6 17.9 - - - +
166C GLY* 5.3 3.6 - - - -
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Residues in contact with ALA 538 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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508A GLY 4.2 2.9 - - - +
509A ARG* 4.0 29.6 - - + +
512A VAL* 3.8 22.2 - - + -
529A GLN* 3.2 3.8 - - - +
530A ALA* 2.8 30.9 + - + +
536A ILE* 3.8 2.8 - - - +
537A ILE* 1.3 81.8 - - - +
539A ARG* 1.3 61.8 + - - +
26C GLN 3.3 11.4 - - - +
27C ILE* 4.2 0.9 - - - +
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Residues in contact with ARG 539 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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512A VAL* 4.7 1.1 - - - +
527A ALA* 5.8 6.7 - - + -
528A ILE 3.4 12.3 - - - +
529A GLN* 3.1 32.2 - - + +
536A ILE* 3.3 33.1 - - + +
538A ALA* 1.3 76.4 - - - +
540A SER* 1.3 62.4 + - - +
541A THR* 6.4 2.5 - - - -
26C GLN 3.5 6.7 + - - -
27C ILE 3.3 19.3 + - - +
28C CYS* 2.6 32.6 - - - +
29C GLY 3.3 1.4 + - - +
30C GLY* 5.8 0.4 - - - -
62C ASP 6.0 1.8 - - - -
63C TYR* 4.5 8.4 - - - +
64C LYS* 3.8 47.6 + - - +
170C GLN* 4.2 6.9 - - - +
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Residues in contact with SER 540 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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512A VAL* 3.5 23.1 - - - +
513A GLU* 5.2 1.8 - - - -
516A LYS* 3.1 31.7 - - - +
527A ALA* 4.8 0.2 - - - -
528A ILE* 2.8 41.5 + - - +
539A ARG* 1.3 77.0 - - - +
541A THR* 1.3 65.5 + - - +
29C GLY* 3.5 18.1 + - - -
30C GLY* 5.4 2.2 - - - -
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Residues in contact with THR 541 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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516A LYS* 4.9 2.9 - - - +
525A ASP* 4.5 9.7 - - - +
526A ILE 3.4 12.3 + - - -
527A ALA* 4.4 11.7 + - - +
539A ARG* 6.4 2.7 - - - -
540A SER* 1.3 80.8 + - - +
542A VAL* 1.3 67.9 + - - +
543A LYS* 3.4 36.9 + - - +
29C GLY* 5.0 2.7 + - - -
62C ASP* 6.3 2.5 - - + -
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Residues in contact with VAL 542 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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516A LYS* 4.0 22.0 - - + +
519A ILE* 3.8 22.2 - - + +
520A PRO 3.6 24.7 - - - +
521A ARG* 3.8 18.4 - - + +
522A GLN 4.9 0.4 - - - +
524A PHE 4.1 2.5 - - - +
525A ASP* 3.7 1.9 - - - -
526A ILE* 2.8 39.7 + - + +
528A ILE* 3.6 28.3 - - + -
541A THR* 1.3 70.4 + - - +
543A LYS* 1.3 64.2 + - - +
544A 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