Contacts of the strand formed by residues 526 - 532 (chain D) 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 ILE 526 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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487D ILE* 4.7 6.1 - - + -
488D ASN* 3.3 23.6 - - - +
519D ILE* 3.7 22.7 - - + -
520D PRO 4.7 1.6 - - - +
522D GLN* 3.5 42.6 - - + +
524D PHE* 3.7 10.8 - - + +
525D ASP* 1.3 79.4 - - - +
527D ALA* 1.3 62.6 + - - +
528D ILE* 3.6 19.8 + - + -
541D THR* 3.4 4.5 - - - -
542D VAL* 2.9 46.0 + - + +
550E LEU* 3.8 14.8 - - + -
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Residues in contact with ALA 527 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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486D LEU 3.6 1.9 - - - +
487D ILE* 3.2 4.6 - - - -
488D ASN* 3.0 37.9 + - - +
489D GLY 4.8 1.4 + - - +
525D ASP 4.2 1.0 - - - -
526D ILE* 1.3 70.0 - - - +
528D ILE* 1.3 63.3 + - - +
529D GLN* 4.0 6.0 + - + +
539D ARG* 5.5 13.7 - - + +
540D SER 4.2 2.7 - - - -
541D THR* 4.4 11.2 - - - +
64F LYS* 6.2 4.3 - - + -
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Residues in contact with ILE 528 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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485D VAL* 4.7 2.5 - - + -
487D ILE* 3.6 26.9 - - + -
512D VAL* 3.9 23.7 - - + +
515D MET* 4.0 31.6 - - + +
516D LYS* 4.0 17.9 - - + +
519D ILE* 4.3 11.9 - - + -
526D ILE* 3.6 11.4 + - + +
527D ALA* 1.3 73.4 - - - +
529D GLN* 1.3 68.2 + - - +
539D ARG* 3.4 3.0 - - - +
540D SER 2.9 38.6 + - - +
542D VAL* 3.8 27.6 - - + -
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Residues in contact with GLN 529 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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485D VAL* 3.4 8.8 - - - +
486D LEU* 3.0 71.7 + - + +
489D GLY* 5.9 1.2 - - - +
512D VAL* 4.3 5.2 - - - -
527D ALA* 4.6 7.3 + - + +
528D ILE* 1.3 78.7 - - - +
530D ALA* 1.3 60.7 + - - +
531D ALA* 4.9 3.1 - - - +
536D ILE* 3.3 29.7 - - + +
538D ALA 3.2 12.1 - - - +
539D ARG* 3.4 35.1 - - + +
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Residues in contact with ALA 530 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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483D VAL* 4.0 19.3 - - + -
484D ASP 3.3 6.1 - - - +
485D VAL* 4.5 5.6 - - + +
508D GLY* 4.2 9.2 - - - +
511D LEU* 5.5 1.8 - - + -
512D VAL* 4.1 9.6 - - + -
529D GLN* 1.3 76.0 - - - +
531D ALA* 1.3 62.3 + - - +
536D ILE* 3.7 3.2 - - - +
537D ILE* 2.9 26.3 + - + +
538D ALA* 2.7 30.7 + - + +
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Residues in contact with ALA 531 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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483D VAL* 3.3 7.4 - - - -
484D ASP* 2.7 43.8 + - + +
486D LEU* 4.7 14.6 - - + -
529D GLN* 4.9 1.1 - - - +
530D ALA* 1.3 76.7 - - - +
532D ILE* 1.3 64.0 + - - +
533D GLY 3.9 14.8 - - - +
534D THR 5.1 0.9 - - - -
535D HIS 3.3 16.2 - - - +
536D ILE* 4.3 8.1 - - + -
537D ILE* 4.3 1.1 - - - -
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Residues in contact with ILE 532 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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481D VAL* 4.3 19.3 - - + -
482D ARG 3.4 21.8 - - - +
483D VAL* 4.3 5.6 - - + -
501D ARG* 5.8 2.9 - - - +
504D SER* 4.1 16.2 - - - +
531D ALA* 1.3 77.7 - - - +
533D GLY* 1.3 65.2 + - - +
534D THR 3.6 0.2 + - - -
535D HIS* 2.9 25.5 + - - +
537D ILE* 3.7 36.5 - - + +
165F THR* 3.8 27.6 - - + +
167F VAL* 4.4 13.5 - - + +
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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