Contacts of the helix formed by residues 525 - 534 (chain D) in PDB entry 1C2O
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 ARG 525 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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330D VAL* 6.0 1.2 - - - +
331D VAL 5.9 0.4 + - - -
332D LYS 4.1 18.0 + - - -
400D ALA* 5.1 9.7 - - - +
404D ASP* 3.3 31.1 + - - +
408D VAL* 4.2 23.9 - - + +
409D CYS* 5.0 0.2 - - - -
429D ILE* 5.8 5.9 - - - +
510D TYR* 5.5 0.6 + - - -
523D GLY 3.3 5.3 + - - -
524D LEU* 1.3 77.9 - - + +
526D ALA* 1.3 53.4 + - - +
527D GLN 3.1 3.5 + - - -
528D THR* 3.1 15.9 + - + -
529D CYS* 2.7 47.7 + - - -
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Residues in contact with ALA 526 (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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385A TRP* 3.4 30.4 - - - +
386A LEU* 4.1 9.6 - - + +
508D GLN* 4.3 5.4 - - - +
523D GLY* 4.2 21.2 + - - -
524D LEU 2.7 10.3 + - - -
525D ARG* 1.3 70.0 - - - +
527D GLN* 1.3 67.2 + - - +
529D CYS* 3.9 2.4 - - - +
530D ALA* 3.0 21.7 + - - +
534D ARG* 5.6 0.2 + - - -
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Residues in contact with GLN 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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380A LEU* 4.8 3.5 - - + +
383A THR 4.2 3.1 + - - +
384A ASP* 2.8 34.4 + - - +
385A TRP* 3.4 30.8 + - + +
386A LEU* 5.1 1.2 + - - +
381D HIS* 4.8 8.7 - - + -
525D ARG 3.1 1.0 + - - -
526D ALA* 1.3 76.6 + - - +
528D THR* 1.3 63.1 + - - +
530D ALA* 2.5 26.2 + - - +
531D PHE* 2.8 11.6 + - - +
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Residues in contact with THR 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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381D HIS* 3.2 28.2 + - + +
382D TYR* 3.2 29.2 - - + +
404D ASP* 3.4 16.4 - - + +
409D CYS* 4.4 1.6 - - - -
525D ARG* 3.1 20.5 + - + -
527D GLN* 1.3 82.6 - - - +
529D CYS* 1.3 57.5 + - - +
531D PHE* 2.9 24.8 + - - +
532D TRP* 3.1 19.9 - - + +
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Residues in contact with CYS 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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408D VAL* 4.3 4.5 - - - -
409D CYS* 2.1 58.6 - - + -
412D ALA* 4.6 5.8 - - + -
524D LEU 4.0 10.3 - - - +
525D ARG* 2.7 37.5 + - - +
526D ALA* 3.9 2.2 - - - +
528D THR* 1.3 71.7 - - - +
530D ALA* 1.3 57.6 + - - +
532D TRP 4.4 0.2 - - - +
533D ASN* 2.7 48.7 + - - +
534D ARG* 5.5 0.4 - - - -
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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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380A LEU* 4.7 2.5 - - - -
385A TRP* 3.3 50.5 - - + +
526D ALA 3.0 8.2 + - - +
527D GLN 2.5 19.8 + - - +
529D CYS* 1.3 70.7 - - - +
531D PHE* 1.3 58.0 + - - +
534D ARG* 2.7 50.6 + - + +
535D PHE* 3.3 1.9 + - - +
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Residues in contact with PHE 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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380A LEU* 4.0 21.0 - - + +
377D ALA* 3.8 18.4 - - + -
378D VAL* 3.7 32.3 - - + -
381D HIS* 4.0 34.3 - + + +
382D TYR* 4.4 1.1 - + - -
527D GLN 2.8 7.3 + - - +
528D THR* 2.9 15.7 - - - +
530D ALA* 1.3 80.0 - - - +
532D TRP* 1.3 83.8 + + - +
535D PHE* 3.2 28.7 + + - +
536D LEU* 2.7 49.1 + - + +
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Residues in contact with TRP 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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367D VAL* 4.2 7.2 - - + -
378D VAL* 4.0 15.7 - - + -
382D TYR* 2.6 42.4 + + - -
401D VAL* 3.9 20.6 - - + -
404D ASP* 3.7 3.5 - - + +
405D HIS* 3.3 53.4 - + + +
409D CYS* 3.5 24.0 - - + -
528D THR* 3.1 26.8 + - + +
531D PHE* 1.3 86.9 - + - +
533D ASN* 1.3 69.7 + - - +
536D LEU* 3.5 36.4 - - + +
537D PRO* 2.9 27.7 - - - +
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Residues in contact with ASN 533 (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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409D CYS* 3.1 40.9 + - - +
410D PRO* 4.3 1.0 - - - +
412D ALA* 4.6 1.2 - - - +
413D GLN* 3.7 39.0 + - + +
529D CYS* 2.7 36.5 + - - +
532D TRP* 1.3 77.3 - - - +
534D ARG* 1.3 62.5 + - + +
537D PRO* 3.8 10.7 - - - +
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Residues in contact with ARG 534 (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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385A TRP* 3.8 43.9 - - + +
388A PRO* 6.3 1.0 - - - +
526D ALA 5.6 0.2 + - - -
529D CYS 5.3 0.4 + - - -
530D ALA* 2.7 34.1 + - + +
533D ASN* 1.3 79.1 - - + +
535D PHE* 1.3 61.3 + - + +
536D LEU 3.8 0.2 - - - -
537D PRO* 3.8 5.9 - - - +
538D LYS* 3.0 25.9 + - - +
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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