Contacts of the helix formed by residues 531 - 539 (chain D) in PDB entry 4CYM
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 THR 531 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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501D HIS* 3.5 2.0 - - - -
522D ALA 3.5 13.5 - - - +
523D GLU* 4.2 13.9 - - - +
524D VAL 3.4 9.6 - - - +
525D GLN* 4.5 3.8 - - + -
530D ASN* 1.3 76.2 - - - +
532D PRO* 1.3 77.9 - - - +
533D LEU* 3.2 11.1 + - - +
534D HIS* 2.7 50.6 + - + +
535D LEU* 3.1 11.3 + - - +
560D ILE* 4.2 21.5 - - + -
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Residues in contact with PRO 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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498D THR* 4.4 1.8 - - + -
500D LEU* 3.7 43.5 - - + +
501D HIS* 3.5 36.5 - - + +
504D CYS* 3.4 23.2 - - + +
521D SER 4.7 0.4 - - - +
522D ALA* 3.3 21.8 - - - +
524D VAL 3.8 2.7 - - - +
531D THR* 1.3 81.9 - - - +
533D LEU* 1.3 60.5 + - - +
535D LEU* 3.1 3.0 + - + +
536D ALA* 3.0 19.2 + - - +
548D LEU* 3.9 6.1 - - + -
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Residues in contact with LEU 533 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522D ALA* 4.8 2.8 + - + +
531D THR* 3.0 10.6 + - - +
532D PRO* 1.3 79.9 - - - +
534D HIS* 1.3 63.5 + - - +
535D LEU 3.2 0.3 + - - -
536D ALA* 3.3 1.4 + - - +
537D CYS* 2.9 34.0 + - - -
545D VAL* 4.1 23.6 - - + +
548D LEU* 3.5 30.7 - - + +
549D VAL* 4.7 3.8 - - + -
556D CYS* 4.8 8.1 - - - -
557D ARG 4.7 8.5 - - - +
558D LEU* 4.2 24.0 - - + -
568D PRO* 3.7 26.9 - - + -
584D LEU* 4.6 3.6 - - + -
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Residues in contact with HIS 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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529D GLY 4.3 4.7 - - - -
530D ASN* 3.2 31.9 - - + +
531D THR* 2.7 51.8 + - + +
533D LEU* 1.3 76.0 - - - +
535D LEU* 1.3 63.4 + - - +
537D CYS* 3.5 4.6 + - - +
538D THR* 3.1 28.9 + - - +
560D ILE* 2.8 35.6 + - + -
562D ASN* 3.7 4.3 + - - -
566D ASP 3.0 21.2 + - - -
568D PRO* 3.8 19.5 - - + +
571D ILE* 3.5 19.6 - - + +
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Residues in contact with LEU 535 (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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501D HIS* 3.6 44.2 - - + +
504D CYS 4.4 2.5 - - - -
505D GLN* 4.3 34.5 - - + +
526D ASP* 4.3 7.2 - - - +
530D ASN* 3.9 27.4 - - + +
531D THR 3.1 12.2 + - - +
532D PRO* 3.6 6.7 - - + +
533D LEU 3.1 0.2 - - - -
534D HIS* 1.3 74.1 - - - +
536D ALA* 1.3 66.4 + - - +
538D THR* 2.9 30.1 + - + +
539D TYR* 3.1 12.8 + - + +
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Residues in contact with ALA 536 (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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504D CYS* 3.6 26.7 + - + +
532D PRO 3.0 12.1 + - - +
533D LEU 3.6 7.4 - - - +
535D LEU* 1.3 75.7 - - - +
537D CYS* 1.3 59.6 + - - +
539D TYR 3.6 0.5 + - - -
540D GLY* 3.2 4.0 + - - -
541D HIS* 3.0 30.1 + - + +
544D CYS* 4.2 5.6 - - + -
545D VAL* 3.8 30.0 - - + +
548D LEU* 4.3 6.3 - - + -
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Residues in contact with CYS 537 (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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533D LEU* 2.9 31.5 + - - +
534D HIS 3.8 5.2 - - - +
535D LEU 3.1 0.2 - - - -
536D ALA* 1.3 76.1 - - - +
538D THR* 1.3 64.2 - - - +
539D TYR 3.3 0.3 + - - -
540D GLY* 3.3 8.4 + - - -
545D VAL* 4.0 6.3 - - - -
568D PRO* 3.7 39.7 - - + +
571D ILE* 3.7 9.8 - - + +
572D ALA* 4.6 3.7 - - - +
577D TYR* 3.4 17.2 - - - -
580D VAL* 3.9 24.9 - - + +
584D LEU* 4.1 4.0 - - - -
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Residues in contact with THR 538 (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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530D ASN* 5.6 3.4 - - - +
534D HIS* 3.1 16.5 + - + +
535D LEU* 2.9 24.6 + - + +
537D CYS* 1.3 75.6 - - - +
539D TYR* 1.3 84.1 + - - +
540D GLY 3.4 0.7 - - - -
571D ILE* 3.3 31.4 - - + -
575D TRP* 3.5 23.2 - - - +
577D TYR* 3.3 14.2 + - - -
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Residues in contact with TYR 539 (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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505D GLN* 3.2 57.6 + - + -
535D LEU* 3.1 10.8 + - + +
538D THR* 1.3 101.0 + - - +
540D GLY* 1.3 64.3 + - - +
541D HIS* 3.0 28.6 + - + +
575D TRP* 5.0 15.5 - + - -
577D TYR* 3.7 10.3 + - - -
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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