Contacts of the helix formed by residues 567 - 575 (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 567 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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534D HIS* 4.0 1.6 - - - -
558D LEU 3.6 8.6 + - - -
559D ASP 3.8 21.5 - - - +
560D ILE 3.7 3.6 - - - +
561D GLY* 5.0 0.4 - - - +
565D GLY 3.4 3.5 + - - +
566D ASP* 1.3 77.4 - - - +
568D PRO* 1.3 75.2 - - - +
569D LEU* 3.2 18.5 + - - +
570D HIS* 3.0 40.8 + - + +
571D ILE* 3.3 12.5 + - - +
590D SER 5.1 2.8 + - - +
593D ILE* 3.8 26.0 - - + +
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Residues in contact with PRO 568 (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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531D THR* 5.1 0.2 - - - +
533D LEU* 3.7 29.8 - - + -
534D HIS* 3.8 23.3 - - + +
537D CYS* 3.7 25.7 - - + +
557D ARG 5.7 0.7 - - - +
558D LEU* 3.6 16.8 - - - +
560D ILE* 3.9 4.9 - - + +
567D THR* 1.3 89.8 - - - +
569D LEU* 1.3 55.4 + - - +
571D ILE* 3.0 13.7 + - + +
572D ALA* 2.9 27.9 + - - +
584D LEU* 4.0 10.3 - - + -
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Residues in contact with LEU 569 (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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558D LEU 5.3 0.6 + - - +
567D THR* 3.2 10.4 + - - +
568D PRO* 1.3 77.3 - - - +
570D HIS* 1.3 66.3 + - - +
572D ALA 4.4 0.2 - - - +
573D ALA* 2.9 22.9 + - - +
581D ILE* 4.0 31.0 - - + +
584D LEU* 3.8 24.5 - - + +
585D LEU* 3.9 17.3 - - + -
589D ALA* 3.8 24.7 - - + -
590D SER 3.3 26.5 - - - +
591D THR* 4.4 0.9 - - + -
601D PRO* 4.0 14.8 - - + -
614D MET* 4.2 10.8 - - + -
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Residues in contact with HIS 570 (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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565D GLY 4.6 1.6 - - - -
566D ASP* 3.4 27.6 - - - +
567D THR* 3.0 51.2 + - + +
569D LEU* 1.3 78.3 - - - +
571D ILE* 1.3 63.8 + - - +
573D ALA* 3.6 2.3 - - - +
574D ARG* 3.0 27.6 + - - +
590D SER 5.6 0.4 - - - -
593D ILE* 3.1 34.2 + - + -
595D ASN* 3.7 10.3 + - + -
599D GLU 3.5 19.8 + - - -
600D THR 3.9 1.1 - - - -
601D PRO* 3.3 29.5 - - + +
604D CYS* 4.0 11.6 - - - +
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Residues in contact with ILE 571 (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* 4.4 5.2 - - - +
534D HIS* 3.5 42.0 - - + +
537D CYS* 3.7 3.8 - - + -
538D THR* 3.3 54.7 - - + +
562D ASN* 4.6 3.6 - - - +
566D ASP* 4.2 17.5 - - + +
567D THR 3.3 6.9 + - - +
568D PRO* 3.0 8.1 + - + +
570D HIS* 1.3 80.4 - - - +
572D ALA* 1.3 63.6 + - - +
574D ARG* 3.3 12.1 + - - +
575D TRP* 3.2 26.8 + - + +
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Residues in contact with ALA 572 (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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537D CYS* 4.6 2.9 - - + +
568D PRO 2.9 14.9 + - - +
569D LEU 3.9 3.4 - - - +
570D HIS 3.3 0.2 - - - -
571D ILE* 1.3 77.9 - - - +
573D ALA* 1.3 57.7 + - - +
575D TRP 3.7 0.5 + - - -
576D GLY 3.1 8.3 + - - -
577D TYR* 3.0 36.4 + - + +
580D VAL* 3.5 33.4 - - + -
581D ILE* 3.5 16.4 - - + +
584D LEU* 4.2 5.8 - - + -
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Residues in contact with ALA 573 (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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569D LEU 2.9 17.7 + - - +
570D HIS 3.6 4.5 - - - +
572D ALA* 1.3 74.3 - - - +
574D ARG* 1.3 66.6 + - - +
576D GLY* 3.0 10.9 + - - -
581D ILE* 4.2 10.8 - - + +
601D PRO 3.6 24.0 - - - +
604D CYS 3.6 3.1 - - - -
605D ALA* 3.7 6.7 - - - +
606D LEU 3.3 16.6 + - - -
610D ILE* 4.6 1.9 - - - +
614D MET* 4.0 20.6 - - + -
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Residues in contact with ARG 574 (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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566D ASP* 2.8 43.7 + - - -
570D HIS* 3.0 22.5 + - - +
571D ILE* 3.3 14.3 + - - +
573D ALA* 1.3 76.6 - - - +
575D TRP* 1.3 76.9 + - + +
576D GLY 3.3 1.9 + - - -
595D ASN* 5.1 1.2 - - - +
599D GLU* 3.4 23.0 + - - -
604D CYS* 3.2 28.4 + - + +
606D LEU* 3.4 23.0 - - - +
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Residues in contact with TRP 575 (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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538D THR* 3.5 22.4 - - - +
539D TYR* 5.0 13.5 - + - -
571D ILE* 3.2 17.2 + - + +
572D ALA 3.8 0.2 - - - -
574D ARG* 1.3 101.8 - - + +
576D GLY* 1.3 66.3 + - - +
577D TYR* 3.2 54.9 + + + -
606D LEU* 4.3 9.4 - - - +
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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