Contacts of the helix formed by residues 567 - 575 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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534E HIS* 4.1 1.3 - - - -
558E LEU 3.6 8.7 + - - -
559E ASP 3.8 22.0 - - - +
560E ILE 3.7 4.5 - - - +
561E GLY* 4.9 0.4 - - - +
565E GLY 3.4 3.1 + - - +
566E ASP* 1.3 77.5 - - - +
568E PRO* 1.4 75.4 - - - +
569E LEU* 3.2 17.5 + - - +
570E HIS* 3.0 35.2 + - + +
571E ILE* 3.3 12.0 + - - +
590E SER 5.0 3.0 + - - +
593E ILE* 3.8 30.7 - - + +
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Residues in contact with PRO 568 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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533E LEU* 3.6 30.7 - - + +
534E HIS* 3.8 22.9 - - + +
537E CYS* 3.7 26.0 - - + +
557E ARG 5.6 0.4 - - - +
558E LEU* 3.6 16.8 - - - +
560E ILE* 3.9 3.6 - - + +
567E THR* 1.4 90.0 - - - +
569E LEU* 1.3 56.2 + - - +
571E ILE* 3.0 13.8 + - + +
572E ALA* 2.9 27.7 + - - +
584E LEU* 4.0 10.1 - - + -
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Residues in contact with LEU 569 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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558E LEU 5.2 1.1 + - - +
567E THR* 3.2 10.2 + - - +
568E PRO* 1.3 77.0 - - - +
570E HIS* 1.3 65.6 + - - +
572E ALA 4.4 0.2 - - - +
573E ALA* 2.9 23.6 + - - +
581E ILE* 4.0 31.6 - - + +
584E LEU* 3.8 24.3 - - + +
585E LEU* 3.9 17.9 - - + -
589E ALA* 3.8 24.2 - - + -
590E SER 3.3 25.6 - - - +
591E THR* 4.4 1.6 - - + -
601E PRO* 4.0 15.9 - - + -
614E MET* 4.2 10.3 - - + -
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Residues in contact with HIS 570 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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565E GLY 4.6 0.2 + - - -
566E ASP* 3.4 27.1 + - - +
567E THR* 3.0 50.1 + - + +
569E LEU* 1.3 78.2 - - - +
571E ILE* 1.3 63.7 + - - +
573E ALA* 3.4 2.3 + - - +
574E ARG* 3.0 29.5 + - - +
590E SER 5.7 0.2 - - - -
593E ILE* 3.1 31.8 + - - +
594E GLN 4.5 0.2 - - - -
595E ASN* 3.6 15.4 - - + +
599E GLU 3.3 22.5 + - - -
601E PRO* 3.4 29.8 - - + +
604E CYS* 4.0 11.5 - - - +
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Residues in contact with ILE 571 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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530E ASN* 4.5 0.7 - - - +
534E HIS* 3.6 37.7 - - + +
537E CYS* 3.7 3.4 - - + -
538E THR* 3.2 56.8 - - + +
562E ASN* 4.2 12.3 - - - +
566E ASP* 4.2 11.0 - - + +
567E THR 3.3 8.9 + - - +
568E PRO* 3.0 9.0 + - + +
570E HIS* 1.3 82.3 - - - +
572E ALA* 1.3 61.4 + - - +
574E ARG* 3.3 17.8 + - - +
575E TRP* 3.2 27.7 + - + +
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Residues in contact with ALA 572 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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537E CYS* 4.6 3.6 - - + -
568E PRO 2.9 14.3 + - - +
569E LEU 3.9 2.9 - - - +
571E ILE* 1.3 78.6 - - - +
573E ALA* 1.3 56.9 + - - +
575E TRP 3.7 0.5 + - - -
576E GLY 3.0 8.8 + - - -
577E TYR* 3.0 36.6 + - + +
580E VAL* 3.5 32.8 - - + -
581E ILE* 3.5 17.0 - - + +
584E LEU* 4.2 6.1 - - + -
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Residues in contact with ALA 573 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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569E LEU 2.9 18.5 + - - +
570E HIS 3.6 4.3 - - - +
572E ALA* 1.3 73.9 - - - +
574E ARG* 1.3 67.4 + - - +
576E GLY* 3.0 11.4 + - - -
581E ILE* 4.1 10.0 - - + +
601E PRO 3.6 24.5 - - - +
604E CYS 3.6 2.2 - - - -
605E ALA* 4.1 6.3 - - - +
606E LEU 3.3 16.8 + - - -
610E ILE* 4.6 1.6 - - - +
614E MET* 4.0 20.4 - - + -
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Residues in contact with ARG 574 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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564E LYS* 5.9 1.6 - - - +
566E ASP* 3.0 41.0 + - - -
570E HIS 3.0 14.3 + - - +
571E ILE* 3.3 20.0 + - - +
573E ALA* 1.3 77.8 - - - +
575E TRP* 1.3 76.4 + - + +
576E GLY 3.3 2.1 + - - -
595E ASN* 4.8 1.4 - - - +
599E GLU* 4.0 11.5 + - - -
604E CYS* 3.2 38.8 + - + +
606E LEU* 3.4 23.0 - - - +
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Residues in contact with TRP 575 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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538E THR* 3.5 21.6 - - - +
539E TYR* 5.0 13.7 - + - -
571E ILE* 3.2 16.7 + - + +
572E ALA 3.7 0.2 - - - -
574E ARG* 1.3 101.1 - - + +
576E GLY* 1.3 65.9 + - - +
577E TYR* 3.2 54.9 + + + -
606E LEU* 4.4 9.1 - - - +
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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