Contacts of the helix formed by residues 567 - 575 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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534F HIS* 4.0 1.8 - - - -
558F LEU 3.6 10.1 + - - +
559F ASP* 3.8 23.8 - - - +
560F ILE 3.7 4.7 - - - +
561F GLY 5.0 0.4 - - - +
565F GLY 3.4 2.9 + - - +
566F ASP* 1.3 76.4 - - - +
568F PRO* 1.3 75.5 - - - +
569F LEU* 3.2 17.2 + - - +
570F HIS* 3.1 36.1 + - + +
571F ILE* 3.3 12.6 + - - +
590F SER 5.1 3.0 + - - +
593F ILE* 3.8 25.8 - - + -
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Residues in contact with PRO 568 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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531F THR* 5.2 0.2 - - - +
533F LEU* 3.7 31.0 - - + -
534F HIS* 3.8 23.6 - - + +
537F CYS* 3.7 25.5 - - + +
557F ARG 5.6 0.7 - - - +
558F LEU* 3.6 17.5 - - - +
560F ILE* 3.9 4.9 - - + +
567F THR* 1.3 89.4 - - - +
569F LEU* 1.3 56.1 + - - +
571F ILE* 3.0 14.6 + - + +
572F ALA* 2.9 27.9 + - - +
584F LEU* 4.0 9.6 - - + -
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Residues in contact with LEU 569 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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558F LEU 5.3 0.8 + - - +
567F THR* 3.1 11.2 + - - +
568F PRO* 1.3 76.5 - - - +
570F HIS* 1.3 65.6 + - - +
572F ALA 4.4 0.2 - - - +
573F ALA* 2.9 23.6 + - - +
581F ILE* 4.0 31.0 - - + +
584F LEU* 3.8 25.0 - - + +
585F LEU* 3.9 17.7 - - + -
589F ALA* 3.8 24.7 - - + -
590F SER 3.3 25.6 - - - +
591F THR* 4.4 1.1 - - + -
601F PRO* 4.0 15.7 - - + -
614F MET* 4.2 10.8 - - + -
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Residues in contact with HIS 570 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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565F GLY 4.7 0.2 + - - -
566F ASP* 3.4 25.3 + - - +
567F THR* 3.1 48.6 + - - +
569F LEU* 1.3 78.2 - - - +
571F ILE* 1.3 63.1 + - - +
573F ALA* 3.6 1.9 - - - +
574F ARG* 3.0 28.2 + - - +
590F SER 5.7 0.2 - - - -
593F ILE* 3.1 32.0 + - - +
595F ASN* 3.6 15.4 - - + +
599F GLU 3.3 22.7 + - - -
601F PRO* 3.4 29.6 - - + +
604F CYS* 4.0 12.4 - - - +
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Residues in contact with ILE 571 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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530F ASN* 4.5 0.7 - - - +
534F HIS* 3.5 40.8 - - + +
537F CYS* 3.7 4.0 - - + -
538F THR* 3.3 54.1 - - + +
562F ASN* 4.2 11.7 - - - +
566F ASP* 4.2 13.7 - - + +
567F THR 3.3 7.2 + - - +
568F PRO* 3.0 8.7 + - + +
570F HIS* 1.3 80.8 - - - +
572F ALA* 1.3 64.0 + - - +
574F ARG* 3.3 12.2 + - - +
575F TRP* 3.2 27.7 + - + +
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Residues in contact with ALA 572 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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537F CYS* 4.6 3.1 - - + +
568F PRO 2.9 14.5 + - - +
569F LEU 3.9 3.1 - - - +
570F HIS 3.4 0.2 - - - -
571F ILE* 1.3 78.9 - - - +
573F ALA* 1.3 57.5 + - - +
575F TRP 3.7 0.7 + - - -
576F GLY* 3.0 21.7 + - - -
577F TYR* 3.0 23.4 + - + +
580F VAL* 3.5 33.9 - - + -
581F ILE* 3.5 16.4 - - + +
584F LEU* 4.2 5.4 - - + -
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Residues in contact with ALA 573 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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569F LEU 2.9 18.1 + - - +
570F HIS 3.6 3.8 - - - +
572F ALA* 1.3 74.5 - - - +
574F ARG* 1.3 67.1 + - - +
576F GLY* 3.0 11.3 + - - -
581F ILE* 4.2 10.0 - - + +
601F PRO 3.6 24.9 - - - +
604F CYS 3.6 3.1 - - - -
605F ALA* 3.7 6.4 - - - +
606F LEU 3.3 16.8 + - - -
610F ILE* 4.6 2.4 - - - +
614F MET* 4.0 19.7 - - + -
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Residues in contact with ARG 574 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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566F ASP* 2.7 42.5 + - - -
570F HIS* 3.0 22.1 + - - +
571F ILE* 3.3 13.9 + - - +
573F ALA* 1.3 77.4 - - - +
575F TRP* 1.3 76.0 + - + +
576F GLY 3.3 2.4 + - - -
595F ASN* 4.8 0.6 + - - -
599F GLU* 3.4 23.0 + - - -
604F CYS* 3.2 29.3 + - + +
606F LEU* 3.4 22.9 - - - +
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Residues in contact with TRP 575 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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538F THR* 3.5 21.2 - - - +
539F TYR* 5.0 14.1 - + - -
571F ILE* 3.2 16.5 + - + +
572F ALA 3.7 0.2 - - - -
574F ARG* 1.3 101.0 - - + +
576F GLY* 1.3 66.9 + - - +
577F TYR* 3.2 56.2 + + + -
606F LEU* 4.4 9.7 - - - +
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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