Contacts of the helix formed by residues 577 - 587 (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 TYR 577 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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537F CYS 3.3 27.4 - - - -
538F THR 3.3 8.1 + - - -
539F TYR* 3.7 5.5 - - - -
540F GLY* 3.4 27.6 + - - -
572F ALA* 3.0 18.5 + - + +
575F TRP* 3.2 59.7 - + + -
576F GLY* 1.3 72.1 - - - -
578F GLN* 1.3 65.9 + - - +
579F GLY 3.0 3.9 + - - -
580F VAL* 3.2 17.9 + - + -
581F ILE* 3.0 22.2 + - - +
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Residues in contact with GLN 578 (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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576F GLY 3.7 4.8 + - - -
577F TYR* 1.3 71.7 - - - +
579F GLY* 1.3 57.8 + - - +
581F ILE* 3.1 12.2 + - - +
582F GLU* 2.8 57.0 + - + +
609F LYS* 6.1 0.5 - - - +
610F ILE* 5.7 7.5 - - + +
613F VAL* 3.3 33.4 - - + +
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Residues in contact with GLY 579 (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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542F GLU* 3.6 25.9 - - - +
577F TYR 3.0 0.8 + - - -
578F GLN* 1.3 76.3 - - - +
580F VAL* 1.3 61.2 + - - +
582F GLU* 3.4 10.7 + - - +
583F THR* 2.7 33.9 + - - -
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Residues in contact with VAL 580 (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* 3.9 15.9 - - + -
540F GLY* 4.4 11.0 - - - -
542F GLU* 3.6 32.3 + - + +
545F VAL* 4.1 14.1 - - + -
572F ALA* 3.5 22.9 - - + -
577F TYR* 3.3 24.0 - - + +
579F GLY* 1.3 72.4 - - - +
581F ILE* 1.3 65.5 - - - +
583F THR* 3.0 10.7 + - - -
584F LEU* 2.9 35.2 + - + +
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Residues in contact with ILE 581 (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* 4.0 16.2 - - + -
572F ALA* 3.5 37.0 - - + +
573F ALA* 4.2 2.9 - - - +
576F GLY 4.3 1.3 - - - -
577F TYR 3.0 27.2 + - - +
578F GLN* 3.1 12.3 + - - +
580F VAL* 1.3 80.3 - - - +
582F GLU* 1.3 64.7 + - + +
584F LEU* 3.3 2.5 + - - +
585F LEU* 3.0 42.4 + - + +
610F ILE* 4.1 24.9 - - + -
613F VAL* 5.1 7.6 - - + -
614F MET* 4.0 15.0 - - + -
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Residues in contact with GLU 582 (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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578F GLN* 2.8 49.5 + - - +
579F GLY* 3.7 7.8 - - - +
581F ILE* 1.3 75.6 - - - +
583F THR* 1.3 53.7 + - - +
585F LEU* 3.1 6.8 + - - +
586F GLN* 2.8 52.4 + - - +
613F VAL* 3.9 18.6 - - + +
617F TYR* 3.9 16.8 - - + +
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Residues in contact with THR 583 (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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542F GLU* 4.1 2.3 + - - +
545F VAL* 4.4 14.1 - - + -
546F LYS* 3.7 40.7 - - + -
549F VAL* 4.8 6.0 - - + +
550F TYR* 4.2 18.4 - - + +
579F GLY 2.7 23.0 + - - -
580F VAL* 3.2 10.3 - - - -
582F GLU* 1.3 75.1 - - - +
584F LEU* 1.3 63.2 + - - +
586F GLN* 3.4 11.1 + - - +
587F ASN* 3.0 29.2 + - - +
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Residues in contact with LEU 584 (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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533F LEU* 4.6 3.6 - - + -
537F CYS* 4.1 4.3 - - - -
545F VAL* 4.5 7.9 - - + -
549F VAL* 4.4 14.6 - - + -
558F LEU* 3.8 28.0 - - + +
568F PRO* 4.0 16.2 - - + +
569F LEU* 3.8 37.7 - - + +
572F ALA* 4.2 1.6 - - + -
580F VAL* 2.9 39.2 + - + +
581F ILE 3.5 6.1 - - - +
583F THR* 1.3 72.9 - - - +
585F LEU* 1.3 64.5 + - - +
587F ASN* 3.1 6.4 + - - -
588F GLY 3.0 16.6 + - - -
589F ALA* 3.1 20.5 + - + +
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Residues in contact with LEU 585 (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* 3.9 26.0 - - + -
581F ILE* 3.0 42.6 + - + +
582F GLU* 3.6 3.6 - - - +
584F LEU* 1.3 75.3 - - - +
586F GLN* 1.3 60.3 + - - +
588F GLY* 2.9 19.4 + - - -
589F ALA 4.0 15.1 + - - +
591F THR* 4.3 15.7 - - + +
613F VAL* 4.5 1.8 - - + +
614F MET* 4.3 15.0 - - + +
617F TYR* 3.9 51.4 - - + -
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Residues in contact with GLN 586 (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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46C VAL* 6.1 1.0 - - - +
47C HIS* 4.4 23.2 + - - -
63C ALA* 5.9 2.0 - - - +
64C LEU* 3.3 28.7 + - + +
550F TYR* 4.7 10.1 + - - +
582F GLU* 2.8 39.8 + - - +
583F THR* 3.7 12.0 - - - +
584F LEU 3.2 0.2 - - - -
585F LEU* 1.3 76.1 - - - +
587F ASN* 1.3 62.7 + - - +
588F GLY 3.5 0.2 - - - -
617F TYR* 3.5 24.9 + - + +
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Residues in contact with ASN 587 (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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64C LEU* 3.6 23.8 - - - +
78C GLN* 5.6 1.8 - - - +
549F VAL* 3.6 30.6 + - + +
550F TYR* 3.3 34.5 + - - -
558F LEU* 3.6 14.8 - - + +
583F THR 3.0 20.6 + - - +
584F LEU* 3.1 6.3 + - - +
585F LEU 3.1 0.6 - - - -
586F GLN* 1.3 81.9 - - - +
588F GLY* 1.3 56.8 + - - +
589F ALA 3.7 0.2 - - - -
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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