Contacts of the helix formed by residues 577 - 587 (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 TYR 577 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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537E CYS 3.3 26.7 - - - -
538E THR 3.3 8.6 + - - -
539E TYR* 3.6 5.9 + - - -
540E GLY* 3.3 28.4 + - - -
572E ALA* 3.0 16.8 + - + +
575E TRP* 3.2 59.8 - + + -
576E GLY* 1.3 71.4 - - - +
578E GLN* 1.3 66.7 + - - +
579E GLY 3.0 3.5 + - - -
580E VAL* 3.2 18.2 + - + -
581E ILE* 3.0 22.4 + - - +
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Residues in contact with GLN 578 (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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576E GLY 3.7 5.1 + - - -
577E TYR* 1.3 71.7 - - - +
579E GLY* 1.3 58.1 + - - +
581E ILE* 3.1 11.6 + - - +
582E GLU* 2.8 55.9 + - + +
610E ILE* 5.7 7.2 - - + -
613E VAL* 3.3 33.4 - - + +
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Residues in contact with GLY 579 (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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542E GLU* 3.6 26.1 + - - +
577E TYR 3.0 1.6 + - - -
578E GLN* 1.3 74.9 - - - +
580E VAL* 1.3 59.3 + - - +
582E GLU* 3.4 10.9 + - - +
583E THR* 2.7 33.4 + - - -
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Residues in contact with VAL 580 (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* 3.9 16.6 - - + -
540E GLY* 4.4 10.5 - - - -
542E GLU* 3.6 33.4 + - + +
545E VAL* 4.1 14.1 - - + -
572E ALA* 3.5 23.3 - - + -
577E TYR* 3.3 24.0 - - + +
579E GLY* 1.3 72.3 - - - +
581E ILE* 1.3 64.2 + - - +
583E THR* 3.0 9.9 + - - -
584E LEU* 2.9 35.2 + - + +
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Residues in contact with ILE 581 (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* 4.0 15.3 - - + -
572E ALA* 3.5 37.2 - - + +
573E ALA* 4.1 2.9 - - - +
576E GLY 4.3 1.1 - - - -
577E TYR 3.0 28.5 + - - +
578E GLN* 3.1 11.4 + - - +
580E VAL* 1.3 81.7 - - - +
582E GLU* 1.3 64.8 + - - +
584E LEU* 3.2 2.8 + - - +
585E LEU* 3.0 43.0 + - + +
610E ILE* 4.1 25.1 - - + -
613E VAL* 5.1 7.6 - - + -
614E MET* 4.0 15.0 - - + -
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Residues in contact with GLU 582 (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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578E GLN* 2.8 45.1 + - - +
579E GLY* 3.7 7.6 - - - +
581E ILE* 1.3 76.7 - - - +
583E THR* 1.3 53.3 + - - +
585E LEU* 3.0 8.9 + - - +
586E GLN* 2.7 57.5 + - - +
613E VAL* 4.0 20.9 - - + +
617E TYR* 4.3 9.2 - - + +
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Residues in contact with THR 583 (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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542E GLU* 4.2 1.9 + - - +
545E VAL* 4.4 13.5 - - + -
546E LYS* 3.7 41.5 - - + -
549E VAL* 4.8 5.1 - - + +
550E TYR* 4.2 17.7 - - + +
579E GLY 2.7 22.8 + - - -
580E VAL* 3.2 10.5 - - - -
582E GLU* 1.3 76.1 - - - +
584E LEU* 1.3 64.3 + - - +
586E GLN* 3.4 11.9 + - - +
587E ASN* 3.0 30.0 + - - +
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Residues in contact with LEU 584 (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* 4.6 4.3 - - + -
537E CYS* 4.1 3.4 - - - -
545E VAL* 4.5 8.5 - - + -
549E VAL* 4.4 15.0 - - + -
558E LEU* 3.8 27.3 - - + +
568E PRO* 4.0 16.6 - - + +
569E LEU* 3.8 38.1 - - + +
572E ALA* 4.2 1.3 - - + -
580E VAL* 2.9 35.6 + - + +
581E ILE 3.5 6.1 - - - +
583E THR* 1.3 76.9 - - - +
585E LEU* 1.3 62.8 + - - +
587E ASN* 3.1 5.9 + - - -
588E GLY 3.0 17.0 + - - -
589E ALA* 3.1 20.2 + - + +
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Residues in contact with LEU 585 (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* 3.9 25.6 - - + -
581E ILE* 3.0 41.5 + - + +
582E GLU* 3.6 7.0 - - - +
584E LEU* 1.3 75.1 - - - +
586E GLN* 1.3 58.2 + - - +
588E GLY* 2.9 20.3 + - - -
589E ALA 4.0 14.5 - - - +
591E THR* 4.3 15.7 - - + +
613E VAL* 4.5 2.7 - - + +
614E MET* 4.3 15.0 - - + +
617E TYR* 4.0 50.1 - - + -
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Residues in contact with GLN 586 (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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46B VAL* 6.1 0.6 - - - +
47B HIS* 4.4 22.3 + - - -
63B ALA* 5.8 2.6 - - - +
64B LEU* 3.3 28.9 + - + +
550E TYR* 4.7 10.1 + - - -
582E GLU* 2.7 41.0 + - - +
583E THR* 3.7 12.0 - - - +
584E LEU 3.2 0.2 - - - -
585E LEU* 1.3 78.2 - - - +
587E ASN* 1.3 59.6 + - - +
588E GLY* 3.5 0.6 + - - -
617E TYR* 3.8 22.1 + - + +
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Residues in contact with ASN 587 (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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64B LEU* 3.5 24.5 - - - +
78B GLN* 5.7 0.5 - - - +
549E VAL* 3.6 31.0 - - + +
550E TYR* 3.6 27.8 + - - -
558E LEU* 3.6 14.1 - - + +
583E THR* 3.0 24.5 + - - +
584E LEU* 3.1 7.6 + - - +
586E GLN* 1.3 81.2 - - - +
588E GLY* 1.3 56.5 + - - +
589E ALA 3.7 0.4 - - - -
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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