Contacts of the helix formed by residues 570 - 578 (chain C) in PDB entry 5V3M
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 CYS 570 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A A 5.3 3.1 - - - -
14A C 5.3 0.9 - - - -
545C GLU* 4.7 7.4 - - - -
548C ARG* 3.3 28.7 - - - -
551C ARG* 4.8 1.8 - - - +
559C TYR* 3.5 18.4 - - - +
568C PHE* 3.1 2.8 - - - +
569C THR* 1.3 79.3 - - - +
571C THR* 1.3 64.0 + - - +
572C THR* 3.3 27.6 - - - -
573C GLU* 3.4 33.4 - - + +
574C LEU 3.6 11.4 + - - -
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Residues in contact with THR 571 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B C 6.3 1.3 - - + -
13B C 4.7 20.1 + - + +
14B T 3.8 23.6 - - + +
551C ARG* 5.6 0.2 - - - +
559C TYR* 4.0 27.1 - - - -
570C CYS* 1.3 77.2 - - - +
572C THR* 1.3 69.5 + - + +
574C LEU* 3.6 4.5 + - - +
575C PHE* 3.3 21.7 + - - +
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Residues in contact with THR 572 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A A 4.2 10.3 - - - +
14A C 3.7 12.3 - - - +
14B T 4.1 13.2 - - - -
15B G 2.5 42.3 + - - +
16B T 3.9 8.5 + - - +
570C CYS* 3.3 22.9 - - - -
571C THR* 1.3 86.2 - - + +
573C GLU* 1.3 68.0 + - + +
575C PHE* 3.2 7.3 + - - +
576C ARG* 3.1 22.7 + - - +
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Residues in contact with GLU 573 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A G 4.1 21.9 + - + +
12A C 3.4 44.9 + - + +
548C ARG* 4.0 5.7 + - - -
568C PHE* 3.7 26.3 - - + +
569C THR* 3.7 15.6 + - - +
570C CYS* 3.4 33.7 - - + +
571C THR 3.3 0.6 - - - -
572C THR* 1.3 80.1 - - + +
574C LEU* 1.3 62.6 + - - +
576C ARG* 3.5 8.9 + - - +
577C HIS* 3.2 21.5 + - - +
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Residues in contact with LEU 574 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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559C TYR* 3.8 29.6 - - + +
560C LYS 4.3 6.3 - - - +
561C CYS* 3.8 30.5 - - + +
568C PHE* 3.7 28.3 - - + -
570C CYS 3.6 12.7 + - - +
571C THR* 3.6 5.2 + - - +
572C THR 3.3 0.2 - - - -
573C GLU* 1.3 78.5 - - - +
575C PHE* 1.3 65.3 + - - +
577C HIS* 3.0 11.5 + - + +
578C GLN* 3.0 45.5 + - + +
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Residues in contact with PHE 575 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B T 3.9 47.3 - + + -
15B G 3.4 30.5 - + - -
571C THR 3.3 14.3 + - - +
572C THR* 3.2 8.8 + - - +
574C LEU* 1.3 81.6 - - - +
576C ARG* 1.3 64.6 + - - +
578C GLN* 3.5 24.6 + - - +
579C LYS* 3.5 38.9 + - - +
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Residues in contact with ARG 576 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A T 5.6 0.2 - - - -
10A G 3.9 18.7 + - - +
11A G 3.3 30.3 + - - -
12A C 3.6 9.9 - - - +
16B T 4.4 21.4 + - + +
17B G 2.6 30.3 + - - -
572C THR 3.1 14.1 + - - +
573C GLU* 3.9 7.0 - - - +
575C PHE* 1.3 76.7 - - - +
577C HIS* 1.3 67.6 + - - +
579C LYS* 3.0 28.8 + - + +
580C VAL* 5.1 0.9 - - - +
597C ILE* 4.8 17.9 - - + +
598C ARG* 3.3 48.9 - - - +
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Residues in contact with HIS 577 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A G 3.0 36.3 + - - +
561C CYS* 3.6 14.6 - - + -
564C CYS* 2.3 20.5 - - + -
566C LYS* 4.9 2.7 - - + -
568C PHE* 3.5 31.7 - + + -
573C GLU 3.2 6.2 + - - +
574C LEU* 3.0 9.9 + - + +
576C ARG* 1.3 79.7 - - - +
578C GLN* 1.3 60.3 + - - +
579C LYS 2.9 6.1 + - - -
580C VAL* 3.2 31.2 + - + +
581C HIS* 3.9 5.2 - + - -
1008C ZN 2.0 37.7 - - - -
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Residues in contact with GLN 578 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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560C LYS 5.8 0.2 + - - -
561C CYS* 4.6 9.7 - - - +
562C LYS* 5.2 4.8 - - - +
574C LEU* 3.0 41.5 + - + +
575C PHE* 3.5 30.8 - - - +
576C ARG 3.3 0.4 - - - -
577C HIS* 1.3 80.6 - - + +
579C LYS* 1.3 56.7 + - - +
580C VAL 2.9 8.4 + - - -
581C HIS* 3.3 22.9 + - + +
582C THR* 3.4 14.7 + - - +
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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
------------------------------------------------------------
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