Contacts of the helix formed by residues 47 - 51 (chain G) in PDB entry 6IY6
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 ARG 47 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45G LEU 3.7 3.9 + - - +
46G VAL* 1.3 75.0 - - - +
48G VAL* 1.3 64.8 + - - +
49G ARG* 3.3 25.6 - - + +
50G ASP* 3.1 36.1 + - - +
51G LEU* 3.7 7.1 + - - +
82G GLN* 3.5 20.1 - - - +
83G GLN* 3.5 29.2 - - - +
213H LYS 5.0 1.6 + - - -
214H GLY* 4.6 8.7 + - - -
263H GLU* 3.9 17.7 + - - +
264H LYS* 3.6 33.7 - - - +
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Residues in contact with VAL 48 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47G ARG* 1.3 68.1 - - - +
49G ARG* 1.3 60.5 + - - +
51G LEU* 3.0 33.8 + - + +
62G VAL* 4.1 21.8 - - + -
64G ALA* 4.4 3.8 - - + -
80G LEU 4.4 10.3 - - - +
82G GLN* 2.7 38.6 + - + +
85G PHE* 4.0 8.3 - - + -
86G ASN* 3.9 36.6 - - - +
87G VAL* 4.0 9.0 - - + +
132G GLN* 3.5 14.9 - - + -
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Residues in contact with ARG 49 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47G ARG* 4.1 28.4 - - + +
48G VAL* 1.3 77.7 - - - +
50G ASP* 1.3 70.7 - - - +
52G THR* 3.6 17.2 - - - +
83G GLN* 4.0 19.1 - - - +
85G PHE* 3.6 48.2 - - + -
132G GLN* 3.6 15.8 + - - +
323G THR* 5.8 4.8 + - - +
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Residues in contact with ASP 50 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46G VAL* 5.1 1.2 - - + +
47G ARG* 3.1 34.2 + - - +
48G VAL 3.1 0.8 - - - -
49G ARG* 1.3 85.9 - - - +
51G LEU* 1.3 58.6 - - - +
52G THR* 3.0 16.5 + - - -
55G LYS* 3.6 34.5 + - - +
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Residues in contact with LEU 51 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46G VAL* 3.8 22.2 - - + -
47G ARG 4.0 6.5 - - - +
48G VAL* 3.0 26.4 + - + +
50G ASP* 1.3 73.3 - - - +
52G THR* 1.3 56.9 + - - +
55G LYS* 5.1 5.6 - - + -
60G VAL* 3.8 10.8 - - + -
62G VAL* 3.9 19.5 - - + -
87G VAL* 4.0 26.5 - - + -
120G VAL* 3.6 26.7 - - + -
132G GLN* 2.7 27.2 + - + +
135G VAL* 3.4 21.2 - - + +
137G LEU* 5.0 8.1 - - + -
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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