Contacts of the helix formed by residues 82 - 89 (chain I) in PDB entry 2YW7
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 82 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33D LEU* 4.9 2.0 - - - -
34D THR* 5.2 3.4 - - - +
37D HIS* 4.1 30.3 - - + +
94D ASP* 2.5 30.9 + - + +
95D TYR* 4.2 24.0 - - + +
80I LYS* 3.7 3.9 - - + -
81I GLY* 1.3 81.0 - - - +
83I PRO* 1.4 73.2 - - - +
85I ALA* 3.0 26.7 + - + +
86I ILE* 3.2 13.6 + - - +
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Residues in contact with PRO 83 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30D ASP* 3.5 40.2 - - - +
33D LEU* 4.8 6.0 - - + -
34D THR* 4.8 2.5 - - - +
83D PRO* 5.0 1.3 - - + +
86D ILE* 3.7 40.4 - - + +
87D ILE* 4.0 7.4 - - + +
90D ARG* 3.9 11.4 - - - +
94D ASP* 3.8 6.7 - - - +
81I GLY 4.8 0.4 - - - +
82I THR* 1.4 87.4 - - - +
84I GLY* 1.3 56.8 + - - +
86I ILE* 3.0 25.9 + - + +
87I ILE* 3.4 15.1 + - - +
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Residues in contact with GLY 84 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87D ILE* 4.7 0.4 - - - -
90D ARG* 3.6 8.4 - - - +
94D ASP* 2.6 27.8 + - - -
83I PRO* 1.3 73.4 - - - +
85I ALA* 1.3 55.2 + - - +
87I ILE* 3.6 18.5 - - - +
88I LYS* 3.3 24.8 + - - +
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Residues in contact with ALA 85 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26I SER* 4.2 0.7 - - - -
80I LYS* 3.8 33.0 - - + +
82I THR* 3.0 34.9 + - - +
84I GLY* 1.3 78.8 - - - +
86I ILE* 1.3 56.6 + - + +
88I LYS* 3.6 6.4 - - - +
89I ASP* 2.7 41.2 + - - +
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Residues in contact with ILE 86 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D LEU* 4.6 4.7 - - + -
83D PRO* 3.8 18.6 - - + -
86D ILE* 5.4 0.2 - - + -
26I SER* 4.0 21.3 - - - +
29I ASN* 3.8 20.2 - - + +
30I ASP* 3.9 26.2 - - + +
33I LEU* 3.8 28.9 - - + -
81I GLY* 5.7 0.9 - - - +
82I THR 3.5 13.7 - - - +
83I PRO* 3.0 12.7 + - + +
85I ALA* 1.3 74.2 - - + +
87I ILE* 1.3 57.1 + - - +
88I LYS 2.8 14.9 + - - -
89I ASP* 3.4 6.7 - - - -
90I ARG* 2.9 32.7 + - + +
92I TRP* 5.2 1.3 - - + -
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Residues in contact with ILE 87 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83D PRO* 4.2 9.0 - - + +
84D GLY* 5.5 0.2 - - - -
87D ILE* 3.7 43.5 - - + -
90D ARG* 6.0 0.2 - - - +
83I PRO 3.9 7.9 - - - +
84I GLY* 3.6 24.7 - - - +
86I ILE* 1.3 74.6 - - - +
88I LYS* 1.3 66.9 + - + +
90I ARG* 3.3 43.1 - - - +
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Residues in contact with LYS 88 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22I GLN* 5.4 2.6 - - - +
80I LYS* 3.6 30.5 - - + +
84I GLY 3.3 18.4 + - - +
85I ALA* 3.6 6.5 - - - +
86I ILE 2.8 1.2 + - - -
87I ILE* 1.3 82.8 - - + +
89I ASP* 1.3 82.8 + - - +
90I ARG 2.9 15.6 + - - +
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Residues in contact with ASP 89 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22I GLN* 3.6 31.9 + - + +
23I LYS* 4.2 28.5 - - + +
26I SER* 2.7 26.4 + - - -
80I LYS* 5.1 0.5 - - - +
85I ALA* 2.7 23.1 - - - +
86I ILE 3.2 1.1 + - - +
88I LYS* 1.3 94.0 + - - +
90I ARG* 1.3 58.0 + - - +
91I THR* 5.0 2.3 - - - +
92I TRP* 4.6 5.0 - - - -
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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