Contacts of the helix formed by residues 82 - 90 (chain H) in PDB entry 1VEQ
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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80H LYS* 3.8 2.9 - - - +
81H GLY* 1.3 78.1 + - - +
83H PRO* 1.3 76.7 - - + +
84H GLY 2.7 3.0 + - - -
85H ALA* 3.2 23.9 + - - +
86H ILE* 3.0 15.6 + - - +
33K LEU* 5.1 1.6 - - - -
34K THR* 4.7 4.0 - - - +
37K HIS* 3.9 26.1 - - + +
94K ASP* 3.6 17.2 + - + -
95K TYR* 3.8 37.8 + - + +
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Residues in contact with PRO 83 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82H THR* 1.3 86.1 - - - +
84H GLY* 1.3 59.4 + - - +
86H ILE* 2.7 25.8 - - + +
87H ILE* 3.3 12.2 + - - +
30K ASP* 2.9 34.8 - - - +
33K LEU* 4.5 15.2 - - + -
34K THR* 4.3 6.5 - - - +
83K PRO* 5.5 3.8 - - + +
86K ILE* 3.4 33.9 - - + -
87K ILE* 5.4 7.9 - - + +
90K ARG* 3.6 13.0 - - - +
94K ASP* 4.0 4.7 - - + -
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Residues in contact with GLY 84 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82H THR* 2.7 2.8 + - - -
83H PRO* 1.3 75.0 - - - +
85H ALA* 1.3 67.8 + - - +
86H ILE 2.7 4.0 + - - -
87H ILE* 2.8 28.4 + - - +
88H LYS* 3.3 5.3 + - - +
87K ILE* 5.7 1.6 - - - -
90K ARG* 4.7 2.0 - - - +
94K ASP* 3.0 27.8 + - - -
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Residues in contact with ALA 85 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26H SER* 4.2 0.7 - - - -
80H LYS* 3.6 52.7 - - + +
82H THR* 3.2 19.2 + - - +
84H GLY* 1.3 72.5 - - - +
86H ILE* 1.3 62.5 + - - +
88H LYS* 3.3 10.1 + - - +
89H ASP* 3.1 33.6 + - - +
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Residues in contact with ILE 86 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26H SER* 3.7 27.6 + - - +
29H ASN* 4.0 13.5 - - + +
30H ASP* 3.6 27.4 - - + +
33H LEU* 5.1 4.5 - - + -
81H GLY* 5.5 2.4 - - - -
82H THR 3.0 13.2 + - - +
83H PRO* 2.7 33.9 - - + +
84H GLY 2.7 4.0 + - - -
85H ALA* 1.3 71.3 - - - +
87H ILE* 1.3 58.3 + - - +
88H LYS 2.8 10.8 + - - -
89H ASP* 3.2 0.7 + - - +
90H ARG* 3.2 26.4 + - + +
33K LEU* 5.2 5.8 - - + -
83K PRO* 3.4 36.1 - - + -
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Residues in contact with ILE 87 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83H PRO 3.4 11.0 - - - +
84H GLY* 2.8 33.9 + - - +
86H ILE* 1.3 78.0 - - + +
88H LYS* 1.3 61.1 + - + +
90H ARG* 3.1 51.9 - - - +
83K PRO* 5.4 9.2 - - + +
84K GLY* 5.7 2.0 - - - -
87K ILE* 5.3 22.9 - - + -
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Residues in contact with LYS 88 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80H LYS* 4.9 13.8 - - - +
84H GLY 3.3 7.9 + - - +
85H ALA* 3.5 13.7 - - - +
86H ILE 2.8 1.6 + - - -
87H ILE* 1.3 79.3 - - + +
89H ASP* 1.3 68.9 + - - +
90H ARG 3.2 10.8 + - - +
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Residues in contact with ASP 89 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22H GLN* 3.3 29.6 + - - +
23H LYS* 4.7 23.5 - - + +
26H SER* 3.1 33.9 + - - +
80H LYS* 5.5 0.9 - - - +
85H ALA* 3.1 14.5 + - - +
86H ILE 3.2 0.2 + - - -
88H LYS* 1.3 83.6 - - - +
90H ARG* 1.3 62.5 + - - +
91H THR* 3.9 9.2 + - - +
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Residues in contact with ARG 90 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26H SER* 5.0 4.5 - - - +
30H ASP* 3.3 18.6 + - + -
86H ILE* 3.2 15.3 + - + +
87H ILE* 3.1 49.5 - - - +
88H LYS 3.2 10.0 - - - +
89H ASP* 1.3 81.5 - - - +
91H THR* 1.3 63.1 + - - +
92H TRP* 3.4 47.3 + - + +
93H ASP* 4.2 1.6 - - - +
94H ASP* 3.1 58.4 + - - +
83K PRO* 3.6 11.3 - - - +
84K GLY* 4.8 0.6 - - - +
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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