Contacts of the helix formed by residues 90 - 97 (chain Y) in PDB entry 6L49
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 ASP 90 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61Y GLU* 4.9 9.9 - - - +
65Y LEU* 3.8 17.5 - - + +
86Y ALA 4.0 2.3 + - - +
87Y ILE 3.5 4.5 - - - +
88Y ARG 4.4 1.2 - - - -
89Y ASN* 1.3 88.7 + - - +
91Y GLU* 1.3 60.9 + - - +
92Y GLU* 3.1 14.2 + - - +
93Y LEU* 2.6 44.3 + - + +
94Y ASN* 3.0 27.2 + - - +
103Z LEU* 5.1 2.1 - - - +
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Residues in contact with GLU 91 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89Y ASN 3.7 3.8 + - - +
90Y ASP* 1.3 72.4 - - - +
92Y GLU* 1.3 73.1 + - - +
94Y ASN* 3.1 10.7 + - + +
95Y LYS* 2.9 38.6 + - - +
100Z PRO* 5.7 1.6 - - - +
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Residues in contact with GLU 92 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90Y ASP* 3.1 11.8 + - - +
91Y GLU* 1.3 88.6 - - - +
93Y LEU* 1.3 60.7 + - - +
95Y LYS* 3.8 0.4 + - - -
96Y LEU* 3.7 13.7 + - - +
100Z PRO* 3.6 36.5 - - + +
101Z GLY 3.7 1.2 + - - -
102Z GLU* 2.8 48.0 + - - +
103Z LEU* 2.9 44.8 + - + +
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Residues in contact with LEU 93 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58Y LEU* 4.0 28.3 - - + +
61Y GLU* 4.1 11.7 - - + +
62Y ILE* 4.1 28.9 - - + +
65Y LEU* 3.8 28.7 - - + -
86Y ALA 4.2 5.6 - - - +
87Y ILE* 3.8 22.3 - - + +
90Y ASP* 2.6 26.4 + - + +
92Y GLU* 1.3 72.3 - - - +
94Y ASN* 1.3 63.3 + - - +
95Y LYS 3.3 0.2 - - - -
96Y LEU* 3.6 7.7 + - + +
97Y LEU* 3.4 20.8 + - + +
62Z PHE* 5.0 11.9 - - + -
103Z LEU* 4.4 9.4 - - + -
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Residues in contact with ASN 94 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87Y ILE 3.8 7.6 - - - +
88Y ARG* 2.7 45.2 + - - +
90Y ASP 3.0 18.8 + - - +
91Y GLU* 3.1 13.6 + - - +
93Y LEU* 1.3 77.4 - - - +
95Y LYS* 1.3 60.4 + - - +
97Y LEU 3.3 0.2 - - - -
98Y GLY* 3.0 32.0 + - - -
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Residues in contact with LYS 95 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91Y GLU* 2.9 26.9 + - - +
92Y GLU* 4.0 6.5 - - - +
93Y LEU 3.3 0.6 - - - -
94Y ASN* 1.3 80.3 - - - +
96Y LEU* 1.3 59.5 + - - +
97Y LEU 3.6 0.2 + - - -
98Y GLY* 4.0 5.9 + - - -
98Z LEU 5.7 4.5 - - - +
100Z PRO* 3.8 37.2 - - + +
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Residues in contact with LEU 96 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58Y LEU* 4.0 25.6 - - + -
92Y GLU 3.7 9.8 + - - +
93Y LEU* 3.6 12.5 + - + +
94Y ASN 3.3 0.6 - - - -
95Y LYS* 1.3 78.8 - - - +
97Y LEU* 1.3 64.6 + - + +
98Y GLY 3.6 1.4 + - - -
100Y VAL* 4.5 2.1 - - - +
62Z PHE* 4.3 7.2 - - + -
66Z ILE* 4.1 16.6 - - + -
69Z ARG* 3.1 53.9 + - - +
98Z LEU* 3.9 22.7 - - + +
99Z LEU* 3.8 32.3 - - + -
100Z PRO* 5.3 2.4 - - + +
103Z LEU* 5.0 1.8 - - + -
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Residues in contact with LEU 97 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98T TYR* 3.4 30.1 - - + +
87Y ILE* 3.3 43.5 - - + -
88Y ARG* 3.2 17.2 + - - +
93Y LEU* 3.4 13.5 + - + +
94Y ASN 3.3 6.3 + - - -
95Y LYS 3.4 0.4 - - - -
96Y LEU* 1.3 89.8 - - + +
98Y GLY* 1.3 61.6 + - - +
99Y ARG 3.5 2.0 - - - -
100Y VAL* 3.6 32.5 + - + +
102Y ILE* 5.1 0.9 - - + -
62Z PHE* 3.9 28.7 - - + -
69Z ARG* 3.7 11.9 - - - +
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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