Contacts of the helix formed by residues 85 - 96 (chain I) in PDB entry 6QY3
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 HIS 85 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62I ASN* 4.0 23.1 + - - +
64I LEU* 5.1 12.8 - - + -
83I ALA 3.8 0.8 + - - -
84I ARG* 1.3 78.0 - - - +
86I ASP* 1.3 65.7 + - - +
87I SER* 3.2 12.8 + - - +
88I SER* 3.5 18.5 + - - +
89I LEU* 4.0 2.4 + - - +
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Residues in contact with ASP 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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85I HIS* 1.3 72.1 - - - +
87I SER* 1.3 58.7 + - - +
88I SER 3.3 0.2 - - - -
89I LEU* 3.0 14.3 + - + +
90I GLN* 2.9 25.7 + - - +
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Residues in contact with SER 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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85I HIS* 3.2 7.9 - - - +
86I ASP* 1.3 79.5 - - - +
88I SER* 1.3 56.9 + - - +
90I GLN* 2.8 25.9 + - - +
91I ILE* 2.9 14.9 + - - +
194I VAL 5.8 1.3 - - - -
195I CYS 4.5 4.7 - - - -
196I GLY* 4.2 27.2 - - - +
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Residues in contact with SER 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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84I ARG* 5.0 10.8 - - - -
85I HIS* 3.5 13.4 + - - +
86I ASP 3.3 0.6 - - - -
87I SER* 1.3 77.7 - - - +
89I LEU* 1.3 61.5 + - - +
91I ILE* 3.6 17.5 + - - +
92I ALA* 4.2 4.2 + - - +
211J GLN* 6.0 7.0 - - - -
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Residues in contact with LEU 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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85I HIS 4.0 2.7 + - - +
86I ASP* 3.0 18.3 + - + +
88I SER* 1.3 77.7 - - - +
90I GLN* 1.3 61.5 + - - +
91I ILE 3.6 0.2 + - - -
92I ALA* 3.7 16.9 + - - +
93I ARG* 4.4 2.3 + - - +
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Residues in contact with GLN 90 (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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86I ASP 2.9 11.6 + - - +
87I SER* 2.8 16.0 + - - +
89I LEU* 1.3 75.4 - - - +
91I ILE* 1.3 61.8 + - - +
92I ALA 3.2 2.0 - - - -
93I ARG* 3.3 18.2 + - + +
94I GLN* 3.5 8.5 + - - +
195I CYS 5.1 8.1 - - - +
196I GLY 6.3 1.3 - - - -
197I CYS* 6.0 1.0 - - - +
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Residues in contact with ILE 91 (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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87I SER 2.9 9.4 + - - +
88I SER* 3.8 13.5 - - - +
89I LEU 3.3 1.0 - - - -
90I GLN* 1.3 74.9 - - - +
92I ALA* 1.3 59.6 + - - +
94I GLN* 3.0 12.4 + - + +
95I ILE* 2.9 26.3 + - - +
196I GLY 4.5 13.7 - - - +
197I CYS* 5.3 4.9 - - - +
198I MET* 5.4 5.4 - - + +
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Residues in contact with ALA 92 (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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88I SER 4.2 4.2 + - - +
89I LEU* 3.7 14.0 + - - +
90I GLN 3.2 0.6 - - - -
91I ILE* 1.3 79.9 - - - +
93I ARG* 1.3 57.3 + - - +
95I ILE* 3.2 11.4 + - - +
96I ALA* 3.0 25.8 + - - +
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Residues in contact with ARG 93 (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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89I LEU 4.4 1.9 + - - +
90I GLN* 3.3 14.8 + - - +
91I ILE 3.2 0.6 - - - -
92I ALA* 1.3 76.2 - - - +
94I GLN* 1.3 61.2 + - - +
96I ALA* 3.0 21.7 + - - +
97I TRP* 3.1 12.8 + - - +
277I LEU 5.6 1.7 - - - +
278I ASN* 4.6 24.1 - - + +
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Residues in contact with GLN 94 (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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90I GLN 3.5 4.6 + - - +
91I ILE* 3.0 17.5 + - + +
93I ARG* 1.3 78.8 - - - +
95I ILE* 1.3 61.3 + - - +
96I ALA 3.4 0.3 + - - -
97I TRP* 3.4 19.6 + - - +
197I CYS* 4.4 22.4 - - + -
198I MET* 5.2 4.3 - - + +
201I ILE* 5.5 9.9 - - + +
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Residues in contact with ILE 95 (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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91I ILE 2.9 11.8 + - - +
92I ALA* 3.2 12.8 + - - +
94I GLN* 1.3 77.0 - - - +
96I ALA* 1.3 58.2 + - - +
97I TRP 3.3 2.7 + - - +
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Residues in contact with ALA 96 (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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92I ALA 3.0 14.4 + - - +
93I ARG* 3.0 11.8 + - - +
95I ILE* 1.3 77.8 - - - +
97I TRP* 1.3 64.5 + - - +
98I LYS* 3.2 5.2 + - - +
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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