Contacts of the helix formed by residues 89 - 97 (chain I) in PDB entry 2HQT
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 89 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87I SER* 3.1 5.6 + - - -
88I LYS* 1.3 83.3 - - - +
90I VAL* 1.3 65.0 + - - +
91I LYS* 3.6 7.3 + - - +
92I SER* 2.6 51.4 + - - +
93I THR* 3.3 10.2 + - - -
48J GLN* 3.7 27.5 + - + +
51J LEU* 3.9 6.6 - - - +
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Residues in contact with VAL 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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35H SER* 6.5 0.4 - - - -
84I VAL* 3.8 23.8 - - + +
87I SER* 3.2 15.6 + - - +
89I ASP* 1.3 72.0 - - - +
91I LYS* 1.3 64.3 + - - +
93I THR* 3.1 4.7 + - - -
94I TYR* 3.0 47.6 + - + +
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Residues in contact with LYS 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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89I ASP* 3.4 9.4 + - - +
90I VAL* 1.3 79.3 - - - +
92I SER* 1.3 57.1 + - - +
94I TYR* 3.4 6.4 + - + +
95I THR* 3.0 38.7 + - - +
98I ARG* 5.9 0.2 - - - +
2005I SO4 3.2 39.9 + - - -
51J LEU* 4.1 16.8 - - + +
54J ARG* 4.1 13.5 - - - +
55J ASP* 5.7 0.4 + - - -
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Residues in contact with SER 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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89I ASP* 2.6 32.3 + - - -
91I LYS* 1.3 77.6 - - - +
93I THR* 1.3 53.2 + - - +
95I THR* 3.6 5.0 + - - +
96I THR* 2.5 37.4 + - - -
47J ASP* 3.7 22.7 - - - +
48J GLN* 3.2 24.7 - - - +
51J LEU* 3.2 21.3 - - - +
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Residues in contact with THR 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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80I ILE* 5.8 0.4 - - + -
83I LEU* 4.5 5.4 - - + -
84I VAL* 3.7 35.7 - - + +
87I SER* 3.1 28.6 + - - -
89I ASP 3.3 1.9 + - - -
90I VAL* 3.1 11.1 + - - -
92I SER* 1.3 75.4 - - - +
94I TYR* 1.3 66.0 + - - +
96I THR* 3.2 13.5 + - - -
97I TYR* 3.2 35.9 + - + +
101I LEU* 4.9 0.2 - - - +
47J ASP* 4.7 9.1 + - - +
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Residues in contact with TYR 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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84I VAL* 3.4 35.7 - - + +
90I VAL* 3.0 39.7 + - + +
91I LYS* 3.9 7.2 - - + +
93I THR* 1.3 77.1 - - - +
95I THR* 1.3 63.1 + - - +
96I THR 3.2 0.3 + - - -
97I TYR 3.2 2.4 + - - -
98I ARG* 3.1 31.7 + - - +
101I LEU* 3.6 27.6 - - + +
119I LEU* 3.9 11.8 - - + +
120I GLU* 3.0 24.9 + - - +
121I ILE* 3.8 27.2 - - + +
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Residues in contact with THR 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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50I ASN* 5.5 0.2 - - - +
91I LYS* 3.0 25.9 + - - +
92I SER* 3.7 7.9 - - - +
93I THR 3.3 0.2 - - - -
94I TYR* 1.3 76.8 - - - +
96I THR* 1.3 61.2 + - - +
98I ARG* 3.2 47.7 + - - +
2005I SO4 3.9 5.5 + - - -
50J ASN* 5.9 3.1 - - - +
51J LEU* 4.5 14.2 - - + +
54J ARG* 4.4 15.0 - - - +
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Residues in contact with THR 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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47I ASP* 5.3 0.5 - - - +
50I ASN* 3.3 15.7 - - - +
92I SER 2.5 22.5 + - - -
93I THR 3.6 5.8 - - - -
94I TYR 3.1 0.8 - - - -
95I THR* 1.3 79.5 - - - +
97I TYR* 1.3 83.5 + - + +
98I ARG 3.7 0.7 - - - -
47J ASP* 3.5 32.2 + - - +
50J ASN* 5.5 2.1 + - - +
96J THR* 3.7 36.2 + - + +
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Residues in contact with TYR 97 (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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46I LEU* 4.1 19.9 - - + +
47I ASP* 3.8 22.7 + - - -
50I ASN* 3.2 12.1 - - + +
80I ILE* 3.9 20.6 - - + -
83I LEU* 3.8 28.6 - - + +
93I THR* 3.2 37.1 + - + +
94I TYR 3.2 6.2 + - - -
96I THR* 1.3 101.2 - - + +
98I ARG* 1.3 62.5 + - - -
99I HIS 3.1 3.3 + - - -
100I ILE* 3.3 20.5 + - + -
101I LEU* 2.9 28.2 + - + +
47J ASP* 4.7 7.8 + - - -
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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