Contacts of the helix formed by residues 89 - 97 (chain Q) 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 Q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87Q SER* 2.9 11.8 + - - -
88Q LYS* 1.3 82.4 - - - +
90Q VAL* 1.3 66.9 + - - +
91Q LYS* 3.7 10.1 + - - +
92Q SER* 2.7 50.5 + - - +
93Q THR* 3.2 6.4 + - - -
48R GLN* 3.9 28.1 + - + +
51R LEU* 4.2 3.3 - - - +
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Residues in contact with VAL 90 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84Q VAL* 3.9 31.9 - - + +
87Q SER* 3.6 12.3 - - - +
89Q ASP* 1.3 73.9 - - - +
91Q LYS* 1.3 63.9 + - - +
93Q THR* 2.9 12.1 + - - -
94Q TYR* 3.0 37.5 + - + -
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Residues in contact with LYS 91 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89Q ASP* 3.3 11.9 + - - +
90Q VAL* 1.3 78.4 - - - +
92Q SER* 1.3 63.0 + - - +
94Q TYR* 3.2 7.7 + - + +
95Q THR* 2.9 35.4 + - - +
2009Q SO4 3.1 42.5 + - - +
51R LEU* 3.9 16.2 - - + +
54R ARG* 3.9 14.8 - - - +
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Residues in contact with SER 92 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89Q ASP* 2.7 31.7 + - - -
91Q LYS* 1.3 75.7 - - - +
93Q THR* 1.3 58.2 + - - +
95Q THR* 3.4 3.4 + - - -
96Q THR* 2.6 33.6 + - - -
47R ASP* 3.7 11.4 - - - -
48R GLN* 3.3 36.8 - - - +
51R LEU* 3.3 20.3 - - - +
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Residues in contact with THR 93 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80Q ILE* 6.1 0.7 - - + -
83Q LEU* 4.5 6.5 + - + +
84Q VAL* 4.0 33.7 - - + +
87Q SER* 2.7 29.7 + - - -
89Q ASP 3.2 2.7 + - - -
90Q VAL* 2.9 10.4 + - - -
92Q SER* 1.3 78.4 - - - +
94Q TYR* 1.3 62.6 + - - +
96Q THR* 3.2 11.7 + - - -
97Q TYR* 3.2 37.2 + - + +
101Q LEU* 4.8 0.6 - - + +
47R ASP* 4.9 9.2 + - - +
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Residues in contact with TYR 94 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84Q VAL* 4.2 23.5 - - + +
90Q VAL* 3.0 36.3 + - + +
91Q LYS* 3.6 11.0 - - + +
93Q THR* 1.3 78.2 - - - +
95Q THR* 1.3 63.4 + - - +
97Q TYR 3.4 1.9 + - - -
98Q ARG* 3.2 34.0 + - - +
101Q LEU* 3.7 27.3 - - + +
119Q LEU* 4.9 2.5 - - + +
120Q GLU* 2.6 28.9 + - - +
121Q ILE* 3.2 17.9 - - + +
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Residues in contact with THR 95 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50Q ASN* 5.5 0.2 - - - +
91Q LYS* 2.9 28.9 + - - +
92Q SER* 3.8 7.0 - - - -
94Q TYR* 1.3 77.2 - - - +
96Q THR* 1.3 61.6 + - - +
98Q ARG* 3.3 47.9 + - - +
2009Q SO4 4.2 3.1 + - - -
51R LEU* 4.5 10.3 - - + +
54R ARG* 4.1 15.3 - - - +
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Residues in contact with THR 96 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47Q ASP* 4.8 1.1 - - - +
50Q ASN* 3.2 16.3 - - - +
92Q SER 2.6 21.7 + - - -
93Q THR 3.7 5.2 - - - -
94Q TYR 3.2 0.4 - - - -
95Q THR* 1.3 77.5 - - - +
97Q TYR* 1.3 82.3 + - + +
98Q ARG 3.5 0.7 - - - -
47R ASP* 3.4 37.2 + - - +
50R ASN* 5.6 1.9 + - - +
96R THR* 3.8 29.6 + - + +
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Residues in contact with TYR 97 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46Q LEU* 4.0 31.0 - - + +
47Q ASP* 3.8 22.8 + - - -
50Q ASN* 3.3 11.2 - - + +
80Q ILE* 4.1 15.5 - - + -
83Q LEU* 4.2 17.6 - - + +
93Q THR* 3.2 40.0 + - + +
94Q TYR 3.6 4.0 - - - -
95Q THR 3.3 0.2 - - - -
96Q THR* 1.3 97.3 - - + +
98Q ARG* 1.3 65.4 + - - +
99Q HIS 3.2 0.2 + - - -
100Q ILE* 3.3 25.1 + - + -
101Q LEU* 2.9 29.2 + - + +
47R ASP* 4.9 7.6 + - - -
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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