Contacts of the helix formed by residues 81 - 90 (chain A) in PDB entry 1QST
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 PRO 81 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79A LYS 3.4 8.5 - - - +
80A MET* 1.3 93.4 - - + +
82A LYS* 1.3 61.0 + - - +
83A GLU* 3.2 19.7 - - - +
84A TYR* 2.8 33.8 + - + +
85A ILE* 3.1 11.5 + - - +
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Residues in contact with LYS 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A LYS* 3.7 18.8 - - + +
71A ASN* 3.0 30.8 - - - +
74A SER* 3.0 28.0 + - - +
75A ARG* 5.0 7.1 - - - +
80A MET 3.2 6.8 + - - -
81A PRO* 1.3 70.6 - - - +
83A GLU* 1.3 64.3 + - - +
85A ILE* 3.1 12.1 + - + +
86A VAL* 3.0 25.7 + - + +
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Residues in contact with GLU 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A PRO* 3.2 15.8 - - - +
82A LYS* 1.3 78.3 - - - +
84A TYR* 1.3 76.1 + - - +
86A VAL* 3.5 9.5 + - - +
87A LYS* 3.0 29.7 + - + +
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Residues in contact with TYR 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A MET* 3.9 28.5 - - - -
81A PRO* 2.8 26.8 + - + +
83A GLU* 1.3 89.2 - - - +
85A ILE* 1.3 63.6 + - - +
87A LYS* 3.3 27.8 + - + +
88A LEU* 3.1 59.2 + - + +
125A PHE* 4.3 5.2 - + - -
192A TYR* 4.3 13.3 + - - -
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Residues in contact with ILE 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A LYS* 3.8 20.0 - - + -
73A PHE* 3.9 24.0 - - + +
74A SER* 3.6 37.7 - - - +
77A LEU* 5.0 1.1 - - + -
80A MET* 3.5 41.3 - - + +
81A PRO 3.1 4.4 + - - +
82A LYS* 3.1 9.4 + - - +
84A TYR* 1.3 77.1 - - - +
86A VAL* 1.3 61.8 + - - +
88A LEU* 3.4 0.9 + - - +
89A VAL* 3.0 40.6 + - + +
125A PHE* 3.9 16.8 - - + -
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Residues in contact with VAL 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A LYS* 3.7 34.3 - - + +
82A LYS* 3.0 22.1 + - + +
83A GLU* 3.6 11.0 - - - +
85A ILE* 1.3 77.6 - - - +
87A LYS* 1.3 64.2 + - - +
90A PHE* 3.0 50.3 + - + +
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Residues in contact with LYS 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A GLU* 3.0 18.1 + - + +
84A TYR* 3.4 35.3 - - + +
86A VAL* 1.3 78.7 - - - +
88A LEU* 1.3 71.1 + - + +
90A PHE* 3.9 1.6 - - - +
91A ASP* 3.3 23.1 + - - +
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Residues in contact with LEU 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A TYR* 3.1 49.7 + - + +
87A LYS* 1.3 90.1 - - + +
89A VAL* 1.3 65.1 + - - +
91A ASP* 2.9 23.5 - - + +
94A HIS* 3.1 44.4 - - + +
111A CYS* 4.6 0.4 - - - -
124A ALA* 4.3 8.1 - - + -
125A PHE* 3.6 34.1 - - + -
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Residues in contact with VAL 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A ASN* 5.2 4.7 - - - +
66A LEU* 4.1 33.7 - - + +
69A LEU* 5.5 1.6 - - + -
70A LYS* 4.6 5.2 - - + +
73A PHE* 4.1 18.8 - - + -
85A ILE* 3.0 36.5 + - + +
86A VAL* 4.0 2.7 - - - +
88A LEU* 1.3 77.1 - - - +
90A PHE* 1.3 83.2 + - + +
91A ASP 3.5 4.5 + - - +
94A HIS* 4.6 8.3 - - - +
95A GLU* 5.9 0.3 - - - -
96A SER* 4.6 6.7 + - - +
111A CYS* 4.1 19.3 - - + -
125A PHE* 4.5 2.0 - - + -
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Residues in contact with PHE 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A ASN* 3.5 26.3 + - - +
63A MET* 3.4 35.0 - - + -
66A LEU* 3.8 26.9 - - + -
67A ILE* 4.0 27.6 - - + -
70A LYS* 4.7 9.9 - - + -
86A VAL* 3.0 48.2 + - + +
87A LYS* 3.9 2.9 - - - +
89A VAL* 1.3 87.8 - - + +
91A ASP* 1.3 63.9 + - - +
92A ARG 3.9 0.5 + - - -
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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