Contacts of the helix formed by residues 73 - 78 (chain Q) in PDB entry 2IAN
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 ALA 73 (chain Q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69Q GLU* 3.1 10.4 + - + +
70Q GLN 4.3 1.6 - - - +
72Q ARG* 1.3 74.0 - - - +
74Q ALA* 1.3 59.8 + - - +
75Q VAL* 3.3 3.6 - - - -
76Q ASP* 3.0 11.1 + - - +
77Q THR* 2.9 27.8 + - + +
49S PRO* 3.3 35.2 - - + -
50S SER* 3.8 25.1 - - - +
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Residues in contact with ALA 74 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26Q LEU* 3.9 7.0 - - + -
70Q GLN 3.2 10.0 + - - +
71Q ARG 3.1 15.1 + - - +
73Q ALA* 1.3 73.0 - - - +
75Q VAL* 1.3 65.0 + - - +
76Q ASP 3.0 2.0 - - - -
77Q THR* 3.3 10.3 - - - -
78Q TYR* 2.7 33.0 + - + -
79Q CYS* 3.0 9.0 + - - -
29R LEU* 3.6 33.4 - - + -
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Residues in contact with VAL 75 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24Q VAL* 3.2 43.0 - - + +
26Q LEU* 3.9 18.8 - - + +
42Q SER* 4.0 13.2 - - - +
71Q ARG 4.3 1.8 + - - +
72Q ARG 4.6 13.2 - - - +
73Q ALA* 4.9 0.9 - - - +
74Q ALA* 1.3 77.1 - - - +
76Q ASP* 1.3 62.9 + - - +
79Q CYS* 3.5 11.0 - - - +
80Q ARG* 3.2 47.9 + - - +
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Residues in contact with ASP 76 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73Q ALA* 3.0 8.9 + - - +
74Q ALA 2.8 4.4 + - - -
75Q VAL* 1.3 78.4 - - - +
77Q THR* 1.3 59.9 + - - +
78Q TYR 3.1 4.7 - - - -
80Q ARG* 2.6 50.0 + - + +
81Q HIS* 3.1 25.6 + - - +
29S ASN* 5.3 0.2 + - - -
50S SER* 4.6 14.2 + - - -
64S ALA* 4.3 20.8 + - + +
65S THR* 4.3 15.2 + - - +
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Residues in contact with THR 77 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70Q GLN* 4.8 2.1 + - - +
73Q ALA* 2.9 30.3 + - + +
74Q ALA* 3.3 9.5 - - - +
76Q ASP* 1.3 70.4 - - + +
78Q TYR* 1.3 59.6 + - - +
81Q HIS* 3.5 4.2 - - - +
29R LEU* 5.5 2.6 - - - +
29S ASN* 3.4 34.3 - - - +
30S ASN* 4.2 19.5 + - - +
49S PRO* 4.2 22.7 - - + +
64S ALA* 4.4 6.7 - - + -
91S GLN* 2.8 31.9 + - - +
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Residues in contact with TYR 78 (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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7P ILE* 6.4 0.2 - - + -
9P GLN* 2.4 44.6 + - - +
24P PHE* 3.4 7.0 - + - -
13Q PHE* 3.8 19.9 + - + -
15Q CYS* 3.8 27.4 - - - -
26Q LEU* 4.4 2.5 - - + -
74Q ALA* 2.7 25.2 + - + +
76Q ASP 3.1 0.4 - - - -
77Q THR* 1.3 76.2 - - - +
79Q CYS* 1.3 63.8 + - - +
80Q ARG 3.6 0.2 - - - -
81Q HIS* 3.8 0.6 - - - +
82Q ASN* 2.9 49.5 + - - +
27R GLY* 3.2 26.5 - - - -
28R THR 4.0 4.7 - - - -
29R LEU* 3.5 41.7 - - + -
91S GLN* 5.1 1.6 - - - +
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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
------------------------------------------------------------
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