Contacts of the strand formed by residues 26 - 30 (chain A) in PDB entry 1QD9
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 MET 26 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A ILE 3.8 0.5 - - - +
22A ILE* 3.3 5.4 - - - +
23A VAL* 2.8 37.3 + - + +
24A ASN* 3.4 3.1 + - + +
25A ASN* 1.3 95.1 - - - +
27A PHE* 1.3 60.2 + - - +
28A TYR* 4.3 19.7 - - + +
72A VAL* 4.1 11.9 - - + -
121A ILE* 3.6 23.6 - - + -
122A ALA 3.5 22.2 - - - +
123A LEU* 4.1 4.5 - - - +
124A VAL* 4.1 3.4 - - - -
23B VAL* 4.0 20.9 - - + -
24B ASN* 3.6 24.0 - - - +
28B TYR* 4.8 5.4 - - - +
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Residues in contact with PHE 27 (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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5A VAL* 3.9 11.2 - - + -
20A GLY* 3.7 14.1 - - - -
21A ILE 3.4 9.4 - - - -
22A ILE* 4.2 1.3 - - + +
26A MET* 1.3 74.3 - - - +
28A TYR* 1.3 76.3 + - - +
29A SER* 3.7 33.4 - - - -
60A VAL* 3.8 25.1 - - + -
61A LEU* 3.7 34.3 - - + -
64A ALA* 3.4 25.1 - - + -
66A ALA* 4.7 1.8 - - + -
120A VAL* 4.3 2.0 - - + -
121A ILE* 3.3 7.3 - - - +
122A ALA* 2.8 44.7 + - + +
124A VAL* 3.8 17.0 - - + -
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Residues in contact with TYR 28 (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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20A GLY* 3.1 2.6 - - - -
21A ILE* 2.9 35.8 + - + +
23A VAL* 3.8 31.0 - - + -
26A MET* 4.3 14.7 - - + +
27A PHE* 1.3 78.6 - - - +
29A SER* 1.3 62.3 + - - +
120A VAL 3.8 3.1 - - - -
121A ILE* 3.9 33.7 - - + -
28B TYR* 4.1 8.5 + - - -
26C MET* 4.7 4.9 - - + +
28C TYR* 4.1 15.2 + - - -
72C VAL* 4.2 14.6 - - + +
73C LYS* 3.8 24.9 - - + -
101C ALA* 3.5 13.8 - - + +
121C ILE* 3.8 29.7 - - + +
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Residues in contact with SER 29 (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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19A GLN 3.7 7.9 - - - -
27A PHE* 3.7 24.0 - - - -
28A TYR* 1.3 76.0 - - - +
30A SER* 1.3 72.7 + - - +
32A GLN* 4.8 0.2 - - - -
57A LEU* 3.9 4.3 - - - +
60A VAL* 4.2 10.1 - - - -
119A GLU* 3.7 4.2 - - - +
120A VAL* 3.0 43.1 + - - +
73C LYS* 3.7 19.8 - - - -
101C ALA* 3.9 3.1 - - - +
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Residues in contact with SER 30 (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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17A TYR* 3.6 15.8 - - - -
18A SER 2.5 25.0 + - - -
19A GLN* 2.9 18.4 + - - -
29A SER* 1.3 88.3 + - - +
31A GLY* 1.3 68.1 + - - +
32A GLN* 3.1 15.6 + - - +
119A GLU* 4.3 0.4 - - - -
101C ALA* 3.4 0.9 - - - +
102C ARG 2.8 35.0 + - - +
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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