Contacts of the strand formed by residues 27 - 33 (chain Q) in PDB entry 3K9Q
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 LEU 27 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2Q ALA* 4.2 0.4 - - - -
3Q VAL* 3.7 33.2 - - + -
5Q VAL* 3.9 13.0 - - + -
21Q ILE* 3.5 28.3 - - + +
24Q VAL* 3.6 32.8 - - + +
25Q GLU 3.3 3.0 - - - +
26Q GLY* 1.3 81.0 + - - +
28Q GLU* 1.3 66.1 + - - +
325Q VAL* 4.1 14.6 - - + -
328Q LEU* 4.0 28.0 - - + -
329Q ALA* 4.2 18.6 - - + -
332Q ALA* 4.8 1.3 - - + -
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Residues in contact with GLU 28 (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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1Q MET* 5.4 7.1 - - - +
2Q ALA* 4.0 18.8 + - + +
3Q VAL 3.0 11.1 + - - +
4Q LYS* 3.8 2.3 - - + -
5Q VAL* 2.9 27.3 + - - +
21Q ILE* 4.4 1.3 - - - -
27Q LEU* 1.3 78.2 - - - +
29Q VAL* 1.3 64.7 + - - +
30Q VAL* 3.5 18.4 + - + +
70Q LYS* 4.3 40.1 + - - +
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Residues in contact with VAL 29 (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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5Q VAL* 3.3 10.8 - - + +
7Q ILE* 3.9 15.5 - - + -
18Q PHE* 3.7 38.3 - - + -
21Q ILE* 3.7 38.8 - - + +
22Q GLN* 4.9 2.5 + - - +
28Q GLU* 1.3 72.5 - - - +
30Q VAL* 1.3 59.9 + - - +
31Q ALA 3.4 24.5 - - - +
32Q VAL* 4.0 9.0 - - + -
71Q GLU 4.7 1.7 - - - +
72Q VAL* 3.8 16.0 - - + +
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Residues in contact with VAL 30 (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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4Q LYS* 4.2 26.9 - - + -
5Q VAL 2.9 10.4 + - - +
28Q GLU* 4.2 25.1 - - + +
29Q VAL* 1.3 76.6 - - - +
31Q ALA* 1.3 63.4 + - + +
71Q GLU 4.2 8.3 - - - +
72Q VAL* 3.7 4.5 - - - -
73Q LYS* 2.9 28.1 + - - +
88Q LEU* 4.5 12.0 - - + +
90Q ILE* 3.6 29.2 - - + -
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Residues in contact with ALA 31 (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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5Q VAL 3.7 1.0 + - - -
6Q ALA* 3.2 9.0 - - + -
7Q ILE 3.0 23.0 + - - -
29Q VAL* 3.4 5.2 - - - +
30Q VAL* 1.3 84.5 - - + +
32Q VAL* 1.3 67.3 + - - +
72Q VAL* 4.2 0.9 - - - -
73Q LYS 3.0 10.5 - - - +
75Q PHE* 4.2 3.6 - - + -
85Q TRP* 3.8 18.8 - - + -
88Q LEU* 3.6 28.3 - - + -
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Residues in contact with VAL 32 (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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7Q ILE* 3.4 11.2 - - + +
10Q PHE* 3.6 54.3 - - + -
18Q PHE* 4.7 0.7 - - + -
29Q VAL* 4.0 10.8 - - + -
31Q ALA* 1.3 81.3 - - - +
33Q ASN* 1.3 65.1 + - - +
41Q LEU* 4.1 20.9 - - + -
65Q PHE* 4.5 5.4 - - + -
72Q VAL* 4.0 18.6 - - + -
73Q LYS 2.9 4.8 + - - +
74Q SER* 3.1 4.8 - - - -
75Q PHE* 2.9 25.7 + - - -
85Q TRP* 5.2 0.9 - - - -
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Residues in contact with ASN 33 (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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0Q NAD 3.2 14.8 + - - -
7Q ILE 2.9 8.4 + - - +
8Q ASN* 2.9 26.3 + - - +
9Q GLY* 2.9 26.5 + - - -
10Q PHE 3.8 2.6 + - - -
32Q VAL* 1.3 77.1 - - - +
34Q ASP* 1.3 63.6 + - - +
75Q PHE* 3.0 22.1 - - + +
77Q GLU 2.8 47.7 + - - -
83Q LEU* 3.4 24.0 - - + +
85Q TRP* 4.4 5.8 - - + -
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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