Contacts of the helix formed by residues 3 - 9 (chain Q) in PDB entry 4PJO
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 3 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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0Q SER* 3.8 22.7 - - - +
2Q LYS* 1.3 74.0 - - - +
4Q VAL* 1.3 66.1 + - - +
5Q ARG 3.1 0.4 - - - -
6Q PHE* 3.3 24.9 + - + +
7Q LEU 3.6 2.6 + - - -
80Q LEU* 4.0 23.1 - - + -
82Q ASP* 5.8 1.1 - - - +
58R ALA* 4.1 9.9 - - + +
59R PHE* 3.8 17.5 - - - +
60R ASP* 3.3 21.0 + - + +
64R ASN* 3.5 35.2 - - + +
66R VAL* 4.2 8.7 - - + +
100R PHE* 3.6 23.6 - - + -
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Residues in contact with VAL 4 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1313 U 4.1 10.5 - - + +
2Q LYS* 4.5 22.0 - - + +
3Q LEU* 1.3 78.5 - - - +
5Q ARG* 1.3 67.4 + - - +
6Q PHE 3.0 0.4 - - - -
7Q LEU* 2.8 24.2 + - + +
8Q MET* 2.9 20.1 + - + +
32Q VAL* 4.9 0.2 - - + -
33Q ASP 4.0 11.0 - - - +
34Q VAL* 3.7 28.9 - - + +
36Q MET* 3.9 40.8 - - + -
60R ASP* 4.6 1.6 + - - +
64R ASN* 4.9 1.6 - - - +
100R PHE* 4.8 1.8 - - - -
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Residues in contact with ARG 5 (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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313 G 4.3 26.8 + - - -
1223 C 4.7 5.7 + - - -
2Q LYS* 3.7 50.8 - - + +
3Q LEU 3.1 0.2 - - - -
4Q VAL* 1.3 78.6 - - - +
6Q PHE* 1.3 59.8 + - - +
8Q MET* 3.3 43.2 + - + +
9Q LYS* 3.5 18.5 + - - +
34Q VAL* 3.9 19.5 - - - +
82Q ASP* 3.9 19.1 - - + +
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Residues in contact with PHE 6 (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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3Q LEU* 3.3 21.6 + - + +
4Q VAL 3.0 1.0 + - - -
5Q ARG* 1.3 74.0 - - - +
7Q LEU* 1.3 80.1 + - + +
8Q MET 3.1 1.3 - - - -
9Q LYS* 3.0 24.7 + - - +
10Q LEU* 3.7 25.2 - - + +
70Q LEU* 4.0 17.0 - - + -
74Q LEU* 4.2 8.3 - - + -
76Q LEU* 4.0 27.6 - - + -
79Q LEU* 3.9 34.5 - - + +
80Q LEU* 3.7 24.5 - - + -
82Q ASP* 3.9 10.2 + - - +
66R VAL* 4.2 12.6 - - + -
100R PHE* 4.1 10.8 - + - -
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Residues in contact with LEU 7 (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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3Q LEU 4.4 1.3 - - - +
4Q VAL* 2.8 17.0 + - + +
6Q PHE* 1.3 79.8 - - + +
8Q MET* 1.3 56.2 + - - +
10Q LEU* 3.1 44.5 + - + +
29Q ILE* 5.2 0.2 - - - +
32Q VAL* 3.7 26.1 - - + +
36Q MET* 3.8 20.6 - - + -
68Q PHE* 3.7 40.4 - - + -
70Q LEU* 5.2 0.2 - - + -
100R PHE* 3.7 52.0 - - + -
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Residues in contact with MET 8 (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 VAL* 2.9 13.3 + - + +
5Q ARG* 3.3 69.5 - - - +
6Q PHE 3.1 0.2 - - - -
7Q LEU* 1.3 75.5 - - - +
9Q LYS* 1.3 60.0 + - + +
10Q LEU 3.5 0.5 + - - -
11Q SER* 3.6 13.2 + - - -
31Q GLY* 6.0 0.3 - - - -
32Q VAL* 3.4 29.5 + - + +
33Q ASP* 3.8 19.1 - - - +
34Q VAL* 3.4 25.6 - - + -
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Residues in contact with LYS 9 (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 ARG* 3.6 14.8 - - - +
6Q PHE* 3.0 12.1 + - - +
8Q MET* 1.3 76.9 - - - +
10Q LEU* 1.3 57.2 + - - +
11Q SER* 3.0 14.4 + - - +
13Q GLU* 5.5 0.3 - - - +
78Q THR 4.9 0.6 + - - -
79Q LEU* 2.8 55.4 + - + +
81Q VAL 3.6 10.7 + - - -
82Q ASP* 3.5 33.3 - - - +
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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