Contacts of the helix formed by residues 13 - 21 (chain J) in PDB entry 2QJK
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 THR 13 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12J ARG* 1.3 78.6 - - - +
14J GLY* 1.3 75.5 + - - +
15J ILE* 3.7 26.2 - - + +
16J GLU* 3.1 27.5 + - - -
17J LYS* 3.0 24.9 + - - +
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Residues in contact with GLY 14 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12J ARG 3.8 0.4 + - - -
13J THR* 1.3 74.5 - - - +
15J ILE* 1.3 66.7 + - - +
17J LYS* 2.9 16.6 + - - +
18J TRP* 2.8 26.1 + - - +
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Residues in contact with ILE 15 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13J THR* 4.2 16.6 - - + -
14J GLY* 1.3 74.0 - - - +
16J GLU* 1.3 58.8 + - + +
18J TRP* 3.3 14.4 + - + +
19J LEU* 2.8 42.9 + - + +
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Residues in contact with GLU 16 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9J TYR* 3.2 33.5 + - - +
10J GLU 4.3 1.4 - - - +
11J PRO* 3.7 6.0 - - + +
12J ARG* 3.1 30.1 + - - +
13J THR* 3.1 31.5 + - - +
14J GLY 3.0 0.4 - - - -
15J ILE* 1.3 81.2 - - + +
17J LYS* 1.3 54.4 + - - +
19J LEU* 3.1 7.7 + - + +
20J HIS* 2.7 36.6 + - - +
26J VAL* 5.5 5.8 - - + -
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Residues in contact with LYS 17 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11J PRO* 3.5 34.5 + - + +
12J ARG* 2.8 27.5 + - - +
13J THR 3.0 13.2 + - - +
14J GLY* 2.9 11.7 + - - +
16J GLU* 1.3 74.3 - - - +
18J TRP* 1.3 57.9 + - - +
20J HIS* 4.1 1.6 - - - +
21J SER* 2.9 25.3 + - - -
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Residues in contact with TRP 18 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126G GLU* 3.8 29.8 + - + -
127G VAL* 4.5 15.0 - - + -
130G ILE* 4.7 8.5 - - + -
348G TRP* 4.6 16.4 - + - -
14J GLY 2.8 15.8 + - - +
15J ILE* 3.4 15.7 - - + +
17J LYS* 1.3 76.4 - - - +
19J LEU* 1.3 84.7 + - + +
21J SER* 2.8 18.4 + - - -
22J ARG* 2.8 66.9 + - - +
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Residues in contact with LEU 19 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127G VAL* 4.4 21.5 - - + -
15J ILE* 2.8 25.5 + - + +
16J GLU* 3.5 7.2 - - + +
18J TRP* 1.3 90.5 - - + +
20J HIS* 1.3 53.5 + - - +
22J ARG* 2.9 6.0 + - - +
23J LEU* 2.7 51.4 + - + +
25J ILE* 4.8 7.9 - - + -
26J VAL* 3.7 28.0 - - + -
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Residues in contact with HIS 20 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9J TYR* 3.4 39.6 + + + +
11J PRO* 3.7 22.4 - - + +
16J GLU 2.7 19.9 + - - +
17J LYS 4.4 2.7 - - - +
19J LEU* 1.3 75.0 - - - +
21J SER* 1.3 64.6 + - - +
22J ARG 3.1 1.0 + - - -
23J LEU 3.9 0.6 + - - -
24J PRO* 3.8 34.5 - - + +
27J ALA* 4.2 10.2 - - + +
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Residues in contact with SER 21 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124G PRO* 5.6 2.5 - - - +
218G SER* 4.6 6.1 - - - +
219G THR* 4.5 7.8 - - - +
17J LYS 2.9 15.6 + - - -
18J TRP* 2.8 18.4 + - - -
20J HIS* 1.3 80.3 - - - +
22J ARG* 1.3 68.5 + - - +
24J PRO* 5.7 0.2 - - - -
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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