Contacts of the helix formed by residues 19 - 26 (chain B) in PDB entry 4KJQ
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 ARG 19 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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454A ALA* 4.6 10.5 - - - +
457A GLU* 3.9 27.1 + - - +
18B ARG* 1.3 79.7 - - - +
20B GLN* 1.3 62.1 + - - +
22B ILE* 3.6 34.4 + - - +
23B ARG* 3.4 26.4 + - - +
26B LEU* 5.6 5.9 - - - +
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Residues in contact with GLN 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B ARG 2.9 7.0 + - - +
19B ARG* 1.3 75.4 - - - +
21B LEU* 1.3 64.9 + - - +
23B ARG* 3.2 10.2 + - + +
24B GLN* 3.0 51.1 + - + +
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Residues in contact with LEU 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A GLU* 3.4 55.9 - - + +
119A GLN* 3.8 12.3 - - + -
208A PHE* 4.1 14.4 - - + -
209A ARG* 5.3 0.2 - - - +
449A LEU* 5.1 1.8 - - + -
453A LEU* 3.8 25.4 - - + -
18B ARG* 2.7 19.1 + - - +
20B GLN* 1.3 74.2 + - - +
22B ILE* 1.3 57.5 + - + +
24B GLN* 2.8 34.7 + - - +
25B LEU* 2.8 33.2 + - + +
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Residues in contact with ILE 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450A ALA* 4.0 22.7 - - + +
453A LEU* 3.7 48.7 - - + +
454A ALA* 3.8 10.8 - - + +
457A GLU* 4.6 4.5 - - - +
18B ARG* 3.1 23.2 + - + +
19B ARG* 3.9 37.0 - - - +
20B GLN 3.4 0.4 - - - -
21B LEU* 1.3 76.5 - - - +
23B ARG* 1.3 57.9 + - - +
25B LEU* 3.9 9.1 + - - +
26B LEU* 3.2 32.9 + - + +
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Residues in contact with ARG 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B ARG* 3.4 20.7 + - - +
20B GLN* 3.2 11.5 + - + +
21B LEU 3.1 0.6 - - - -
22B ILE* 1.3 77.0 - - - +
24B GLN* 1.3 67.2 + - + +
26B LEU* 3.7 9.3 + - - +
27B GLU* 3.3 48.1 + - - +
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Residues in contact with GLN 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208A PHE* 3.1 63.0 + - + +
20B GLN* 3.0 39.9 + - + +
21B LEU* 2.8 33.8 + - - +
23B ARG* 1.3 77.9 - - + +
25B LEU* 1.3 63.2 + - - +
26B LEU 3.2 0.2 - - - -
27B GLU* 3.0 14.9 + - - +
28B ARG 3.1 7.1 + - - -
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Residues in contact with LEU 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A GLU* 5.8 2.0 - - + +
207A GLN* 5.9 0.4 - - + -
208A PHE* 3.6 24.2 - - + -
442A LYS* 5.1 2.6 - - - +
443A PRO* 5.0 4.5 - - - +
446A SER* 3.8 50.3 - - - +
447A ALA* 5.7 0.3 - - - -
449A LEU* 3.9 33.2 - - + -
450A ALA* 4.0 14.1 - - + +
453A LEU* 4.5 4.5 - - + -
21B LEU* 2.8 36.6 + - + +
22B ILE* 4.1 6.5 - - - +
24B GLN* 1.3 72.3 - - - +
26B LEU* 1.3 62.6 + - - +
27B GLU 3.1 0.7 + - - -
28B ARG* 3.4 15.9 + - - +
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Residues in contact with LEU 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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442A LYS* 2.7 55.9 + - + +
447A ALA* 5.1 10.1 - - + +
450A ALA* 4.3 17.5 - - + -
451A ARG* 6.2 2.9 - - + -
19B ARG* 5.6 6.5 - - - +
22B ILE* 3.2 31.9 + - + +
23B ARG* 4.1 9.0 - - - +
24B GLN 3.2 0.4 - - - -
25B LEU* 1.3 77.3 - - - +
27B GLU* 1.3 64.7 + - + +
28B ARG 3.5 0.6 - - - +
30B LYS* 4.7 3.3 - - - +
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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