Contacts of the helix formed by residues 17 - 27 (chain B) in PDB entry 1JB0
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 17 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16B THR* 1.3 68.7 - - - +
18B ARG* 1.3 63.8 + - - +
19B ARG 3.0 4.3 + - - -
20B ILE* 3.1 20.0 + - + +
21B TRP* 3.4 16.0 + - - -
701B ASP* 4.0 24.2 - - + +
702B LYS 3.0 11.7 + - - +
703B PRO* 4.1 2.9 - - + -
704B VAL* 3.2 32.6 + - - +
1238B CLA 3.6 55.9 - - + +
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Residues in contact with ARG 18 (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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584A GLY* 6.2 0.9 - - - -
10B ASP* 5.4 1.2 + - - +
11B LEU* 3.6 22.6 - - - +
14B ASP* 2.8 24.0 + - - +
16B THR* 3.2 14.0 + - - +
17B THR* 1.3 79.6 + - - +
19B ARG* 1.3 62.5 + - - +
20B ILE 3.3 0.2 + - - -
21B TRP* 3.4 10.1 + - - +
22B TYR* 2.9 73.9 + - + +
704B VAL* 4.1 10.1 - - + +
707B SER* 4.9 10.3 - - - +
710B GLN* 5.3 2.7 - - - +
5002B LMG 4.8 10.3 + - - -
69C GLY 5.1 1.8 + - - -
70C ALA* 5.2 1.8 - - - +
71C GLU* 3.5 34.8 + - - +
76C MET* 4.3 15.3 - - + -
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Residues in contact with ARG 19 (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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2B THR* 3.1 31.4 + - - +
4B PHE* 2.8 43.6 + - + +
5B PRO* 4.2 3.6 - - + -
11B LEU* 3.3 36.4 - - - +
12B ALA* 4.1 1.8 - - - +
14B ASP* 3.7 24.9 + - + +
16B THR 3.2 13.4 + - - +
17B THR 3.0 0.6 - - - -
18B ARG* 1.3 78.7 - - - +
20B ILE* 1.3 65.9 + - - +
22B TYR* 3.9 1.0 - - - +
23B ALA* 2.9 31.5 + - - +
700B LYS* 5.2 0.2 - - - +
701B ASP* 2.8 29.5 + - - -
34I ILE 2.8 30.1 + - - -
35I GLU* 3.9 7.3 + - - -
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Residues in contact with ILE 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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1131A CLA 4.0 26.0 - - + -
4B PHE* 4.3 11.2 - - + -
17B THR* 3.1 13.8 + - + +
19B ARG* 1.3 89.8 - - + +
21B TRP* 1.3 67.5 + - + +
23B ALA* 3.2 2.6 + - - +
24B ILE* 3.0 43.2 + - + +
701B ASP* 4.0 21.5 - - + +
1238B CLA 3.9 32.8 - - + -
34I ILE* 4.2 20.0 - - + -
35I GLU* 4.2 1.8 - - - +
4019L BCR 4.4 5.4 - - + -
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Residues in contact with TRP 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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1131A CLA 4.3 10.8 - - + -
17B THR* 3.4 24.0 - - - -
18B ARG* 3.4 7.8 + - - +
20B ILE* 1.3 75.8 - - + +
22B TYR* 1.3 62.6 + - + +
24B ILE* 3.1 14.9 + - + +
25B ALA* 2.9 25.8 + - - +
704B VAL* 6.0 0.7 - - + -
706B LEU* 3.5 14.5 - - + +
710B GLN* 3.0 37.5 - - - +
1238B CLA 3.6 40.2 - - + +
1239B CLA 3.9 36.6 - - + -
2002B PQN 4.0 47.8 - - + -
5002B LMG 3.9 20.4 - - + +
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Residues in contact with TYR 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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11B LEU* 3.7 21.8 - - + -
18B ARG* 2.9 66.9 + - + +
21B TRP* 1.3 71.3 - - + +
23B ALA* 1.3 67.1 + - - +
25B ALA* 4.2 5.4 - - - -
26B MET* 2.9 36.3 + - - +
707B SER* 2.6 34.7 + - - -
709B VAL* 4.6 6.6 - - - +
710B GLN* 4.4 2.5 - - - -
5002B LMG 3.5 66.0 + - + -
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Residues in contact with ALA 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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4B PHE* 3.4 33.0 - - + -
5B PRO* 3.7 21.1 - - + -
7B PHE* 3.4 11.3 - - - -
11B LEU* 3.7 10.9 - - - +
19B ARG 2.9 20.8 + - - +
20B ILE 3.2 1.3 + - - +
22B TYR* 1.3 74.3 - - - +
24B ILE* 1.3 63.9 + - - +
27B ALA* 3.1 22.2 + - - +
1201B CLA 4.2 2.2 - - - +
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Residues in contact with ILE 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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4B PHE* 4.9 2.0 - - + -
20B ILE* 3.0 32.5 + - + +
21B TRP* 3.4 14.6 - - + +
23B ALA* 1.3 80.1 - - - +
25B ALA* 1.3 60.3 + - - +
26B MET 3.4 0.7 + - - -
27B ALA* 3.6 12.3 + - - +
1201B CLA 3.7 41.1 - - + +
1226B CLA 3.5 18.3 - - + +
2002B PQN 4.3 19.7 - - + -
5002B LMG 4.2 14.1 - - + -
4019L BCR 4.0 37.2 - - + -
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Residues in contact with ALA 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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21B TRP 2.9 9.1 + - - +
22B TYR 3.2 4.5 + - - +
24B ILE* 1.3 76.0 - - - +
26B MET* 1.3 59.2 + - - +
27B ALA 3.5 0.2 - - - -
29B ASP* 5.4 0.2 - - - +
1226B CLA 2.9 35.4 - - + +
5002B LMG 3.2 67.1 - - + +
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Residues in contact with MET 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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7B PHE* 4.1 14.4 - - + -
8B SER* 5.9 3.4 - - - +
11B LEU* 4.1 19.3 - - + -
22B TYR* 2.9 24.1 + - - +
23B ALA 3.9 0.2 - - - -
25B ALA* 1.3 79.1 - - - +
27B ALA* 1.3 65.7 + - - +
28B HIS 3.2 2.7 - - - -
29B ASP* 3.1 20.4 + - + +
32B SER* 4.1 25.6 - - - +
33B HIS* 3.0 17.6 + - + -
1226B CLA 4.1 0.7 - - - -
5002B LMG 4.0 58.3 - - - +
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Residues in contact with ALA 27 (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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7B PHE* 3.7 10.8 - - + -
23B ALA 3.1 15.0 + - - +
24B ILE 3.7 7.4 - - - +
25B ALA 3.5 1.4 - - - -
26B MET* 1.3 78.3 - - - +
28B HIS* 1.3 62.3 + - + +
30B PHE* 3.6 1.9 - - - -
33B HIS* 2.9 23.4 - - - -
1201B CLA 3.4 57.5 - - + +
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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