Contacts of the helix formed by residues 33 - 43 (chain B) in PDB entry 1JIH
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 ALA 33 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B MET 3.6 0.2 + - - -
32B ASN* 1.3 74.0 - - - +
34B PHE* 1.3 65.4 + - - +
35B PHE 3.3 2.2 - - - -
36B ALA* 2.9 15.7 + - + +
37B GLN* 2.9 12.3 + - + +
61B ALA* 4.9 7.0 - - - -
62B VAL 3.5 28.7 - - - +
63B SER* 4.0 13.2 - - - -
64B TYR* 4.4 9.2 - - + +
67B ARG* 4.1 11.5 - - - +
155B ASP* 5.4 1.0 + - - -
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Residues in contact with PHE 34 (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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31B MET* 3.2 46.4 + - + +
32B ASN 3.0 3.4 + - - -
33B ALA* 1.3 74.9 - - - +
35B PHE* 1.3 69.8 + + + +
37B GLN* 3.0 11.2 + - + +
38B VAL* 2.8 56.3 + - + +
131B TYR* 3.4 21.5 - - - -
134B GLU* 3.7 3.4 - - + -
135B SER* 3.6 33.7 - - - -
154B ILE* 4.1 8.1 - - + -
155B ASP* 3.6 26.9 + - + +
258B TYR* 4.2 13.9 - + - -
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Residues in contact with PHE 35 (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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33B ALA 3.2 1.2 + - - -
34B PHE* 1.3 88.4 - + + +
36B ALA* 1.3 62.4 + - - +
38B VAL* 3.4 2.8 + - - +
39B GLU* 3.2 28.6 + - - +
53B CYS* 3.9 9.9 - - - -
60B ILE* 3.7 29.2 - - + -
61B ALA* 3.6 17.5 - - + +
128B LEU* 4.0 22.9 - - + -
131B TYR* 3.6 52.2 - + + -
154B ILE* 4.3 21.5 - - + -
155B ASP* 5.6 1.6 - - - -
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Residues in contact with ALA 36 (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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33B ALA* 2.9 10.6 + - + +
35B PHE* 1.3 77.0 - - - +
37B GLN* 1.3 60.2 + - - +
39B GLU* 3.3 2.1 + - - +
40B GLN* 2.9 30.5 + - - +
51B VAL* 3.8 19.9 - - + +
53B CYS* 4.3 5.2 - - - +
61B ALA* 3.8 16.6 - - + +
63B SER* 3.9 36.3 - - - +
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Residues in contact with GLN 37 (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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31B MET* 3.8 5.2 - - - +
32B ASN* 2.8 33.5 + - - +
33B ALA* 2.9 9.7 + - + +
34B PHE* 3.3 9.0 - - + +
36B ALA* 1.3 77.0 - - - +
38B VAL* 1.3 62.6 + - - +
40B GLN* 3.3 19.9 + - - +
41B MET* 2.9 28.3 + - - +
63B SER* 6.5 0.4 - - - -
257B GLY 4.4 2.4 + - - -
258B TYR* 3.4 24.6 - - + +
259B THR* 3.0 56.6 + - - +
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Residues in contact with VAL 38 (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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34B PHE* 2.8 47.2 + - + +
35B PHE 3.6 7.4 - - - +
36B ALA 3.2 0.2 - - - -
37B GLN* 1.3 73.6 - - - +
39B GLU* 1.3 62.0 + - - +
41B MET* 3.4 2.1 + - - +
42B ARG* 3.0 31.1 + - + +
104B TYR* 4.7 5.6 - - - +
130B PRO* 4.6 5.8 - - + +
131B TYR* 3.8 28.5 - - + -
134B GLU* 3.9 19.7 - - + -
258B TYR* 3.6 19.8 + - + +
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Residues in contact with GLU 39 (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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35B PHE 3.2 15.7 + - - +
36B ALA 3.8 4.0 - - - +
38B VAL* 1.3 75.7 - - - +
40B GLN* 1.3 62.5 + - - +
42B ARG* 2.8 39.1 + - - +
43B CYS* 3.0 30.8 + - - +
51B VAL* 4.6 3.8 - - + -
53B CYS* 4.2 12.1 - - + -
90B ILE* 3.8 30.5 - - + +
91B HIS 4.7 1.8 - - - -
104B TYR* 2.6 27.9 + - - -
131B TYR* 2.6 29.3 + - - +
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Residues in contact with GLN 40 (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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36B ALA 2.9 17.5 + - - +
37B GLN* 3.4 23.7 + - - +
39B GLU* 1.3 79.0 - - - +
41B MET* 1.3 80.7 + - - +
43B CYS 3.3 0.2 + - - -
44B GLY 3.2 4.2 + - - -
45B LEU* 2.8 65.5 + - + +
46B SER* 3.3 29.9 - - - +
47B LYS* 3.4 13.6 - - - +
51B VAL* 4.3 12.7 - - + +
257B GLY 5.2 2.4 + - - -
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Residues in contact with MET 41 (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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37B GLN* 2.9 20.1 + - + +
38B VAL 4.0 2.7 - - - +
40B GLN* 1.3 97.9 - - - +
42B ARG* 1.3 63.7 + - - +
44B GLY* 3.2 12.3 + - - +
45B LEU 4.6 4.3 - - - +
256B LEU 3.7 20.4 - - - +
257B GLY* 3.9 19.5 - - - +
258B TYR* 3.8 25.8 - - + +
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Residues in contact with ARG 42 (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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38B VAL* 3.0 20.6 + - + +
39B GLU* 2.8 32.4 + - - +
40B GLN 3.3 0.2 - - - -
41B MET* 1.3 77.4 - - - +
43B CYS* 1.3 76.4 + - - +
44B GLY 3.4 0.7 + - - -
90B ILE* 3.4 6.5 - - - +
104B TYR* 3.2 46.1 - - - +
106B ASP* 2.8 43.0 + - - -
130B PRO* 6.1 0.4 - - - -
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Residues in contact with CYS 43 (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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39B GLU 3.0 17.4 + - - +
40B GLN 3.3 0.2 + - - -
41B MET 3.2 0.4 - - - -
42B ARG* 1.3 112.6 - - - +
44B GLY* 1.3 63.4 + - - +
45B LEU* 3.3 24.9 + - + +
90B ILE* 4.0 12.6 - - + -
106B ASP* 4.4 7.9 - - - -
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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