Contacts of the helix formed by residues 30 - 38 (chain A) in PDB entry 1JX6
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 GLY 30 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28A TYR 3.9 0.8 + - - -
29A TRP* 1.3 76.9 - - - +
31A TYR* 1.3 61.0 + - - +
32A GLN 3.5 2.0 - - - -
33A GLU* 2.8 25.4 + - - -
34A PHE* 2.8 26.5 + - - +
162A THR* 4.7 4.0 - - - -
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Residues in contact with TYR 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A TRP 3.7 1.0 + - - -
30A GLY* 1.3 72.7 - - - +
32A GLN* 1.3 88.9 + - + +
34A PHE* 3.3 5.0 + - - +
35A LEU* 3.2 38.5 + - + +
45A THR* 3.3 21.7 - - - +
49A SER* 5.6 0.3 + - - -
161A THR* 3.3 27.5 + - - +
162A THR* 4.4 3.8 - - - +
179A ASP* 3.6 28.8 + - + +
335A VAL* 3.6 33.0 - - + -
337A SER* 3.1 43.5 + - - -
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Residues in contact with GLN 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A GLY 3.5 0.2 - - - -
31A TYR* 1.3 103.9 - - + +
33A GLU* 1.3 60.1 + - - +
35A LEU* 3.2 1.8 + - - +
36A ASP* 2.8 40.0 + - - +
42A ARG* 2.9 38.9 + - - +
185A ARG* 5.8 5.6 - - - +
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Residues in contact with GLU 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A TYR 4.3 0.7 - - - +
29A TRP* 3.7 15.9 - - + -
30A GLY* 2.8 30.2 + - - +
31A TYR 3.2 0.6 - - - -
32A GLN* 1.3 79.5 - - - +
34A PHE* 1.3 56.4 + - - +
36A ASP* 3.4 5.6 + - - +
37A GLU* 3.0 27.9 + - + +
165A ARG* 3.0 29.6 + - - -
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Residues in contact with PHE 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A TRP* 3.9 24.5 - + + -
30A GLY 2.8 18.4 + - - +
31A TYR 3.5 4.0 - - - +
32A GLN 3.2 0.2 - - - -
33A GLU* 1.3 78.0 - - - +
35A LEU* 1.3 62.1 + - + +
37A GLU 3.2 0.9 + - - -
38A PHE* 3.0 59.0 + + - +
41A GLN* 3.7 31.0 - - + -
163A PRO* 3.7 29.6 - - + -
168A ASP* 5.3 1.6 - - - -
171A GLN* 5.0 8.7 - - + -
334A THR* 3.8 32.5 - - + -
335A VAL* 3.9 23.8 - - + -
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Residues in contact with LEU 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A TYR* 3.2 49.4 + - + +
32A GLN* 3.2 3.1 + - - +
34A PHE* 1.3 83.5 - - + +
36A ASP* 1.3 60.0 + - - +
38A PHE 3.2 20.3 - - - +
39A PRO* 3.8 2.3 - - - +
41A GLN* 3.8 15.7 - - + +
42A ARG* 3.5 53.7 + - + +
45A THR* 3.5 28.3 - - + +
46A ASN* 6.0 0.7 - - - +
335A VAL* 3.9 15.7 - - + -
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Residues in contact with ASP 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A GLN* 2.8 23.2 + - - +
33A GLU* 3.9 5.6 - - - +
35A LEU* 1.3 75.1 - - - +
37A GLU* 1.3 65.7 + - - +
38A PHE 3.5 0.2 + - - -
39A PRO* 4.1 8.5 - - - +
42A ARG* 2.6 30.5 + - - +
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Residues in contact with GLU 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A TRP* 3.5 36.0 - - + -
33A GLU* 3.0 18.2 + - + +
34A PHE 3.2 4.5 + - - +
36A ASP* 1.3 79.2 - - - +
38A PHE* 1.3 75.2 + - + +
39A PRO* 3.4 7.7 - - - +
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Residues in contact with PHE 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A TRP* 4.1 18.2 - + - -
34A PHE* 3.0 54.1 + + - +
35A LEU 3.2 10.8 - - - +
37A GLU* 1.3 102.4 - - + +
39A PRO* 1.3 57.6 - - - +
40A GLU* 3.2 3.4 - - + +
41A GLN* 2.8 49.0 + - + +
42A ARG 3.2 0.5 + - - -
168A ASP* 5.2 7.0 - - + -
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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