Contacts of the helix formed by residues 32 - 44 (chain A) in PDB entry 5JRB
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 32 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30A GLN 3.6 4.6 + - - +
31A TYR* 1.3 75.8 - - - +
33A ALA* 1.3 60.3 + - - +
34A GLU* 3.6 19.7 + - - +
35A GLU* 3.3 26.6 + - - +
36A TYR* 2.8 28.9 + - - +
208J CYS* 4.2 1.8 - - - -
203K ALA 4.9 3.6 + - - -
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Residues in contact with ALA 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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32A THR* 1.3 72.7 - - - +
34A GLU* 1.3 69.7 + - - +
36A TYR* 3.4 1.8 + - - +
37A GLN* 2.9 32.2 + - - +
205J TYR* 3.5 31.2 - - + +
208J CYS* 3.5 40.8 + - + +
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Residues in contact with GLU 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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32A THR* 3.6 19.7 + - - +
33A ALA* 1.3 92.1 + - - +
35A GLU* 1.3 61.9 + - - +
37A GLN* 3.4 10.2 + - - +
38A ALA* 3.0 20.3 + - - +
205J TYR* 4.9 8.4 + - - +
203K ALA* 3.6 27.2 - - + +
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Residues in contact with GLU 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* 3.5 24.1 - - + -
32A THR* 3.3 21.7 + - - +
34A GLU* 1.3 74.9 - - - +
36A TYR* 1.3 67.9 + - - +
38A ALA* 3.3 1.7 + - - +
39A ILE* 3.0 36.6 + - + +
79A PHE 4.5 1.9 - - - +
116A LYS* 2.9 29.3 + - - -
200K VAL* 5.0 2.2 - - + -
203K ALA* 3.6 17.8 - - + +
204K ARG* 2.9 43.7 + - + +
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Residues in contact with TYR 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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31A TYR* 4.2 11.3 - - + +
32A THR 2.8 21.8 + - - +
33A ALA 3.7 5.4 - - - +
35A GLU* 1.3 73.8 - - - +
37A GLN* 1.3 65.6 + - + +
39A ILE 3.4 0.2 + - - -
40A GLN* 2.9 52.0 + - + +
201J GLU* 2.9 39.8 + - - -
204J ARG* 2.9 42.8 + - + -
205J TYR* 4.7 10.1 - + - -
208J CYS* 4.3 18.4 - - - -
80K GLY* 4.5 1.3 - - - -
81K TYR* 3.5 23.7 - + - -
82K ASN* 3.8 17.7 - - - +
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Residues in contact with GLN 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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33A ALA 2.9 16.7 + - - +
34A GLU* 3.7 6.9 - - - +
36A TYR* 1.3 86.2 - - - +
38A ALA* 1.3 64.2 + - - +
40A GLN* 3.4 1.7 + - - +
41A LYS* 3.1 25.3 + - + +
201J GLU* 5.2 6.5 - - - +
205J TYR* 3.1 43.9 + - + -
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Residues in contact with ALA 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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34A GLU 3.0 17.1 + - - +
35A GLU 4.0 2.7 - - - +
37A GLN* 1.3 77.7 - - - +
39A ILE* 1.3 57.6 + - - +
41A LYS* 3.5 5.4 + - - +
42A ALA* 2.8 30.5 + - - +
199K SER* 3.7 37.3 - - - +
200K VAL* 3.7 15.6 - - + +
203K ALA* 4.4 3.4 - - + -
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Residues in contact with ILE 39 (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* 3.7 11.7 - - + -
35A GLU* 3.0 39.9 + - + +
38A ALA* 1.3 72.5 - - - +
40A GLN* 1.3 61.6 + - - +
42A ALA* 3.7 1.5 - - - +
43A LEU* 2.8 49.3 + - + +
78A MET* 3.7 19.1 - - + +
79A PHE* 4.2 13.0 - - + -
81K TYR* 3.4 38.1 - - + +
200K VAL* 3.5 24.0 - - + -
204K ARG* 3.9 1.6 - - - +
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Residues in contact with GLN 40 (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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36A TYR* 2.9 44.9 + - + +
37A GLN* 3.8 3.8 - - - +
39A ILE* 1.3 78.6 - - - +
41A LYS* 1.3 62.0 + - - +
43A LEU* 3.6 9.2 + - - +
44A ARG* 3.4 29.9 + - - +
201J GLU* 3.8 14.0 + - - +
204J ARG* 4.7 1.0 - - - +
76K ASN* 3.3 21.7 + - - +
77K GLU* 3.4 23.8 + - - +
80K GLY* 3.4 4.0 - - - -
81K TYR* 2.9 40.2 + - + +
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Residues in contact with LYS 41 (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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37A GLN* 3.1 18.1 + - + +
38A ALA* 4.0 3.4 - - - +
40A GLN* 1.3 76.3 - - - +
42A ALA* 1.3 65.6 + - - +
44A ARG* 3.3 38.5 + - - +
45A GLN* 4.1 8.4 + - - +
199K SER* 5.8 5.8 - - - -
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Residues in contact with ALA 42 (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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38A ALA 2.8 19.6 + - - +
39A ILE 3.1 3.3 + - - +
41A LYS* 1.3 79.2 - - - +
43A LEU* 1.3 62.6 + - - +
44A ARG 3.1 1.0 + - - -
45A GLN* 3.0 32.2 + - - +
78A MET* 3.8 13.0 - - - -
161A ALA* 3.6 4.0 - - - +
197K GLU* 3.8 16.8 - - - +
199K SER* 6.4 1.1 - - - -
200K VAL* 3.8 19.5 - - + -
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Residues in contact with LEU 43 (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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39A ILE* 2.8 38.9 + - + +
40A GLN* 4.1 4.3 - - - +
41A LYS 3.3 0.4 - - - -
42A ALA* 1.3 72.2 - - - +
44A ARG* 1.3 57.5 + - - +
45A GLN 3.2 0.2 - - - -
78A MET* 3.9 17.9 - - + -
79A PHE* 4.4 2.0 - - + -
158A PHE* 3.3 31.6 - - + +
159A GLY* 4.5 2.9 - - - +
160A ASN 3.0 10.6 + - - -
161A ALA* 2.8 33.4 + - + -
162A LEU* 3.7 34.1 - - + -
81K TYR* 3.5 28.3 - - + -
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Residues in contact with ARG 44 (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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40A GLN* 3.4 34.4 + - - +
41A LYS* 3.3 29.8 + - - +
42A ALA 3.1 1.0 - - - -
43A LEU* 1.3 77.2 - - + +
45A GLN* 1.3 64.4 + - - +
46A ARG* 3.3 2.8 + - - +
160A ASN* 2.8 26.7 + - - +
196J LEU* 3.7 18.9 - - - +
201J GLU* 4.9 9.7 + - - +
77K GLU* 2.6 54.8 + - - +
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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