Contacts of the helix formed by residues 39 - 51 (chain A) in PDB entry 1UJN
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 VAL 39 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A PHE* 5.2 0.7 - - + -
36A ASP* 2.8 22.3 + - + +
38A ARG* 1.3 103.1 - - - +
40A GLU* 1.3 63.2 + - - +
41A GLY 3.2 2.7 - - - +
42A PHE* 3.2 11.1 + - + +
43A ALA* 2.9 19.0 + - - +
91A VAL* 4.0 30.3 - - + +
118A THR* 4.1 30.1 - - + +
158A ALA* 5.1 4.9 - - + +
161A THR* 4.8 11.9 - - + -
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Residues in contact with GLU 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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35A PHE* 3.7 29.7 - - + -
36A ASP 3.7 0.8 + - - -
37A ARG* 3.3 15.9 + - - +
38A ARG 3.6 0.6 - - - -
39A VAL* 1.3 75.9 - - - +
41A GLY* 1.3 54.2 + - - +
43A ALA* 3.0 7.7 + - + +
44A GLN* 2.7 68.8 + - + +
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Residues in contact with GLY 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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39A VAL* 3.2 1.8 - - - +
40A GLU* 1.3 79.9 - - - +
42A PHE* 1.3 60.4 + - - +
44A GLN* 3.4 7.7 + - - +
45A GLU* 3.2 18.9 + - - +
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Residues in contact with PHE 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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20A VAL* 5.0 0.9 - - + -
21A LEU* 4.4 16.6 - - + -
39A VAL* 3.2 13.8 + - + +
41A GLY* 1.3 73.1 - - - +
43A ALA* 1.3 60.4 + - - +
45A GLU* 3.0 22.8 + - - +
46A VAL* 2.8 50.2 + - + +
91A VAL* 3.7 25.4 - - + -
116A PHE* 4.3 18.2 - + + -
117A PRO 5.4 0.4 - - - -
118A THR* 4.1 15.9 - - + -
155A GLU* 3.4 40.8 - - + -
157A ARG* 4.4 8.7 - - - +
158A ALA* 4.3 11.7 - - + -
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Residues in contact with ALA 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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33A LEU* 3.7 9.4 - - + +
35A PHE* 3.6 42.2 - - + -
39A VAL 2.9 13.2 + - - +
40A GLU* 3.0 9.8 + - + +
42A PHE* 1.3 78.0 - - - +
44A GLN* 1.3 57.6 + - + +
46A VAL* 3.3 6.6 + - - +
47A ALA* 2.9 28.1 + - - +
55A LEU* 4.6 2.0 - - + -
91A VAL* 4.4 12.3 - - + +
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Residues in contact with GLN 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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35A PHE* 4.7 4.6 - - - -
40A GLU* 2.7 55.1 + - + +
41A GLY* 3.7 6.7 - - - +
43A ALA* 1.3 72.8 - - - +
45A GLU* 1.3 58.2 + - - +
47A ALA* 3.4 5.4 + - - +
48A LYS* 2.9 29.8 + - - +
55A LEU* 3.5 25.8 - - - +
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Residues in contact with GLU 45 (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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21A LEU* 3.9 17.2 - - + +
41A GLY 3.2 12.0 + - - +
42A PHE* 3.0 18.9 + - + +
44A GLN* 1.3 75.4 - - - +
46A VAL* 1.3 65.3 + - - +
48A LYS* 3.4 5.4 + - - +
49A ALA* 3.0 25.3 + - + +
157A ARG* 2.7 38.9 + - - -
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Residues in contact with VAL 46 (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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21A LEU* 3.8 18.6 - - + -
33A LEU* 3.7 17.7 - - + -
42A PHE* 2.8 50.7 + - + +
43A ALA* 3.5 7.4 - - - +
45A GLU* 1.3 78.0 - - - +
47A ALA* 1.3 62.4 + - - +
49A ALA* 3.4 0.9 + - - +
50A LEU* 3.1 26.2 + - + +
89A LEU* 3.9 17.9 - - + -
91A VAL* 4.4 5.4 - - + -
116A PHE* 4.0 23.8 - - + -
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Residues in contact with ALA 47 (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 LEU* 4.1 6.3 - - + -
43A ALA 2.9 16.8 + - - +
44A GLN* 3.6 6.7 - - - +
46A VAL* 1.3 79.1 - - - +
48A LYS* 1.3 57.9 + - - +
51A GLY* 2.9 25.8 + - - -
52A VAL* 2.9 36.2 + - + +
55A LEU* 3.7 26.7 - - + -
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Residues in contact with LYS 48 (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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44A GLN 2.9 18.5 + - - +
45A GLU* 3.9 6.1 - - - +
46A VAL 3.3 0.2 - - - -
47A ALA* 1.3 77.8 - - - +
49A ALA* 1.3 63.5 + - - +
50A LEU 3.4 0.3 + - - -
51A GLY* 3.5 7.5 + - - -
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Residues in contact with ALA 49 (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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21A LEU* 4.0 23.3 - - + +
45A GLU* 3.0 19.1 + - + +
46A VAL 3.8 3.4 - - - +
47A ALA 3.3 0.2 - - - -
48A LYS* 1.3 78.3 - - - +
50A LEU* 1.3 69.1 + - + +
51A GLY 3.8 0.2 + - - -
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Residues in contact with LEU 50 (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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21A LEU* 4.3 12.3 - - + +
24A VAL* 4.0 42.2 - - + +
25A PRO 4.6 5.4 - - - +
26A PRO* 4.9 7.9 - - + -
27A LEU* 3.7 31.7 + - + +
46A VAL* 3.1 23.8 + - + +
49A ALA* 1.3 84.0 - - + +
51A GLY* 1.3 62.4 + - - +
52A VAL* 3.4 5.4 - - + -
89A LEU* 3.6 25.6 - - + -
114A LEU* 5.2 0.9 - - + -
116A PHE* 4.2 5.8 - - + -
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Residues in contact with GLY 51 (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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27A LEU* 5.4 0.4 - - - -
47A ALA 2.9 6.3 + - - -
48A LYS 3.5 6.4 + - - -
49A ALA 3.5 3.0 - - - -
50A LEU* 1.3 80.4 - - - +
52A VAL* 1.3 62.3 + - - +
53A ARG* 3.7 17.0 + - - +
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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