Contacts of the helix formed by residues 34 - 45 (chain A) in PDB entry 4DKE
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 GLU 34 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A CYS* 1.3 86.4 + - + +
36A THR* 3.1 30.4 + - - +
37A VAL* 3.1 22.9 + - - +
38A THR* 3.3 18.2 + - - +
176A TYR* 5.5 7.6 - - + -
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Residues in contact with CYS 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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34A GLU* 1.3 90.5 - - + +
36A THR* 1.3 61.6 + - - +
38A THR* 3.3 3.9 + - - -
39A GLY* 2.9 21.7 + - - -
176A TYR* 5.5 0.9 - - - -
179A CYS 3.1 11.0 - - - -
180A CYS* 2.0 61.5 - - + -
183A SER* 3.9 19.7 - - - +
185A VAL* 4.1 6.0 - - + +
188A TRP* 3.4 12.4 + - + -
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Residues in contact with THR 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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34A GLU* 3.5 35.7 + - - +
35A CYS* 1.3 80.4 - - - +
37A VAL* 1.3 76.8 + - + +
39A GLY* 3.7 4.5 + - - -
40A PHE* 3.3 27.3 + - - -
185A VAL* 3.8 22.1 - - - +
187A ASN* 5.5 0.5 + - - -
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Residues in contact with VAL 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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34A GLU 3.1 15.8 + - - +
36A THR* 1.3 86.7 - - + +
38A THR* 1.3 66.0 + - + +
39A GLY 3.1 1.6 - - - -
40A PHE* 3.1 27.4 + - + +
41A LEU* 3.8 5.8 + - + +
125A LEU* 4.7 3.4 - - + +
128A ASN* 4.5 11.0 - - + -
129A VAL* 3.3 40.2 - - + +
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Residues in contact with THR 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 3.3 11.6 + - - +
35A CYS* 3.3 12.1 + - - -
37A VAL* 1.3 72.5 - - + +
39A GLY* 1.3 68.7 + - - +
41A LEU* 2.9 19.0 + - - +
42A ARG* 3.0 10.6 + - - +
94A TRP* 5.1 1.8 - - + -
129A VAL* 4.2 25.4 - - + -
172A MET* 3.8 13.5 - - - +
176A TYR* 3.9 36.6 - - + -
180A CYS* 4.5 0.2 - - - -
188A TRP* 3.4 23.2 + - - -
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Residues in contact with GLY 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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35A CYS 2.9 16.1 + - - -
36A THR 4.0 2.5 - - - -
37A VAL 3.1 0.6 - - - -
38A THR* 1.3 75.9 + - - +
40A PHE* 1.3 56.5 + - - +
42A ARG* 2.8 27.8 + - - +
43A ASP 3.0 5.4 + - - -
185A VAL* 4.6 0.7 - - - -
187A ASN* 3.7 21.6 + - - -
188A TRP* 3.2 23.1 - - - -
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Residues in contact with PHE 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 THR* 3.3 32.7 + - - -
37A VAL* 3.1 14.7 + - - +
39A GLY* 1.3 73.8 - - - +
41A LEU* 1.3 57.7 + - - +
43A ASP* 3.0 13.2 + - + +
44A LYS* 2.8 27.4 + - - +
125A LEU* 4.2 24.9 - - + +
187A ASN* 4.2 9.6 - - - +
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Residues in contact with LEU 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 VAL* 3.9 14.4 - - + +
38A THR* 2.9 9.6 + - - +
40A PHE* 1.3 73.2 - - - +
42A ARG* 1.3 57.5 + - - +
44A LYS* 2.9 6.0 + - + +
45A LEU* 2.6 57.6 + - + +
94A TRP* 5.4 1.6 - - + -
122A VAL* 4.1 9.2 - - + +
125A LEU* 3.0 52.9 - - + +
126A LEU* 4.0 26.5 - - + +
129A VAL* 4.4 8.5 - - + -
172A MET* 3.8 16.6 - - - -
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Residues in contact with ARG 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 THR 3.0 7.5 + - - +
39A GLY* 2.8 19.4 + - - +
41A LEU* 1.3 72.5 - - - +
43A ASP* 1.3 60.2 + - - +
46A GLN* 3.5 15.8 + - - +
169A PHE* 3.7 24.5 - - + -
172A MET* 3.6 14.2 - - + +
173A GLU* 2.7 36.8 + - - +
187A ASN* 2.9 28.9 + - + +
188A TRP* 3.3 42.2 - - + +
190A ASP* 3.9 16.4 + - - -
191A CYS* 3.3 29.8 - - - +
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Residues in contact with ASP 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 GLY 3.0 9.4 + - - +
40A PHE* 3.4 15.9 - - + +
41A LEU 3.0 0.8 - - - -
42A ARG* 1.3 75.7 - - - +
44A LYS* 1.3 68.4 + - - +
46A GLN* 3.2 42.2 + - - +
187A ASN* 4.2 18.5 - - - +
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Residues in contact with LYS 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 PHE 2.8 17.9 + - - +
41A LEU* 2.9 4.7 + - + +
43A ASP* 1.3 77.9 + - - +
45A LEU* 1.3 60.0 + - + +
46A GLN 3.3 2.9 + - - -
49A SER* 3.7 10.0 + - - -
53A TYR* 5.2 4.8 + - - -
118A TYR* 2.8 48.3 + - + -
121A GLU* 3.5 39.9 + - + -
122A VAL* 4.5 10.8 - - + +
125A LEU* 4.0 25.1 - - + -
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Residues in contact with LEU 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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41A LEU* 2.6 46.9 + - + +
42A ARG 3.8 3.6 - - - -
44A LYS* 1.3 74.6 - - + +
46A GLN* 1.3 53.3 + - - +
50A ARG* 2.6 47.1 + - - -
118A TYR* 3.9 14.4 - - - +
122A VAL* 4.6 13.0 - - + -
165A LEU* 3.9 30.3 - - + +
168A CYS* 4.0 27.4 - - + -
169A PHE* 3.7 21.1 - - + +
172A MET* 4.9 4.9 - - + -
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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