Contacts of the helix formed by residues 41 - 54 (chain D) in PDB entry 2IDK
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 41 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40D ARG* 1.3 73.6 - - - +
42D ALA* 1.3 64.8 + - - +
43D GLU* 3.8 7.7 + - - +
44D TYR* 3.2 21.1 + - - +
45D LYS* 3.2 17.0 + - - +
191D ASN 5.0 2.2 - - - +
192D ILE* 2.9 30.8 + - - +
193D TYR 3.1 8.3 + - - +
194D TYR 3.9 19.3 - - - -
195D LYS* 4.1 13.9 - - + +
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Residues in contact with ALA 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40D ARG 4.0 0.2 + - - -
41D THR* 1.3 73.2 - - - +
43D GLU* 1.3 62.5 + - - +
45D LYS* 3.6 12.6 + - - +
46D ALA* 3.1 25.3 + - - +
195D LYS* 5.3 2.0 - - - +
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Residues in contact with GLU 43 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41D THR* 3.2 8.3 + - - +
42D ALA* 1.3 81.3 - - - +
44D TYR* 1.3 55.9 + - - +
46D ALA* 3.5 5.3 + - - +
47D TRP* 3.0 27.9 + - - +
192D ILE* 5.2 9.5 - - - +
269D ASP 4.8 3.8 - - - +
270D PHE* 3.6 30.6 - - + +
271D LYS* 5.6 6.1 - - - +
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Residues in contact with TYR 44 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40D ARG* 3.5 33.4 - - + -
41D THR* 3.2 19.4 + - - +
43D GLU* 1.3 76.8 - - - +
45D LYS* 1.3 66.2 + - - +
47D TRP* 3.2 10.2 + + - +
48D LEU* 2.9 32.3 + - + +
70D ASP* 2.8 43.6 + - - -
73D MET* 4.6 6.5 - - + -
136D LEU* 3.2 25.4 - - + +
192D ILE 4.1 3.1 - - - +
193D TYR* 3.4 31.9 - + - +
270D PHE* 3.6 32.7 - + + -
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Residues in contact with LYS 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40D ARG* 3.7 28.0 + - + +
41D THR 3.2 13.6 + - - +
42D ALA* 3.9 9.6 - - - +
44D TYR* 1.3 76.0 - - - +
46D ALA* 1.3 59.6 + - - +
48D LEU* 4.1 0.8 - - - +
49D LEU* 2.8 44.2 + - + +
73D MET* 3.3 41.1 - - + -
195D LYS* 5.5 3.2 - - - +
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Residues in contact with ALA 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42D ALA 3.1 16.3 + - - +
43D GLU* 3.6 6.5 - - - +
45D LYS* 1.3 79.0 - - - +
47D TRP* 1.3 57.1 + - - +
49D LEU* 4.3 3.1 - - - +
50D GLY* 2.8 27.9 + - - -
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Residues in contact with TRP 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43D GLU 3.0 18.2 + - - +
44D TYR* 3.6 13.5 - + - +
46D ALA* 1.3 75.9 - - - +
48D LEU* 1.3 83.5 + - + +
50D GLY* 3.2 1.3 + - - -
51D LEU* 2.7 60.9 + - + +
136D LEU* 4.2 7.9 - - + -
171D VAL* 3.5 25.4 - - + -
193D TYR* 5.3 0.2 - + - -
267D LEU* 3.3 35.4 - - + +
270D PHE* 3.5 56.1 - + + -
285D ILE* 3.7 15.3 - - + -
287D VAL* 5.7 0.2 - - + -
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Residues in contact with LEU 48 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44D TYR* 2.9 42.9 + - + +
45D LYS* 4.1 2.7 - - - +
47D TRP* 1.3 96.4 - - + +
49D LEU* 1.3 60.9 + - - +
51D LEU* 3.2 7.0 + - + +
52D LEU* 2.8 47.2 + - + +
70D ASP* 5.0 4.3 - - + -
73D MET* 4.6 10.3 - - - -
74D LEU* 4.0 29.2 - - + -
134D ILE* 4.5 15.0 - - + -
136D LEU* 4.3 11.7 - - + -
171D VAL* 5.2 1.1 - - + -
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Residues in contact with LEU 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45D LYS* 2.8 30.0 + - + +
46D ALA* 4.3 3.1 - - - +
48D LEU* 1.3 70.5 - - - +
50D GLY* 1.3 69.1 + - - +
52D LEU* 3.3 3.0 + - - +
53D ARG* 2.8 45.5 + - - +
73D MET* 4.4 15.3 - - + -
74D LEU* 4.2 13.0 - - + -
77D GLU* 3.6 36.6 - - + +
79D PHE* 3.6 32.5 - - + -
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Residues in contact with GLY 50 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46D ALA 2.8 22.0 + - - -
47D TRP* 3.5 1.1 - - - -
49D LEU* 1.3 79.6 - - - +
51D LEU* 1.3 63.8 + - - +
53D ARG* 3.1 5.5 + - - +
54D GLN* 3.1 25.9 + - - +
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Residues in contact with LEU 51 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47D TRP* 2.7 56.2 + - + +
48D LEU* 3.6 8.3 - - + +
50D GLY* 1.3 72.8 - - - +
52D LEU* 1.3 62.6 + - + +
53D ARG 3.5 0.2 + - - -
54D GLN* 3.6 14.8 + - - +
55D HIS* 3.1 44.2 + - + -
169D LEU* 4.1 7.5 - - + +
171D VAL* 3.5 30.7 - - + -
267D LEU* 5.7 1.3 - - + -
287D VAL* 4.3 20.9 - - + -
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Residues in contact with LEU 52 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48D LEU* 2.8 36.6 + - + +
49D LEU* 4.1 1.3 - - - +
51D LEU* 1.3 73.7 - - + +
53D ARG* 1.3 63.5 + - - +
55D HIS 3.7 0.7 + - - -
56D GLY 3.5 1.0 + - - -
57D CYS* 3.2 35.3 + - + +
60D VAL* 4.0 9.6 - - + -
74D LEU* 3.8 39.9 - - + -
79D PHE* 3.8 27.4 - - + -
132D ALA* 3.8 28.7 - - + -
134D ILE* 4.8 7.4 - - + -
169D LEU* 4.5 6.7 - - + -
171D VAL* 5.1 3.8 - - + -
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Residues in contact with ARG 53 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49D LEU* 2.8 46.5 + - - +
50D GLY* 3.8 4.3 - - - +
52D LEU* 1.3 72.8 - - - +
54D GLN* 1.3 54.7 + - - +
55D HIS 2.5 18.6 + - - -
56D GLY* 2.6 17.1 + - - +
77D GLU* 3.5 42.2 + - - -
79D PHE* 4.0 16.6 - - - -
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Residues in contact with GLN 54 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50D GLY 3.1 11.4 + - - +
51D LEU* 3.8 19.1 - - - +
52D LEU 3.5 0.4 - - - -
53D ARG* 1.3 76.3 - - - +
55D HIS* 1.3 84.2 + - + +
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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