Contacts of the helix formed by residues 43 - 58 (chain B) in PDB entry 5HJS
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 SER 43 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41B GLN 3.2 4.7 + - - -
42B LEU* 1.3 74.9 - - - +
44B PRO* 1.4 75.4 - - - +
45B GLU* 3.4 15.0 + - - +
46B GLN* 3.0 38.6 + - - +
47B LEU* 2.9 22.5 + - - +
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Residues in contact with PRO 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B LEU 4.7 0.9 - - - +
43B SER* 1.4 88.1 - - - +
45B GLU* 1.3 72.3 + - - +
47B LEU* 3.4 13.4 + - + +
48B GLY* 3.0 26.2 + - - -
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Residues in contact with GLU 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B SER* 3.4 19.5 + - - +
44B PRO* 1.3 93.5 - - - +
46B GLN* 1.3 58.3 + - + +
48B GLY* 4.0 1.0 - - - -
49B MET* 3.0 28.2 + - - +
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Residues in contact with GLN 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B GLN 3.9 4.7 - - - +
42B LEU* 3.7 22.0 - - + +
43B SER* 3.0 35.8 + - - +
45B GLU* 1.3 73.1 - - + +
47B LEU* 1.4 66.0 + - - +
49B MET* 3.3 9.4 + - + +
50B ILE* 3.0 31.7 + - - +
220B THR 5.0 1.4 + - - +
223B GLU* 3.9 16.8 + - - +
224B ALA* 3.7 37.3 - - + +
227B ALA* 3.9 4.6 - - - +
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Residues in contact with LEU 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B LEU* 3.9 26.8 - - + +
43B SER 2.9 18.2 + - - +
44B PRO* 3.4 11.7 - - + +
46B GLN* 1.4 76.3 - - - +
48B GLY* 1.3 61.7 + - - +
50B ILE* 3.4 4.7 + - + +
51B GLU* 3.1 55.5 + - + +
228B TYR* 6.4 0.9 - - + -
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Residues in contact with GLY 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B PRO 3.0 16.4 + - - -
45B GLU* 4.0 1.1 - - - -
47B LEU* 1.3 73.3 - - - +
49B MET* 1.3 64.5 + - - +
51B GLU* 3.6 10.4 + - - +
52B LYS* 3.1 43.5 + - - +
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Residues in contact with MET 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B GLU 3.0 18.8 + - - +
46B GLN* 3.6 7.2 - - + +
48B GLY* 1.3 76.2 - - - +
50B ILE* 1.4 67.6 + - + +
52B LYS* 3.4 8.3 + - - +
53B LEU* 3.0 33.4 + - - +
112B PRO* 4.0 25.7 - - + +
194B LEU* 4.1 4.7 - - + -
220B THR* 4.7 5.2 - - - +
221B TYR* 3.8 33.4 - - + -
224B ALA* 3.6 31.0 - - + -
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Residues in contact with ILE 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B LEU* 3.9 18.8 - - + -
46B GLN 3.0 22.1 + - - +
47B LEU* 3.8 4.0 - - + +
49B MET* 1.4 81.8 - - + +
51B GLU* 1.3 61.3 + - + +
53B LEU* 3.1 8.9 + - - +
54B VAL* 2.9 28.4 + - + +
190B ALA* 3.7 32.5 - - + +
193B ALA* 6.1 0.4 - - + -
194B LEU* 3.9 24.9 - - + -
224B ALA* 3.9 10.8 - - + +
228B TYR* 3.8 36.8 - - + -
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Residues in contact with GLU 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B LEU* 3.1 45.1 + - + +
48B GLY* 3.9 9.5 - - - +
50B ILE* 1.3 78.0 - - + +
52B LYS* 1.3 59.2 + - + +
54B VAL* 3.2 8.4 + - - +
55B ALA* 2.9 30.1 + - - +
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Residues in contact with LYS 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B GLY* 3.1 32.7 + - - +
49B MET* 3.7 6.3 - - - +
51B GLU* 1.3 74.1 - - + +
53B LEU* 1.3 60.4 + - + +
55B ALA* 3.7 7.2 - - - +
56B ALA* 2.9 29.8 + - - +
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Residues in contact with LEU 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B MET* 3.0 36.9 + - - +
50B ILE* 3.4 7.9 - - - +
52B LYS* 1.3 77.3 - - + +
54B VAL* 1.4 60.8 + - - +
56B ALA* 3.4 3.2 + - + -
57B GLN* 3.1 19.9 + - - +
107B PHE* 3.4 18.7 - - + -
110B GLN 4.5 5.2 - - - +
111B LEU* 3.5 30.5 - - + +
112B PRO* 4.1 20.2 - - + -
193B ALA* 3.9 28.7 - - + +
194B LEU* 4.0 20.0 - - + -
197B ALA* 4.5 0.2 - - + -
221B TYR* 4.2 9.6 - - + -
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Residues in contact with VAL 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B ILE* 2.9 20.7 + - + +
51B GLU* 3.2 10.1 + - - +
53B LEU* 1.4 74.0 - - - +
55B ALA* 1.3 62.1 - - - +
57B GLN* 3.2 15.5 + - - +
58B GLN* 3.2 38.1 + - - +
189B ASP* 3.8 21.8 - - + +
190B ALA* 3.6 36.3 - - + +
193B ALA* 4.6 4.3 - - + -
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Residues in contact with ALA 55 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51B GLU 2.9 16.6 + - - +
52B LYS* 3.7 8.3 - - - +
54B VAL* 1.3 73.3 - - - +
56B ALA* 1.4 62.6 + - - +
58B GLN* 3.3 27.2 + - - +
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Residues in contact with ALA 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B LYS 2.9 18.2 + - - +
53B LEU* 3.7 8.5 - - - +
54B VAL 3.3 0.2 - - - -
55B ALA* 1.4 74.7 - - - +
57B GLN* 1.3 61.3 + - - +
58B GLN 4.2 3.8 - - - +
107B PHE* 4.2 12.2 - - + +
110B GLN* 3.7 45.1 + - + +
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Residues in contact with GLN 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B LEU 3.1 8.9 + - - +
54B VAL* 3.2 10.0 + - - +
56B ALA* 1.3 76.5 - - - +
58B GLN* 1.4 64.3 + - - +
103B GLU* 5.1 6.1 - - - +
107B PHE* 3.4 41.9 - - + +
133B VAL* 5.9 0.6 - - - +
137B GLU* 2.8 26.5 + - - -
140B ARG* 3.2 27.6 + - - +
193B ALA* 3.8 19.4 - - - +
196B ILE* 3.5 12.0 - - - +
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Residues in contact with GLN 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B VAL* 3.2 37.3 + - - +
55B ALA* 3.3 21.2 + - - +
56B ALA 4.2 3.1 - - - +
57B GLN* 1.4 79.7 - - - +
189B ASP* 3.6 17.6 + - - +
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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