Contacts of the helix formed by residues 42 - 54 (chain H) in PDB entry 5TJ4
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 LYS 42 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12H ASN* 5.9 0.4 + - - -
40H PRO 4.0 0.2 + - - -
41H ASP* 1.3 74.5 - - + +
43H LEU* 1.3 51.4 + - - +
44H GLU* 3.4 14.6 - - - +
45H GLU* 3.2 28.5 + - + +
46H LYS* 2.8 30.8 + - - +
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Residues in contact with LEU 43 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10H TRP* 3.4 35.8 - - + -
11H ILE 3.9 15.3 - - - +
12H ASN* 4.6 7.1 + - - +
40H PRO* 3.5 38.8 - - + +
41H ASP 2.9 4.2 + - - -
42H LYS* 1.3 73.3 - - - +
44H GLU* 1.3 67.7 + - - +
46H LYS* 3.8 6.0 - - - +
47H PHE* 2.9 31.5 + - - +
60H ILE* 4.3 15.0 - - + -
61H PHE 4.1 11.0 - - - +
62H TRP* 3.9 25.4 - - + -
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Residues in contact with GLU 44 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12H ASN* 5.1 0.7 - - - +
42H LYS* 3.5 10.6 - - - +
43H LEU* 1.3 89.0 + - - +
45H GLU* 1.3 73.8 + - + +
48H PRO* 3.1 14.2 - - - +
60H ILE* 5.4 0.7 - - - -
62H TRP* 3.3 49.0 - - + +
66H ARG* 3.7 35.1 + - + +
70H TYR* 2.6 30.5 + - - +
153H GLU* 5.4 3.5 - - - +
344H ARG* 5.5 3.8 + - - -
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Residues in contact with GLU 45 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42H LYS* 3.2 25.0 + - + +
44H GLU* 1.3 95.4 - - + +
46H LYS* 1.3 65.5 + - - +
48H PRO* 3.2 16.6 - - - +
49H GLN* 4.0 7.8 + - - +
66H ARG* 4.5 4.9 + - - +
341H TYR* 3.4 38.1 + - - +
344H ARG* 4.8 6.9 + - - -
1368H GLN* 4.8 8.8 - - + +
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Residues in contact with LYS 46 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10H TRP* 4.2 14.6 - - + -
40H PRO* 5.2 4.0 - - + -
41H ASP 4.5 5.8 - - - +
42H LYS 2.8 15.9 + - - +
43H LEU* 3.3 9.2 + - - +
45H GLU* 1.3 75.4 - - - +
47H PHE* 1.3 64.8 + - - +
49H GLN* 3.2 9.4 + - - +
50H VAL* 3.1 29.3 + - + +
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Residues in contact with PHE 47 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10H TRP* 3.9 10.4 - - + -
43H LEU 2.9 15.2 + - - +
46H LYS* 1.3 72.9 - - - +
48H PRO* 1.3 63.6 - - + +
50H VAL* 3.3 1.6 + - - +
51H ALA* 2.7 60.6 + - + +
57H PRO* 3.8 29.6 - - + -
59H ILE 5.9 0.2 - - - -
60H ILE* 3.3 45.5 - - + -
70H TYR* 3.9 34.8 - + + +
75H LEU* 3.9 27.4 - - + -
76H LEU* 4.5 4.0 - - + -
267H ASN* 4.1 16.4 - - + -
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Residues in contact with PRO 48 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44H GLU 3.1 23.3 - - - +
45H GLU* 3.2 17.0 - - - +
47H PHE* 1.3 95.5 - - + +
49H GLN* 1.3 57.9 + - - +
52H ALA* 3.2 25.1 + - - +
70H TYR* 4.0 16.6 - - + -
75H LEU* 3.6 26.5 - - + +
1368H GLN* 3.7 27.9 - - + +
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Residues in contact with GLN 49 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45H GLU 4.1 8.3 - - - +
46H LYS* 3.2 11.2 + - - +
48H PRO* 1.3 83.8 - - - +
50H VAL* 1.3 67.6 + - + +
52H ALA* 3.4 12.1 + - - +
53H THR* 3.7 12.5 + - + +
1367H GLU 4.3 11.4 - - - +
1368H GLN* 3.6 22.3 + - - +
1369H ASN 5.2 5.4 - - - +
1370H TRP* 5.4 5.6 - - + -
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Residues in contact with VAL 50 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10H TRP* 4.4 17.0 - - + -
46H LYS* 3.1 21.6 + - + +
47H PHE* 3.8 2.9 - - - +
49H GLN* 1.3 78.5 - - + +
51H ALA* 1.3 60.9 + - - +
53H THR* 2.7 28.4 + - - -
55H ASP* 3.3 16.1 + - + +
56H GLY* 3.2 36.8 - - - +
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Residues in contact with ALA 51 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47H PHE* 2.7 52.5 + - + +
50H VAL* 1.3 73.7 - - - +
52H ALA* 1.3 61.4 + - - +
54H GLY* 3.3 12.4 + - - -
55H ASP 3.3 11.6 + - - +
56H GLY* 4.8 0.4 - - - -
75H LEU* 4.0 20.9 - - + +
267H ASN* 4.1 10.3 - - - +
269H ALA* 4.7 6.1 - - - +
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Residues in contact with ALA 52 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48H PRO 3.2 20.7 + - - +
49H GLN* 3.6 6.5 - - - +
50H VAL 3.2 0.4 - - - -
51H ALA* 1.3 76.7 - - - +
53H THR* 1.3 63.3 + - + +
54H GLY 3.4 0.3 + - - -
75H LEU* 4.4 14.3 - - + +
1368H GLN 5.6 1.8 - - - +
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Residues in contact with THR 53 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49H GLN* 3.9 12.6 - - + +
50H VAL* 2.7 18.9 + - - -
52H ALA* 1.3 78.4 - - + +
54H GLY* 1.3 55.7 + - - +
55H ASP* 3.3 15.5 + - - +
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Residues in contact with GLY 54 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1H LYS* 5.3 4.2 - - - +
2H ILE* 5.0 10.0 - - - +
50H VAL 3.5 0.2 + - - -
51H ALA 3.3 10.1 + - - -
52H ALA 3.2 4.8 - - - -
53H THR* 1.3 76.6 - - - +
55H ASP* 1.3 63.1 + - - +
269H ALA* 3.3 28.0 - - - +
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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