Contacts of the helix formed by residues 42 - 54 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12F ASN* 5.9 0.6 + - - -
40F PRO 4.0 0.2 + - - -
41F ASP* 1.3 75.3 - - + +
43F LEU* 1.3 58.8 + - - +
44F GLU* 3.5 15.5 - - - +
45F GLU* 3.2 27.6 + - + +
46F LYS* 2.8 24.4 + - - +
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Residues in contact with LEU 43 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10F TRP* 4.5 10.2 - - + -
11F ILE* 3.4 14.4 - - - +
12F ASN* 3.4 38.5 + - + +
40F PRO* 3.5 35.0 + - + +
41F ASP 2.9 4.0 + - - -
42F LYS* 1.3 74.2 - - - +
44F GLU* 1.3 67.2 + - - +
46F LYS* 4.0 6.5 - - - -
47F PHE* 2.9 33.1 + - - +
60F ILE* 4.2 20.2 - - + -
61F PHE 4.2 6.7 - - - +
62F TRP* 3.7 24.0 - - + -
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Residues in contact with GLU 44 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12F ASN* 5.1 0.7 - - - +
42F LYS* 3.9 9.5 - - - +
43F LEU* 1.3 89.7 + - - +
45F GLU* 1.3 74.0 + - + +
48F PRO* 3.1 14.4 - - - +
60F ILE* 5.4 0.2 - - - -
62F TRP* 3.3 51.1 - - + +
66F ARG* 3.7 32.2 + - + +
70F TYR* 2.6 31.1 + - - +
153F GLU* 5.4 3.8 - - - +
344F ARG* 5.5 2.6 + - - -
1368F GLN* 4.9 0.7 + - - -
2P GLC 4.8 5.1 + - - +
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Residues in contact with GLU 45 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42F LYS* 3.2 24.1 + - + +
44F GLU* 1.3 97.0 - - + +
46F LYS* 1.3 63.5 + - - +
48F PRO* 3.2 13.6 - - - +
49F GLN* 4.0 6.6 + - - +
66F ARG* 4.5 6.8 + - - +
341F TYR* 6.0 1.2 - - - -
344F ARG* 4.8 13.7 + - - -
1367F GLU* 6.5 1.1 - - + -
1368F GLN* 3.4 34.5 - - + +
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Residues in contact with LYS 46 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10F TRP* 4.2 13.9 - - + -
40F PRO* 5.2 4.3 - - + -
41F ASP 4.5 4.9 - - - +
42F LYS 2.8 16.3 + - - +
43F LEU* 3.3 10.0 + - - +
45F GLU* 1.3 75.8 - - - +
47F PHE* 1.3 65.8 + - - +
49F GLN* 3.2 8.4 + - - +
50F VAL* 3.0 29.3 + - + +
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Residues in contact with PHE 47 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10F TRP* 3.9 10.0 - - + -
43F LEU 2.9 12.2 + - - +
46F LYS* 1.3 75.9 - - - +
48F PRO* 1.3 61.6 - - + +
50F VAL* 3.3 1.2 + - - +
51F ALA* 2.7 61.9 + - + +
57F PRO* 3.8 26.2 - - + -
59F ILE 5.9 0.2 - - - -
60F ILE* 3.3 44.4 - - + -
70F TYR* 3.9 35.7 - + + +
75F LEU* 3.9 27.6 - - + -
76F LEU* 4.5 3.8 - - + -
267F ASN* 4.0 18.4 - - + -
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Residues in contact with PRO 48 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44F GLU 3.1 24.0 - - - +
45F GLU 3.2 15.7 - - - +
47F PHE* 1.3 95.2 - - + +
49F GLN* 1.3 58.0 + - - +
52F ALA* 3.2 26.0 + - - +
70F TYR* 4.0 17.3 - - + -
75F LEU* 3.6 25.8 - - + +
1368F GLN* 3.7 25.7 - - + +
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Residues in contact with GLN 49 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45F GLU 4.1 8.1 - - - +
46F LYS* 3.2 10.2 + - - +
48F PRO* 1.3 83.8 - - - +
50F VAL* 1.3 66.9 + - + +
52F ALA* 3.4 12.4 + - - +
53F THR* 3.7 11.8 + - - +
1367F GLU 4.7 10.1 - - - +
1368F GLN* 3.7 19.6 + - - +
1370F TRP* 5.5 11.7 - - + +
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Residues in contact with VAL 50 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10F TRP* 4.4 17.0 - - + -
46F LYS* 3.0 21.8 + - + +
47F PHE* 3.8 3.1 - - - +
49F GLN* 1.3 79.7 - - + +
51F ALA* 1.3 60.1 + - - +
53F THR* 2.7 27.6 + - - -
55F ASP* 3.3 16.3 + - + +
56F GLY* 3.2 36.6 - - - +
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Residues in contact with ALA 51 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47F PHE* 2.7 53.3 + - + +
50F VAL* 1.3 72.7 - - - +
52F ALA* 1.3 61.1 + - - +
54F GLY* 3.3 12.5 + - - -
55F ASP 3.3 11.8 + - - +
56F GLY* 4.9 0.6 - - - -
75F LEU* 4.0 21.0 - - + +
267F ASN* 4.0 9.6 - - - +
269F ALA* 4.7 6.1 - - - +
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Residues in contact with ALA 52 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48F PRO 3.2 20.3 + - - +
49F GLN* 3.6 7.0 - - - +
50F VAL 3.2 0.4 - - - -
51F ALA* 1.3 78.8 - - - +
53F THR* 1.3 61.3 + - + +
54F GLY* 3.4 0.5 + - - -
75F LEU* 4.4 13.4 - - + +
1368F GLN 5.4 3.4 - - - +
1369F ASN* 6.5 0.9 - - - -
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Residues in contact with THR 53 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1F LYS 5.7 1.4 + - - -
49F GLN 3.7 12.5 + - - +
50F VAL* 2.7 19.2 + - - -
52F ALA* 1.3 77.7 - - + +
54F GLY* 1.3 55.2 + - - +
55F ASP* 3.3 14.8 + - - +
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Residues in contact with GLY 54 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1F LYS 4.6 8.6 + - - -
2F ILE* 4.1 13.0 - - - +
50F VAL 3.5 0.2 + - - -
51F ALA 3.3 10.4 + - - -
52F ALA 3.2 4.4 - - - -
53F THR* 1.3 78.1 - - - +
55F ASP* 1.3 64.3 + - - +
269F ALA* 3.3 26.5 - - - +
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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