Contacts of the helix formed by residues 66 - 74 (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 ARG 66 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44F GLU* 3.7 24.9 + - + +
45F GLU* 4.5 6.9 + - - +
62F TRP* 3.4 31.0 - - + +
63F ALA 3.5 1.9 + - - +
64F HIS 3.3 1.0 - - - -
65F ASP* 1.3 78.9 + - - +
67F PHE* 1.3 64.4 + - + +
68F GLY 3.4 0.2 - - - -
69F GLY* 3.2 13.6 + - - -
70F TYR* 3.2 46.3 + - + +
337F SER* 4.6 28.7 + - - +
340F TRP* 4.5 12.7 - - - +
344F ARG* 4.4 9.5 - - - +
1368F GLN* 4.4 17.8 - - - +
2P GLC 2.4 42.7 + - - +
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Residues in contact with PHE 67 (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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60F ILE* 3.7 16.6 - - + -
62F TRP* 3.3 33.2 - - + -
63F ALA 3.5 14.4 - - - -
64F HIS* 3.1 17.0 + - + +
66F ARG* 1.3 78.4 - - + +
68F GLY* 1.3 56.5 + - - +
70F TYR* 3.2 11.7 + + - -
71F ALA* 2.7 36.4 + - - +
76F LEU* 3.4 23.4 - - + +
97F VAL* 6.3 1.6 - - + -
104F ILE* 3.8 13.7 - - + -
105F ALA* 3.6 23.1 - - + -
263F SER* 3.4 23.3 - - - -
265F GLY* 3.6 24.2 - - - -
332F ASN* 5.7 1.1 - - + -
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Residues in contact with GLY 68 (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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64F HIS 4.2 0.6 + - - -
66F ARG 3.4 0.2 - - - -
67F PHE* 1.3 77.4 - - - +
69F GLY* 1.3 57.3 + - - +
71F ALA* 3.2 4.9 + - - +
72F GLN* 2.9 31.0 + - - +
99F TYR* 3.9 22.6 - - - -
104F ILE* 4.1 3.0 - - - +
332F ASN* 3.0 25.8 + - - +
334F PRO* 3.8 8.8 - - - +
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Residues in contact with GLY 69 (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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66F ARG 3.2 8.2 + - - -
68F GLY* 1.3 74.1 - - - +
70F TYR* 1.3 65.4 + - - +
72F GLN* 3.5 2.8 + - - +
73F SER* 3.3 26.3 + - - -
332F ASN 4.2 0.4 + - - -
333F ILE 4.4 0.6 + - - -
334F PRO* 3.7 30.3 - - - +
337F SER* 5.5 4.7 - - - -
1224F LEU* 6.3 0.4 - - - -
1385F GLU* 5.3 2.0 - - - +
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Residues in contact with TYR 70 (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* 2.6 44.4 + - - +
47F PHE* 3.9 31.7 - + + +
48F PRO* 4.0 25.6 - - + +
60F ILE* 4.2 12.0 - - + +
62F TRP* 5.3 2.2 - - + -
66F ARG* 3.2 34.0 + - + +
67F PHE* 3.2 27.9 + + - +
69F GLY* 1.3 76.2 - - - +
71F ALA* 1.3 64.2 + - - +
73F SER* 3.3 2.6 + - - -
74F GLY 3.1 5.2 + - - -
75F LEU* 3.1 31.5 + - + +
76F LEU* 3.7 18.2 - - + -
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Residues in contact with ALA 71 (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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67F PHE 2.7 20.1 + - - +
68F GLY 3.5 5.2 - - - +
70F TYR* 1.3 73.6 - - - +
72F GLN* 1.3 58.6 + - - +
74F GLY* 2.9 20.5 + - - +
75F LEU 4.7 0.4 - - - +
76F LEU* 3.8 14.9 - - + +
99F TYR* 3.8 17.5 - - + -
104F ILE* 3.7 28.3 - - + -
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Residues in contact with GLN 72 (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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68F GLY 2.9 16.5 + - - +
69F GLY 3.8 4.9 + - - +
70F TYR 3.3 0.2 - - - -
71F ALA* 1.3 76.9 - - - +
73F SER* 1.3 60.7 + - - +
74F GLY* 3.1 1.8 + - - -
99F TYR* 3.4 24.4 + - + +
334F PRO* 3.7 20.4 - - + +
335F GLN* 5.1 0.3 + - - -
1224F LEU* 3.3 26.7 + - - +
1226F ILE* 3.7 35.0 - - + +
1227F HIS* 3.8 14.4 + - + +
1385F GLU* 4.2 21.4 + - - -
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Residues in contact with SER 73 (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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69F GLY 3.3 12.0 + - - -
70F TYR* 3.7 2.2 - - - -
72F GLN* 1.3 76.7 - - - +
74F GLY* 1.3 57.2 + - - +
75F LEU* 3.2 34.6 - - - +
1385F GLU* 3.0 26.8 + - - -
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Residues in contact with GLY 74 (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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70F TYR 3.1 0.4 + - - -
71F ALA 2.9 17.9 + - - -
72F GLN 3.1 1.9 - - - -
73F SER* 1.3 78.5 - - - +
75F LEU* 1.3 62.6 + - - +
76F LEU 3.4 6.0 - - - +
268F ALA* 3.6 15.1 - - - +
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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