Contacts of the helix formed by residues 49 - 57 (chain F) in PDB entry 5ITZ
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 49 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19F LEU* 3.6 3.6 - - - -
40F VAL 4.9 0.7 - - - -
41F ASN* 4.4 14.8 - - + +
42F ALA 3.2 11.0 - - - +
43F THR* 3.6 17.7 - - + -
47F GLY 3.9 4.5 - - - +
48F LEU* 1.3 73.3 - - - +
50F PRO* 1.3 76.7 - - - +
51F LEU* 3.6 10.3 + - - +
52F HIS* 2.9 42.4 + - - +
53F LEU* 3.1 13.5 + - - +
72F ASP 5.1 1.0 + - - -
75F ALA* 4.0 19.6 - - + +
83F PRO* 5.0 0.3 - - - +
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Residues in contact with PRO 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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18F LEU* 3.7 24.0 - - + -
19F LEU* 3.5 20.2 - - + +
22F ALA* 3.5 23.2 - - + +
39F ASP 4.4 1.8 - - - +
40F VAL 3.4 22.9 - - - +
42F ALA* 3.1 17.7 - - + +
49F THR* 1.3 85.4 - - - +
51F LEU* 1.3 56.0 + - - +
53F LEU* 3.2 2.5 + - + +
54F ALA* 2.9 26.9 + - - +
66F LEU* 3.5 22.0 - - + -
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Residues in contact with LEU 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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40F VAL 5.1 1.0 + - - +
49F THR* 3.2 9.0 + - - +
50F PRO* 1.3 76.0 - - - +
52F HIS* 1.3 64.8 + - - +
54F ALA* 4.6 0.4 - - - -
55F ALA* 2.9 27.1 + - - +
63F VAL* 4.0 43.3 - - + +
66F LEU* 3.4 12.0 - - + +
67F LEU* 3.7 26.9 - - + -
71F ALA* 4.1 14.3 - - + +
72F ASP 3.7 9.0 - - - +
73F VAL* 3.7 20.6 - - - -
83F PRO* 3.9 14.8 - - + -
99F LEU* 4.1 10.3 - - + -
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Residues in contact with HIS 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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47F GLY 4.0 12.6 - - - -
48F LEU* 3.6 24.7 - - + -
49F THR* 2.9 39.3 + - - +
51F LEU* 1.3 77.2 - - - +
53F LEU* 1.3 59.0 + - - +
55F ALA* 3.6 2.1 - - - +
56F THR* 2.8 34.0 + - - -
75F ALA* 3.0 35.7 + - + -
76F ILE 4.0 1.8 - - - -
77F ASP 4.0 1.7 + - - -
81F SER 2.8 27.6 + - - -
83F PRO* 3.3 25.2 - - + +
86F LEU* 3.6 18.3 - - + +
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Residues in contact with LEU 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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19F LEU* 3.6 44.9 - - + +
22F ALA 4.3 2.2 - - - -
23F ARG* 3.9 46.1 - - + +
44F ASP* 5.0 5.4 - - + +
48F LEU* 4.1 29.8 - - + -
49F THR 3.1 8.7 + - - +
50F PRO* 3.8 6.3 - - + +
52F HIS* 1.3 77.4 - - - +
54F ALA* 1.3 62.9 - - - +
56F THR* 3.3 4.4 + - - +
57F TYR* 3.1 42.4 + - + +
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Residues in contact with ALA 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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22F ALA* 3.8 14.2 + - + +
50F PRO 2.9 16.8 + - - +
51F LEU 4.1 1.3 - - - +
53F LEU* 1.3 73.2 - - - +
55F ALA* 1.3 65.5 + - - +
57F TYR 3.5 0.5 + - - -
58F GLY* 3.1 3.8 + - - -
59F HIS* 2.9 33.9 + - + +
62F ILE* 3.8 26.2 - - + -
63F VAL* 3.8 18.8 - - + +
66F LEU* 4.3 3.1 - - + -
95F ILE* 3.9 1.2 - - - +
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Residues in contact with ALA 55 (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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51F LEU* 2.9 20.2 + - + +
52F HIS 3.6 4.0 - - - +
54F ALA* 1.3 79.5 - - - +
56F THR* 1.3 56.7 + - - +
63F VAL* 3.7 9.5 - - + +
83F PRO* 3.9 30.1 - - + +
86F LEU* 5.1 0.4 - - + -
87F ALA* 4.0 9.5 - - + +
92F HIS* 3.0 27.0 - - - -
95F ILE* 4.0 19.2 - - + +
99F LEU* 4.4 2.0 - - + -
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Residues in contact with THR 56 (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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403B ALA* 4.4 15.3 - - + -
404B PHE* 4.5 2.3 - - + -
52F HIS 2.8 22.0 + - - -
53F LEU* 3.7 8.7 - - - +
54F ALA 3.3 0.2 - - - -
55F ALA* 1.3 78.1 - - - +
57F TYR* 1.3 85.1 + - + +
86F LEU* 3.4 30.6 - - + +
90F ILE* 3.5 26.5 - - + +
92F HIS* 2.9 17.8 + - - -
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Residues in contact with TYR 57 (chain F).
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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402B LYS 5.2 0.9 + - - -
403B ALA* 4.8 1.9 - - - -
404B PHE* 3.7 47.6 + + - -
406B HIS* 3.3 29.5 + + - -
407B TRP* 5.4 1.3 - + - -
23F ARG* 3.7 42.3 + - + +
53F LEU* 3.1 34.4 + - + +
56F THR* 1.3 94.2 - - + +
58F GLY* 1.3 60.6 + - - +
59F HIS* 3.4 33.4 - - + +
92F HIS* 3.7 4.5 - - - -
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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