Contacts of the helix formed by residues 36 - 45 (chain A) in PDB entry 1FBA
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 GLY 36 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A SER* 1.3 71.2 - - - +
37A PRO* 1.3 65.8 - - - +
39A MET* 3.8 0.9 - - - +
40A GLY 2.9 23.0 + - - -
50A ASN* 2.9 17.0 + - - +
55A ARG* 4.1 27.8 - - - -
79A PHE* 4.1 11.2 - - - -
81A GLU* 5.5 0.4 - - - -
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Residues in contact with PRO 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A SER* 3.6 12.8 - - - +
36A GLY* 1.3 87.3 - - - +
38A THR* 1.3 66.3 + - - +
40A GLY* 3.2 9.4 + - - -
41A LYS* 3.2 20.7 + - - +
50A ASN* 4.4 4.5 - - - +
79A PHE* 6.0 0.2 - - + -
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Residues in contact with THR 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A GLU* 4.0 19.3 - - + -
35A SER* 3.2 20.5 + - - -
37A PRO* 1.3 73.3 - - - +
39A MET* 1.3 67.2 + - - +
40A GLY 2.9 1.1 - - - -
41A LYS* 3.0 23.5 + - + +
42A ARG* 3.3 44.1 + - - +
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Residues in contact with MET 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A GLU* 4.0 21.9 - - + +
35A SER 2.8 16.9 + - - +
38A THR* 1.3 77.9 - - - +
40A GLY* 1.3 56.6 + - - +
42A ARG* 3.2 26.0 + - + -
43A LEU* 3.0 44.1 + - + +
50A ASN* 4.6 0.2 - - - -
55A ARG* 3.8 35.2 - - + -
58A TYR* 4.1 24.2 - - + -
59A ARG* 3.8 30.5 - - - +
306A GLN* 5.7 0.4 - - - +
310A LEU* 4.6 5.8 - - + -
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Residues in contact with GLY 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A GLY 2.9 9.7 + - - -
37A PRO 3.4 4.9 - - - -
38A THR 2.9 0.8 - - - -
39A MET* 1.3 78.1 - - - +
41A LYS* 1.3 56.1 + - - +
43A LEU* 3.9 2.5 - - - +
44A GLN* 3.1 29.3 + - - +
48A VAL 4.8 0.3 - - - +
50A ASN* 3.2 40.3 - - - +
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Residues in contact with LYS 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A PRO 3.2 16.8 - - - +
38A THR* 3.0 12.9 + - + +
40A GLY* 1.3 76.2 - - - +
42A ARG* 1.3 75.3 + - - +
44A GLN* 3.6 13.0 + - - +
45A ASP* 3.2 30.2 + - - +
358A VAL* 5.3 10.3 - - - +
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Residues in contact with ARG 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A GLU* 5.0 9.6 + - + +
38A THR* 3.4 39.7 + - + +
39A MET* 3.2 26.3 + - + -
41A LYS* 1.3 89.1 - - - +
43A LEU* 1.3 65.3 + - - +
45A ASP* 3.4 21.7 + - - +
46A ILE* 3.8 11.1 + - - +
303A ARG* 3.3 61.6 - - - +
310A LEU* 4.1 22.2 - - + +
358A VAL* 5.1 8.6 - - - +
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Residues in contact with LEU 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A MET* 3.0 29.9 + - + +
40A GLY* 3.9 4.0 - - - +
42A ARG* 1.3 72.5 - - - +
44A GLN* 1.3 56.1 + - - +
45A ASP 3.0 1.6 - - - -
46A ILE* 2.8 28.2 + - + +
48A VAL* 2.9 37.5 + - + +
49A GLU 4.1 16.8 - - - +
50A ASN* 4.3 6.3 - - - +
54A ASN* 4.3 10.5 - - + -
55A ARG* 4.0 28.7 - - + +
58A TYR* 4.6 5.4 - - + -
310A LEU* 4.4 11.2 - - + -
313A TRP* 3.8 30.5 - - + -
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Residues in contact with GLN 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A GLY 3.1 18.7 + - - +
41A LYS* 3.7 14.0 + - - +
43A LEU* 1.3 77.2 - - - +
45A ASP* 1.3 75.5 + - - +
47A GLY* 2.9 19.8 + - - -
48A VAL 3.2 12.7 + - - +
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Residues in contact with ASP 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A LYS* 3.2 16.4 + - - +
42A ARG* 3.4 17.8 - - - +
44A GLN* 1.3 96.1 + - - +
46A ILE* 1.3 62.6 + - + +
47A GLY 3.2 1.8 + - - -
303A ARG* 4.9 10.9 + - - -
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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