Contacts of the helix formed by residues 39 - 48 (chain A) in PDB entry 2F5O
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 ASP 39 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37A PRO* 3.2 7.2 - - + +
38A ARG* 1.3 76.8 - - - +
40A SER* 1.3 65.2 + - - +
41A GLU* 2.7 46.2 + - - +
42A ALA* 3.0 27.9 + - + +
43A PHE 3.2 8.3 + - - -
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Residues in contact with SER 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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28A ILE* 3.6 33.0 - - - +
31A PRO* 4.2 20.8 - - - +
34A ILE* 4.1 26.2 - - - -
38A ARG 3.4 5.1 + - - -
39A ASP* 1.3 74.9 + - - +
41A GLU* 1.3 67.3 + - - +
43A PHE* 3.4 2.5 + - - +
44A ALA* 3.1 18.0 + - - +
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Residues in contact with GLU 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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39A ASP* 2.7 28.1 + - - +
40A SER* 1.3 77.7 + - - +
42A ALA* 1.3 54.7 + - - +
44A ALA* 3.6 5.7 + - - +
45A ALA* 3.0 28.8 + - - +
301A GOL 4.4 2.4 + - - -
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Residues in contact with ALA 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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37A PRO* 3.9 18.2 - - + -
39A ASP* 3.0 21.9 + - + +
41A GLU* 1.3 74.9 - - - +
43A PHE* 1.3 65.4 + - - +
45A ALA* 3.9 6.5 - - - +
46A ARG* 3.0 27.9 + - - +
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Residues in contact with PHE 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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26A VAL* 4.0 17.5 - - + -
28A ILE* 4.0 9.0 - - + -
34A ILE* 3.7 43.3 - - + -
36A HIS 3.7 11.2 - - - -
37A PRO* 3.5 13.1 - - + +
39A ASP 3.2 4.6 + - - +
40A SER 3.5 8.1 - - - +
42A ALA* 1.3 81.0 - - - +
44A ALA* 1.3 63.1 + - - +
46A ARG* 3.3 6.9 - - - +
47A MET* 3.0 28.4 - - + +
71A LEU* 4.5 2.2 - - + -
96A VAL* 4.8 1.6 - - + -
98A PHE* 4.1 16.4 - + - -
117A MET* 3.9 40.8 - - + -
119A VAL* 3.1 35.9 - - + -
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Residues in contact with ALA 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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26A VAL* 3.8 35.4 - - + +
28A ILE* 4.1 7.4 - - + -
40A SER 3.1 16.3 + - - +
41A GLU* 3.8 5.6 - - - +
43A PHE* 1.3 77.2 - - - +
45A ALA* 1.3 64.1 + - - +
47A MET* 3.3 9.2 + - - +
48A ILE* 3.2 20.4 + - - +
301A GOL 3.4 17.7 - - - +
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Residues in contact with ALA 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 GLU 3.0 19.0 + - - +
42A ALA* 3.9 6.7 - - - +
44A ALA* 1.3 78.4 - - - +
46A ARG* 1.3 63.1 + - - +
47A MET 3.3 0.5 + - - -
48A ILE* 3.4 16.3 + - - +
301A GOL 3.6 30.3 + - - +
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Residues in contact with ARG 46 (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 HIS* 4.4 8.7 - - - -
37A PRO* 4.1 27.7 - - - +
42A ALA 3.0 16.8 + - - +
43A PHE 3.3 11.9 - - - +
45A ALA* 1.3 77.6 - - - +
47A MET* 1.3 64.0 + - + +
48A ILE 3.6 3.3 + - - +
50A GLN* 2.8 25.1 - - - +
68A ARG* 3.4 23.1 - - - +
69A ASP* 3.0 37.7 + - - +
119A VAL* 3.7 23.0 + - + +
120A TYR* 4.1 1.8 - - - +
121A ALA* 3.9 13.7 - - - +
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Residues in contact with MET 47 (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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23A ILE* 3.6 20.4 - - + +
26A VAL* 3.7 24.2 - - + -
43A PHE* 3.0 29.8 - - + +
44A ALA 3.3 1.3 + - - +
45A ALA 3.3 0.6 - - - -
46A ARG* 1.3 77.3 - - + +
48A ILE* 1.3 66.0 + - - +
49A GLY 3.3 0.5 + - - -
50A GLN* 3.2 32.9 + - - +
66A LEU* 4.3 19.3 - - + -
69A ASP* 4.2 8.7 - - + +
71A LEU* 4.5 7.2 - - + -
98A PHE* 4.5 16.2 - - - -
119A VAL* 3.8 39.0 - - + -
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Residues in contact with ILE 48 (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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23A ILE* 3.8 5.2 - - + +
24A GLU* 3.6 15.3 - - + +
25A ASP* 3.3 38.4 - - - +
26A VAL* 3.7 10.8 - - + +
44A ALA 3.2 18.8 - - - +
45A ALA* 3.6 15.9 - - - +
46A ARG 3.3 6.5 - - - +
47A MET* 1.3 78.5 - - - +
49A GLY* 1.3 64.8 + - - +
50A GLN* 3.5 2.1 + - - +
301A GOL 4.2 18.2 - - - +
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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