Contacts of the helix formed by residues 45 - 56 (chain D) in PDB entry 5FFO
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 PRO 45 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136B LYS* 5.6 5.8 - - - +
340C TYR* 4.3 10.8 - - - +
345C PRO* 5.8 4.7 - - + -
43D PRO* 4.1 6.3 - - + +
44D LEU* 1.3 86.5 - - + +
46D GLU* 1.3 59.2 + - - +
47D ALA* 3.0 13.5 - - + +
48D VAL* 3.2 51.5 - - + +
49D LEU* 3.4 7.0 + - - +
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Residues in contact with GLU 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132B LEU* 5.4 6.9 - - + +
136B LYS* 5.6 8.4 - - - +
185B TYR* 3.0 25.3 + - - -
213B GLN 5.5 2.0 - - - -
214B LYS* 3.4 39.5 - - - +
215B ILE* 4.0 12.4 - - - +
44D LEU 3.5 3.5 + - - +
45D PRO* 1.3 72.2 - - - +
47D ALA* 1.3 57.9 + - - +
48D VAL 3.4 0.2 - - - -
49D LEU* 3.7 23.4 - - + +
50D ALA* 3.2 24.8 + - - +
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Residues in contact with ALA 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45D PRO* 3.0 11.5 - - + +
46D GLU* 1.3 77.6 - - - +
48D VAL* 1.3 63.6 + - + +
50D ALA* 3.6 7.4 + - - +
51D LEU* 3.5 21.0 + - - +
81D ARG* 5.0 5.0 + - - +
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Residues in contact with VAL 48 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338C VAL* 5.2 12.6 - - + +
340C TYR* 6.0 0.4 - - - +
345C PRO* 5.1 17.3 - - + +
347C VAL* 4.1 24.6 - - + +
44D LEU* 5.0 5.6 - - + -
45D PRO* 3.2 40.8 + - + +
47D ALA* 1.3 77.4 - - + +
49D LEU* 1.3 67.3 + - + +
50D ALA 3.3 0.4 - - - -
51D LEU* 3.4 14.0 + - + +
52D TYR* 3.1 26.2 + - - +
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Residues in contact with LEU 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284C GLU* 5.2 14.4 - - + -
44D LEU* 4.6 14.8 - - + +
45D PRO 3.4 14.5 + - - +
46D GLU* 3.8 26.2 - - + +
47D ALA 3.3 0.6 - - - -
48D VAL* 1.3 86.4 - - + +
50D ALA* 1.3 56.7 + - - +
52D TYR* 3.9 10.8 - - + +
53D ASN* 3.0 43.5 + - - +
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Residues in contact with ALA 50 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46D GLU 3.2 16.9 + - - +
47D ALA* 3.8 5.4 - - - +
48D VAL 3.3 0.4 - - - -
49D LEU* 1.3 75.5 - - - +
51D LEU* 1.3 60.2 + - - +
53D ASN* 4.0 7.5 - - - +
54D SER* 3.0 28.2 + - - -
81D ARG* 3.3 37.0 + - - +
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Residues in contact with LEU 51 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347C VAL* 4.4 20.6 - - + -
47D ALA 3.5 11.8 + - - +
48D VAL* 3.4 14.7 + - + +
49D LEU 3.3 0.4 - - - -
50D ALA* 1.3 78.4 - - - +
52D TYR* 1.3 60.2 + - - +
54D SER* 2.8 20.5 + - - +
55D THR* 3.3 17.0 + - + +
79D VAL* 3.8 28.3 - - + +
80D THR* 3.6 17.5 - - + -
81D ARG* 3.4 46.2 - - + +
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Residues in contact with TYR 52 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284C GLU* 4.2 24.9 - - + -
285C PRO* 3.3 34.2 - - + +
335C LEU* 5.1 1.7 - - - +
336C PRO* 3.1 41.0 + - + +
337C ILE 4.8 0.2 - - - -
338C VAL* 4.0 22.4 - - + -
347C VAL* 4.7 5.5 - - + +
48D VAL 3.1 16.8 + - - +
49D LEU* 4.0 13.2 - - + +
51D LEU* 1.3 76.5 - - - +
53D ASN* 1.3 68.2 + - - +
55D THR* 2.9 18.5 + - - -
56D ARG* 3.4 43.5 + - - +
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Residues in contact with ASN 53 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49D LEU* 3.0 31.0 + - - +
50D ALA* 4.0 7.4 - - - +
51D LEU 3.2 0.2 - - - -
52D TYR* 1.3 85.4 - - - +
54D SER* 1.3 58.0 + - - +
55D THR 3.4 0.2 - - - -
56D ARG* 3.8 20.0 + - - +
57D ASP* 3.1 28.3 + - - +
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Residues in contact with SER 54 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50D ALA 3.0 14.5 + - - -
51D LEU* 2.8 27.0 + - - +
53D ASN* 1.3 76.1 - - - +
55D THR* 1.3 58.2 + - - +
57D ASP* 3.6 10.5 + - - +
81D ARG* 4.7 13.2 + - - +
127D ARG* 2.2 46.8 + - - -
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Residues in contact with THR 55 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336C PRO* 3.6 27.7 - - + +
347C VAL* 5.9 2.5 - - + -
349C GLN* 5.0 13.1 + - - +
51D LEU 3.4 13.3 + - - +
52D TYR* 2.9 18.2 + - - -
54D SER* 1.3 80.1 - - - +
56D ARG* 1.3 60.0 + - - +
57D ASP 3.5 0.2 + - - -
58D ARG* 3.6 26.1 + - - +
79D VAL* 3.7 33.4 - - + -
127D ARG* 4.2 7.2 - - - +
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Residues in contact with ARG 56 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335C LEU* 6.2 1.6 - - - -
336C PRO* 3.7 21.1 - - + -
52D TYR* 3.4 49.3 + - - +
53D ASN* 4.0 21.6 + - - +
54D SER 3.4 0.2 - - - -
55D THR* 1.3 74.2 + - - +
57D ASP* 1.3 62.7 + - - +
58D ARG* 3.5 2.6 + - - +
59D VAL* 5.4 2.6 - - - +
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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