Contacts of the helix formed by residues 46 - 57 (chain x) in PDB entry 6FF7
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 HIS 46 (chain x).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61v VAL* 5.3 7.4 - - + -
112v CYS* 5.0 2.4 - - - +
1098v GLY 6.0 0.2 - - - +
42x SER 3.4 18.4 + - - +
43x TYR 3.0 18.4 - - - +
44x MET 4.0 3.1 - - - +
45x GLY* 1.3 76.2 - - - +
47x PHE* 1.3 63.4 + - - +
48x ASP* 4.1 5.4 - - + +
49x LEU* 4.1 17.9 - - + +
50x LEU* 3.7 6.4 + - - +
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Residues in contact with PHE 47 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15v SER* 4.3 23.6 - - - -
35v GLY* 4.9 14.8 - - - -
61v VAL* 5.4 7.0 - - + +
62v ILE 6.0 1.8 - - - +
45x GLY 3.6 4.2 + - - -
46x HIS* 1.3 71.9 - - - +
48x ASP* 1.3 57.2 + - - +
50x LEU* 3.3 8.9 + - - +
51x ASN* 2.9 26.7 + - - +
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Residues in contact with ASP 48 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1049v LYS 5.3 3.0 - - - +
1050v PHE 4.9 6.1 - - - +
1098v GLY 3.4 25.8 - - - +
1099v GLU* 4.2 14.6 - - + -
1100v THR* 4.5 8.9 - - - +
1122v LEU* 5.5 4.7 - - + +
46x HIS* 3.2 5.0 - - + +
47x PHE* 1.3 77.1 - - - +
49x LEU* 1.3 59.6 + - - +
51x ASN* 3.2 8.4 + - - +
52x TYR* 2.9 28.4 + - - +
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Residues in contact with LEU 49 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1049v LYS 5.2 6.9 + - - +
1050v PHE* 6.3 2.0 - - - -
42x SER 4.5 1.6 - - - +
43x TYR* 4.0 27.6 - - + +
46x HIS* 4.0 12.4 + - + +
47x PHE 3.5 0.2 - - - -
48x ASP* 1.3 76.7 - - - +
50x LEU* 1.3 58.8 + - - +
52x TYR* 3.4 7.6 + - - +
53x PHE* 2.9 30.5 + - - +
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Residues in contact with LEU 50 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43x TYR* 3.8 9.2 + - - +
44x MET* 5.6 3.1 - - - +
46x HIS 3.7 11.7 + - - +
47x PHE* 3.3 12.5 + - - +
49x LEU* 1.3 76.7 - - - +
51x ASN* 1.3 58.7 + - - +
53x PHE* 3.4 5.4 + - - +
54x ALA* 2.9 31.1 + - - +
61x LYS* 6.0 7.2 - - + +
64x VAL* 5.6 5.6 - - + +
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Residues in contact with ASN 51 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1122v LEU* 5.4 13.2 - - + +
1123v SER* 6.2 3.6 - - - -
47x PHE 2.9 13.9 + - - +
48x ASP* 3.2 12.1 + - - +
50x LEU* 1.3 76.2 - - - +
52x TYR* 1.3 56.1 + - - +
54x ALA* 3.1 5.9 + - - +
55x ILE* 3.0 29.1 + - - +
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Residues in contact with TYR 52 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1049v LYS* 5.0 14.6 - - + +
1100v THR* 5.2 8.5 - - - -
1122v LEU* 6.0 3.5 - - + +
48x ASP 2.9 17.2 + - - +
49x LEU* 3.8 7.9 - - - +
50x LEU 3.3 0.2 - - - -
51x ASN* 1.3 77.5 - - - +
53x PHE* 1.3 60.1 + - - +
55x ILE* 3.8 13.6 + - - +
56x ALA* 4.2 6.9 + - - +
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Residues in contact with PHE 53 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1299u GLU* 6.0 6.3 - - + +
49x LEU 2.9 18.5 + - - +
50x LEU* 4.0 4.7 - - - +
52x TYR* 1.3 76.0 - - - +
54x ALA* 1.3 60.6 + - - +
55x ILE 3.4 0.2 - - - -
56x ALA* 4.1 10.0 + - - +
57x GLU* 4.2 10.6 + - - +
64x VAL* 5.6 10.3 - - + +
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Residues in contact with ALA 54 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50x LEU 2.9 18.8 + - - +
51x ASN* 3.1 6.7 + - - +
53x PHE* 1.3 77.1 - - - +
55x ILE* 1.3 59.2 + - - +
56x ALA 3.4 0.4 - - - -
57x GLU* 2.9 19.8 - - - +
58x ASN* 4.9 0.3 - - - -
59x GLU* 4.2 18.8 - - - +
60x SER 4.7 10.3 - - - +
61x LYS* 5.2 6.5 - - + -
64x VAL* 5.4 5.8 - - + -
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Residues in contact with ILE 55 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1304u LEU* 5.7 8.7 - - + -
406v PRO* 5.9 6.7 - - + -
429v ARG* 5.3 11.0 - - - +
784v THR* 4.9 13.0 - - - -
51x ASN 3.0 15.2 + - - +
52x TYR* 3.8 8.9 + - - +
53x PHE 3.4 0.6 - - - -
54x ALA* 1.3 77.3 - - - +
56x ALA* 1.3 65.6 + - - +
57x GLU 3.1 6.4 - - - +
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Residues in contact with ALA 56 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1302u TYR* 6.4 1.6 - - + -
1303u ILE 5.0 11.9 - - - +
1304u LEU* 5.7 6.9 - - + +
802v THR 5.2 1.2 - - - +
803v ASP* 4.8 3.5 - - - +
804v HIS* 3.7 25.7 + - + +
52x TYR 4.2 7.1 + - - +
53x PHE* 4.1 7.5 + - - +
54x ALA 3.4 0.4 - - - -
55x ILE* 1.3 79.8 - - - +
57x GLU* 1.3 60.7 + - - +
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Residues in contact with GLU 57 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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804v HIS* 4.3 12.8 - - + +
805v ASN* 5.8 3.1 - - + -
53x PHE 4.2 10.6 + - - +
54x ALA* 2.9 22.4 - - - +
55x ILE 3.1 7.7 - - - +
56x ALA* 1.3 80.6 - - - +
58x ASN* 1.3 59.8 + - - +
59x GLU* 3.3 17.7 - - + +
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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