Contacts of the helix formed by residues 51 - 65 (chain J) in PDB entry 1FQV
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 ASN 51 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8J SER* 3.6 1.6 - - - -
9J SER* 3.3 13.9 + - - +
10J ASP* 3.5 20.7 + - - +
49J ASN 4.3 0.6 + - - -
50J VAL* 1.3 77.9 - - - +
52J ALA* 1.3 59.2 + - - +
53J ALA* 2.9 29.1 - - - +
54J ILE* 3.2 31.4 + - - +
55J LEU* 3.1 25.6 + - - +
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Residues in contact with ALA 52 (chain J).
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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8J SER* 3.3 9.8 - - - +
10J ASP* 3.0 22.7 + - - +
12J GLU* 3.0 43.1 - - + +
14J PHE* 3.3 21.9 - - - -
51J ASN* 1.3 73.2 - - - +
53J ALA* 1.3 64.1 + - - +
56J LYS* 3.3 12.3 + - - +
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Residues in contact with ALA 53 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51J ASN* 2.9 19.0 - - - +
52J ALA* 1.3 75.0 - - - +
54J ILE* 1.3 70.1 + - + +
56J LYS* 3.4 10.9 - - - +
57J LYS* 3.3 24.1 + - - +
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Residues in contact with ILE 54 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50J VAL* 4.0 7.6 - - + -
51J ASN* 3.2 19.0 + - - +
53J ALA* 1.3 76.6 - - + +
55J LEU* 1.3 55.6 + - - +
57J LYS* 2.7 28.4 + - + +
58J VAL* 2.8 15.9 + - + -
99J THR* 3.9 26.2 - - + +
102J GLU* 3.3 38.8 - - + +
103J LEU* 3.7 14.6 - - + +
106J ALA* 3.3 34.5 - - + -
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Residues in contact with LEU 55 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6J LEU* 4.0 18.6 - - + -
8J SER* 4.2 16.6 - - - +
14J PHE* 3.8 25.6 - - + -
27J ILE* 5.5 1.1 - - + -
47J LEU* 3.7 27.4 - - + -
50J VAL* 3.5 16.4 - - + +
51J ASN 3.1 18.8 + - - +
52J ALA 4.3 3.1 - - - +
54J ILE* 1.3 76.5 - - - +
56J LYS* 1.3 58.5 + - - +
58J VAL* 3.1 14.0 + - + -
59J ILE* 2.9 49.7 + - + +
110J LEU* 5.0 4.0 - - + -
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Residues in contact with LYS 56 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12J GLU* 6.1 1.1 - - - +
14J PHE* 3.8 24.2 - - + -
52J ALA 3.3 18.0 + - - +
53J ALA* 3.4 9.2 - - - +
54J ILE 3.1 0.2 - - - -
55J LEU* 1.3 80.1 - - - +
57J LYS* 1.3 59.0 + - + +
59J ILE* 3.7 4.5 + - - +
60J GLN* 3.1 29.5 + - - +
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Residues in contact with LYS 57 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53J ALA 3.3 17.3 - - - +
54J ILE* 2.7 18.0 + - + +
56J LYS* 1.3 78.0 - - + +
58J VAL* 1.3 56.8 + - - +
60J GLN* 3.0 14.3 + - - +
61J TRP 2.8 26.3 + - - -
92J PHE* 3.1 61.1 + - + +
95J VAL* 4.1 14.0 - - - +
99J THR* 5.0 5.4 - - + -
103J LEU* 3.6 27.6 - - + -
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Residues in contact with VAL 58 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27J ILE* 6.3 0.4 - - + -
50J VAL* 5.0 0.2 - - + -
54J ILE* 2.8 36.5 + - + +
55J LEU* 3.5 14.8 - - + +
57J LYS* 1.3 72.6 - - - +
59J ILE* 1.3 58.8 + - + +
61J TRP* 3.9 5.2 - - - +
62J CYS* 3.0 32.1 + - - -
103J LEU* 4.3 8.7 - - + +
106J ALA* 4.1 13.5 - - + -
107J ALA 5.1 2.2 - - - +
110J LEU* 3.7 16.6 - - + -
112J ILE* 3.3 33.0 - - + -
115J LEU* 5.4 8.3 - - + -
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Residues in contact with ILE 59 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6J LEU* 4.0 4.0 - - + -
14J PHE* 3.6 31.9 - - + -
16J VAL* 3.2 39.7 - - + -
20J ILE* 4.9 5.2 - - + -
55J LEU* 2.9 41.5 + - + +
56J LYS* 4.0 4.5 - - - +
58J VAL* 1.3 74.8 - - + +
60J GLN* 1.3 57.8 + - - +
62J CYS* 3.9 4.1 - - - +
63J THR* 2.6 48.1 + - - +
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Residues in contact with GLN 60 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56J LYS* 3.1 19.1 + - - +
57J LYS* 3.0 19.7 + - - +
59J ILE* 1.3 77.2 - - - +
61J TRP* 1.3 62.0 + - - +
63J THR* 3.3 6.6 + - - -
64J HIS* 3.0 23.7 + - - +
88J TRP* 4.0 18.3 + - + -
91J GLU* 5.3 1.2 - - - +
92J PHE* 3.4 25.6 - - - -
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Residues in contact with TRP 61 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23J GLN* 4.5 5.8 - - - -
57J LYS 2.8 16.0 + - - +
58J VAL 3.9 3.8 - - - +
60J GLN* 1.3 77.4 - - - +
62J CYS* 1.3 78.1 + - - +
64J HIS* 3.3 2.1 + - - +
65J HIS* 2.9 65.8 + + + -
88J TRP* 3.9 17.5 - + - -
89J ASP* 3.5 13.2 + - - +
92J PHE* 3.5 28.0 - + + -
112J ILE* 4.2 9.4 - - + -
114J GLY* 3.2 35.0 - - - -
115J LEU* 3.3 46.5 - - + +
118J VAL* 3.8 11.3 - - + +
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Residues in contact with CYS 62 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20J ILE* 3.6 21.1 - - + -
23J GLN* 3.0 42.6 + - - +
24J SER 5.7 0.2 - - - -
58J VAL* 3.0 28.6 + - - +
59J ILE* 3.9 1.6 - - - +
61J TRP* 1.3 86.7 - - - +
63J THR* 1.3 60.4 + - - +
65J HIS 3.0 1.6 - - - +
66J LYS* 2.8 24.8 + - - -
112J ILE* 3.9 28.9 - - - -
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Residues in contact with THR 63 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20J ILE* 3.6 27.6 - - + +
59J ILE* 2.6 33.3 + - - +
60J GLN* 3.5 7.8 - - - +
62J CYS* 1.3 77.8 - - - +
64J HIS* 1.3 65.1 + - - +
66J LYS* 2.9 31.3 + - + +
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Residues in contact with HIS 64 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60J GLN 3.0 6.9 + - - +
61J TRP 3.5 4.5 - - - +
63J THR* 1.3 79.5 - - - +
65J HIS* 1.3 88.4 + + - +
66J LYS* 3.8 1.2 + - - +
68J ASP* 3.7 1.2 - - - +
86J PRO* 6.0 1.8 - - - +
88J TRP* 3.3 72.1 + + + +
89J ASP* 4.3 0.8 + - - -
243M ASN* 5.1 0.5 - - - +
269M ARG* 2.9 64.4 + - + +
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Residues in contact with HIS 65 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23J GLN* 3.9 8.6 - - - +
61J TRP* 2.9 61.0 + + + +
62J CYS 3.0 5.6 - - - +
63J THR 3.0 0.6 - - - -
64J HIS* 1.3 96.9 + + - +
66J LYS* 1.3 62.7 + - - +
67J ASP 3.1 2.9 - - - -
68J ASP* 3.0 55.5 + - + +
86J PRO* 5.2 5.3 - - - +
88J TRP* 3.8 3.4 - + - -
89J ASP* 3.0 40.8 + - - -
269M ARG* 4.7 0.9 + - - -
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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