Contacts of the helix formed by residues 52 - 66 (chain A) in PDB entry 1F3Y
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 52 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47A ILE* 4.2 0.2 - - - -
51A GLU* 1.3 84.2 + - - +
53A PRO* 1.3 79.5 - - + +
54A ARG* 4.4 2.5 - - + +
55A ASN* 3.9 27.4 + - - +
56A ALA* 3.0 28.6 + - - +
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Residues in contact with PRO 53 (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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17A VAL* 3.5 22.6 - - + +
47A ILE* 3.8 4.9 - - + -
51A GLU 4.4 1.6 - - - +
52A ASP* 1.3 96.2 - - - +
54A ARG* 1.3 60.2 + - + +
56A ALA* 3.0 1.7 + - - +
57A ALA* 2.6 37.6 + - - +
79A TRP* 3.9 26.7 - - + -
106A LYS* 4.1 15.3 - - + +
108A PHE* 3.3 21.4 - - + -
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Residues in contact with ARG 54 (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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52A ASP* 5.2 2.5 - - + +
53A PRO* 1.3 82.6 - - + +
55A ASN* 1.3 92.5 + - - +
57A ALA* 3.3 2.1 + - - +
58A ILE* 2.9 59.4 + - - +
72A VAL* 3.2 33.6 - - + +
75A GLU* 5.0 4.0 - - - +
108A PHE* 3.1 34.6 - - + -
110A PHE* 3.9 5.4 - - - -
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Residues in contact with ASN 55 (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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51A GLU* 4.4 19.4 + - + +
52A ASP* 3.7 25.8 + - + +
53A PRO 3.2 0.4 - - - -
54A ARG* 1.3 105.4 + - - +
56A ALA* 1.3 61.0 + - - +
58A ILE* 3.2 6.7 + - - +
59A ARG* 2.8 42.8 + - - +
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Residues in contact with ALA 56 (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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17A VAL* 3.6 12.6 - - + -
46A GLY 4.5 4.3 - - - +
47A ILE* 3.9 28.3 - - + +
48A ASP* 4.7 7.6 - - - +
51A GLU* 4.6 3.8 - - + +
52A ASP 3.0 19.9 + - - +
53A PRO 3.4 3.8 - - - +
55A ASN* 1.3 75.5 - - - +
57A ALA* 1.3 55.3 + - - +
59A ARG* 4.5 5.4 - - - +
60A GLU* 2.7 40.0 + - + +
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Residues in contact with ALA 57 (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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17A VAL* 3.2 16.5 - - + +
18A GLY 3.8 1.8 - - - +
19A ILE* 2.9 34.0 - - + +
53A PRO 2.6 20.3 + - - +
54A ARG 3.3 5.6 - - - +
56A ALA* 1.3 72.5 - - - +
58A ILE* 1.3 57.7 + - - +
61A LEU* 2.9 27.4 + - - +
108A PHE* 3.4 23.3 - - + -
110A PHE* 4.3 0.7 - - + -
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Residues in contact with ILE 58 (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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19A ILE* 4.5 1.8 - - - -
54A ARG* 2.9 57.3 + - - +
55A ASN* 3.6 7.0 - - - +
57A ALA* 1.3 74.7 - - - +
59A ARG* 1.3 65.4 + - + +
61A LEU* 3.1 21.3 - - - +
62A ARG* 3.1 9.2 + - - +
67A VAL 4.9 1.7 - - - +
68A THR* 5.9 7.2 - - + +
70A ALA 6.1 0.9 - - - +
72A VAL* 4.8 1.1 - - + -
110A PHE* 3.4 26.7 - - + -
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Residues in contact with ARG 59 (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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48A ASP* 5.9 1.8 - - - -
51A GLU* 4.4 20.8 + - - -
55A ASN* 2.8 31.9 + - - +
56A ALA* 3.9 4.9 - - - +
58A ILE* 1.3 72.4 - - + +
60A GLU* 1.3 58.5 + - + +
62A ARG* 2.7 32.4 + - - +
63A GLU* 3.0 21.3 + - + +
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Residues in contact with GLU 60 (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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19A ILE* 4.4 1.3 - - + -
43A PRO* 5.4 0.4 - - - -
44A GLN 4.4 3.4 - - - -
45A GLY* 3.1 30.4 - - - +
46A GLY 2.9 34.3 + - - +
56A ALA* 2.7 28.4 + - - +
57A ALA 4.0 2.0 - - - +
59A ARG* 1.3 72.6 - - + +
61A LEU* 1.3 62.7 + - - +
63A GLU* 3.4 10.9 + - - +
64A GLU* 3.0 39.8 + - - +
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Residues in contact with LEU 61 (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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19A ILE* 3.2 31.6 - - + +
21A LEU* 4.6 14.1 - - + -
43A PRO* 3.6 27.8 - - + +
57A ALA 2.9 17.9 + - - +
58A ILE* 3.1 8.5 - - - +
60A GLU* 1.3 78.2 - - - +
62A ARG* 1.3 55.5 + - - +
64A GLU* 3.9 1.2 - - - +
65A THR* 2.8 37.6 + - - +
67A VAL* 3.0 50.5 - - + +
70A ALA* 6.0 2.0 - - + -
110A PHE* 4.6 13.9 - - + -
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Residues in contact with ARG 62 (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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58A ILE* 3.1 7.8 + - + +
59A ARG* 2.7 19.7 + - - +
61A LEU* 1.3 70.4 - - - +
63A GLU* 1.3 66.2 + - - +
64A GLU 2.7 12.8 + - - -
66A GLY* 2.5 39.4 + - - +
67A VAL 3.8 8.5 - - - +
68A THR* 3.4 35.7 - - + +
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Residues in contact with GLU 63 (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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59A ARG* 3.0 21.7 + - + +
60A GLU* 4.0 13.9 - - - +
62A ARG* 1.3 86.5 + - + +
64A GLU* 1.3 66.9 + - - +
122A LEU 4.2 10.7 - - - +
123A GLY* 5.3 2.8 - - - -
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Residues in contact with GLU 64 (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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43A PRO* 5.1 2.9 - - + -
44A GLN 4.5 16.9 - - - +
60A GLU* 3.0 33.1 + - - +
61A LEU* 3.9 4.3 - - - +
62A ARG 2.7 6.3 + - - -
63A GLU* 1.3 87.1 - - - +
65A THR* 1.3 62.0 + - + +
121A LEU* 3.8 13.3 - - - -
122A LEU 4.1 4.1 - - - +
130A GLU* 2.8 45.5 - - + +
131A PHE* 3.6 25.8 - - + -
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Residues in contact with THR 65 (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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29A PHE* 3.2 32.7 - - + -
43A PRO* 4.6 2.4 - - + +
61A LEU* 2.8 18.3 + - - +
62A ARG 3.0 0.8 + - - -
64A GLU* 1.3 73.3 - - + +
66A GLY* 1.3 59.9 + - - +
67A VAL* 3.0 18.4 + - - +
118A GLU 3.3 13.2 - - - +
119A ILE* 3.3 11.3 - - - -
120A ASN* 3.4 10.5 + - - +
121A LEU* 3.2 25.4 - - + +
131A PHE* 3.1 31.6 - - + -
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Residues in contact with GLY 66 (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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62A ARG* 2.5 31.7 + - - +
64A GLU 3.8 0.2 - - - -
65A THR* 1.3 69.9 - - - +
67A VAL* 1.3 62.9 + - - +
68A THR* 3.0 17.2 + - - +
118A GLU* 3.4 21.8 - - - +
120A ASN* 4.3 5.6 + - - -
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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