Contacts of the helix formed by residues 50 - 63 (chain A) in PDB entry 5UFL
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 ILE 50 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49A GLN* 1.3 86.6 - - + +
51A LEU* 1.3 66.6 + - + +
52A THR* 3.1 4.4 - - - +
53A SER* 3.0 35.3 + - - -
54A GLU* 3.7 2.9 + - - +
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Residues in contact with LEU 51 (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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7A LEU* 3.4 28.5 - - + -
8A LYS* 3.6 27.1 - - + +
11A LEU* 4.5 8.7 - - + -
50A ILE* 1.3 82.4 - - + +
52A THR* 1.3 51.7 + - - +
54A GLU* 3.2 23.2 + - + -
55A CYS* 2.8 46.2 + - - -
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Residues in contact with THR 52 (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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7A LEU* 5.9 1.2 - - - +
45A PHE* 3.4 27.0 - - - +
48A ASN* 3.4 43.3 + - + +
49A GLN 4.1 17.6 - - - +
50A ILE* 4.2 2.6 - - - +
51A LEU* 1.3 77.9 - - - +
53A SER* 1.3 60.7 + - - +
55A CYS* 3.8 7.1 - - - +
56A LEU* 3.0 40.2 + - + +
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Residues in contact with SER 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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50A ILE* 3.0 24.3 + - - -
52A THR* 1.3 81.9 - - - +
54A GLU* 1.3 58.9 + - - +
56A LEU* 3.7 7.9 + - - +
57A SER* 3.0 28.5 + - - -
92A CYS* 4.2 22.6 - - - -
96A THR* 5.1 9.0 - - - +
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Residues in contact with GLU 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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11A LEU* 4.7 9.0 - - + -
50A ILE 3.7 2.5 + - - +
51A LEU* 3.2 28.6 + - + +
53A SER* 1.3 77.4 - - - +
55A CYS* 1.3 58.8 + - - +
57A SER* 3.7 9.0 - - - -
58A CYS* 3.1 35.4 + - - +
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Residues in contact with CYS 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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7A LEU* 3.7 33.9 - - - -
10A LEU* 5.0 11.4 - - + +
11A LEU* 3.9 17.5 - - - -
45A PHE* 4.4 15.3 - - + -
51A LEU* 2.8 38.5 + - - +
52A THR* 3.8 8.5 - - - +
53A SER 3.4 0.2 - - - -
54A GLU* 1.3 74.3 - - - +
56A LEU* 1.3 62.7 + - + +
58A CYS* 3.3 19.7 - - - -
59A LEU* 3.3 14.4 + - - +
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Residues in contact with LEU 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A PHE* 4.4 20.6 - - + -
52A THR* 3.0 32.9 + - - +
53A SER* 4.0 7.2 - - - +
55A CYS* 1.3 77.8 - - - +
57A SER* 1.3 58.8 + - - +
59A LEU* 3.2 12.6 + - + +
60A VAL* 2.8 41.8 + - + +
80A LEU* 6.3 2.5 - - + -
83A LEU* 4.7 27.4 - - + -
89A THR* 5.8 5.4 - - + +
92A CYS* 6.1 4.7 - - + -
93A LEU* 5.5 14.8 - - + +
96A THR* 5.3 9.2 - - + +
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Residues in contact with SER 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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53A SER 3.0 19.4 + - - -
54A GLU* 3.4 15.7 + - - -
56A LEU* 1.3 76.1 - - - +
58A CYS* 1.3 56.0 + - - +
60A VAL* 3.6 5.9 + - - +
61A GLU* 3.1 30.6 + - - +
96A THR* 4.8 17.6 - - - +
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Residues in contact with CYS 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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10A LEU* 5.5 2.2 - - - -
11A LEU* 4.1 24.0 - - + -
14A VAL* 4.0 28.4 - - + +
54A GLU* 3.1 22.7 + - - +
55A CYS* 3.3 26.0 - - - -
57A SER* 1.3 75.5 - - - +
59A LEU* 1.3 62.8 + - - +
61A GLU* 3.6 9.3 + - - +
62A LEU* 3.5 14.2 + - - +
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Residues in contact with LEU 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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10A LEU* 5.3 5.4 - - + -
14A VAL* 4.4 20.4 - - + -
29A LEU* 5.5 1.3 - - + -
33A LEU* 4.4 20.6 - - + -
45A PHE* 6.5 0.9 - - + -
55A CYS 3.3 18.9 + - - +
56A LEU* 3.2 14.3 + - + +
58A CYS* 1.3 78.3 - - - +
60A VAL* 1.3 65.0 + - + +
62A LEU* 3.3 25.7 - - + +
63A LEU* 3.8 3.6 + - - -
76A ILE* 3.8 48.8 - - + +
79A LEU* 5.7 5.8 - - + -
80A LEU* 5.4 8.7 - - + -
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Residues in contact with VAL 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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56A LEU* 2.8 27.3 + - + +
57A SER* 3.9 5.8 - - - +
59A LEU* 1.3 77.9 - - + +
61A GLU* 1.3 62.6 + - - +
62A LEU 3.4 0.7 + - - -
63A LEU* 3.4 24.6 + - + +
64A GLU* 3.7 8.6 + - + +
80A LEU* 5.6 6.1 - - + -
96A THR* 4.5 24.0 - - - +
99A LEU* 3.9 24.0 - - + -
102A VAL* 3.7 28.7 - - + -
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Residues in contact with GLU 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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18A LYS* 5.6 2.5 + - - -
57A SER* 3.1 21.1 + - - +
58A CYS* 3.8 10.7 - - - +
59A LEU 3.3 0.4 - - - -
60A VAL* 1.3 74.4 - - - +
62A LEU* 1.3 64.0 + - - +
64A GLU* 3.5 22.8 + - + +
65A ASP* 4.4 3.6 + - - +
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Residues in contact with LEU 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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14A VAL* 4.1 26.5 - - + +
17A TYR* 4.4 25.6 - - + -
18A LYS* 5.7 9.9 - - - +
29A LEU* 4.3 22.2 - - + -
58A CYS 3.5 9.0 + - - +
59A LEU* 3.3 19.2 + - + +
60A VAL 3.2 0.6 - - - -
61A GLU* 1.3 79.8 - - - +
63A LEU* 1.3 60.7 + - - +
64A GLU 3.2 3.0 + - - -
65A ASP* 3.2 26.8 + - - +
69A SER* 5.5 6.1 - - - +
72A LEU* 4.9 17.7 - - + -
73A ILE* 5.8 3.4 - - + -
76A ILE* 4.7 15.3 - - + -
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Residues in contact with LEU 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 LEU 3.8 5.9 + - - +
60A VAL* 3.4 16.8 + - - +
62A LEU* 1.3 78.3 - - - +
64A GLU* 1.3 55.4 + - - +
65A ASP 3.2 5.8 - - - +
73A ILE* 4.9 12.3 - - + -
76A ILE* 3.5 33.0 - - + -
77A ILE* 5.4 2.7 - - + -
80A LEU* 4.9 10.3 - - + -
99A LEU* 4.9 7.0 - - + -
102A VAL* 3.9 31.8 - - + +
103A LEU* 4.5 15.5 - - + -
106A VAL* 3.9 22.1 - - + +
109A ARG* 3.0 24.8 + - - -
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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