Contacts of the helix formed by residues 50 - 64 (chain A) in PDB entry 3U53
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 50 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48A GLY 3.8 1.6 + - - -
49A GLU* 1.3 75.9 - - - +
51A ASP* 1.3 70.9 + - - +
52A LEU* 3.7 17.1 + - - +
53A GLU* 2.8 41.2 + - + +
54A THR* 3.2 8.8 + - - -
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Residues in contact with ASP 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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4A ARG* 3.0 41.8 + - - -
6A CYS* 3.5 29.2 - - - +
45A VAL* 3.9 9.5 - - - +
49A GLU 4.6 2.6 - - - +
50A ASP* 1.3 80.0 + - - +
52A LEU* 1.3 62.7 + - - +
54A THR* 3.1 16.4 + - - -
55A ALA* 3.3 9.0 + - - +
92A ILE* 3.9 6.9 - - - +
94A TRP* 3.9 14.5 - - + -
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Residues in contact with LEU 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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50A ASP* 3.4 12.0 + - - +
51A ASP* 1.3 75.6 - - - +
53A GLU* 1.3 64.0 + - - +
55A ALA* 3.4 7.8 + - + -
56A LEU* 3.2 33.0 + - + +
72A ILE* 3.7 33.9 - - + -
74A GLU* 5.5 4.9 - - - +
94A TRP* 3.5 52.0 - - + +
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Residues in contact with GLU 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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48A GLY 5.1 0.3 - - - +
49A GLU* 3.6 18.5 - - + +
50A ASP* 2.8 44.3 + - + +
52A LEU* 1.3 76.9 - - - +
54A THR* 1.3 57.8 + - - +
56A LEU* 4.0 7.8 - - + +
57A ARG* 2.9 29.8 + - - +
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Residues in contact with THR 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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6A CYS* 3.8 12.6 - - + +
43A GLY 3.5 24.2 - - - +
44A HIS 3.6 19.7 - - - +
45A VAL* 3.5 15.9 - - + +
49A GLU* 3.0 21.9 + - - +
50A ASP 3.2 10.1 + - - -
51A ASP 3.1 9.1 + - - -
53A GLU* 1.3 77.1 - - - +
55A ALA* 1.3 57.7 + - - +
57A ARG* 3.9 3.6 - - - +
58A GLU* 2.6 45.0 + - - +
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Residues in contact with ALA 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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6A CYS* 3.9 2.6 - - + +
7A GLY* 3.4 41.7 - - - +
8A LEU* 3.7 14.5 - - + +
51A ASP 3.3 9.0 + - - +
52A LEU* 3.7 7.9 - - + +
53A GLU 3.4 0.2 - - - -
54A THR* 1.3 78.9 - - - +
56A LEU* 1.3 55.4 + - - +
58A GLU* 4.1 0.5 - - - +
59A THR* 2.7 37.5 + - - -
94A TRP* 4.2 9.4 - - + -
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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
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8A LEU* 4.1 11.7 - - + -
52A LEU* 3.2 28.0 + - + +
53A GLU* 4.0 6.7 - - + +
55A ALA* 1.3 75.0 - - - +
57A ARG* 1.3 67.4 + - - +
59A THR* 3.2 10.9 + - - -
60A GLN* 3.2 12.5 + - - +
65A ILE 4.9 0.9 - - - +
67A ALA* 4.8 17.7 - - + -
70A LEU* 4.0 26.8 - - + +
72A ILE* 4.3 18.2 - - + -
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Residues in contact with ARG 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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44A HIS 3.4 10.9 + - - -
46A GLU* 3.9 18.9 + - - +
49A GLU* 2.3 53.1 + - - +
53A GLU 2.9 19.3 + - - +
54A THR* 3.9 6.9 - - - +
56A LEU* 1.3 79.1 - - - +
58A GLU* 1.3 89.2 + - - +
60A GLN* 3.1 12.5 + - + +
61A GLU* 3.0 52.1 + - - +
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Residues in contact with GLU 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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6A CYS 4.1 3.4 - - - +
41A PRO* 4.7 2.0 - - - -
42A LYS* 3.0 9.9 - - - +
43A GLY* 2.9 48.8 - - - +
44A HIS 3.6 2.4 + - - +
54A THR* 2.6 25.5 + - - +
55A ALA 4.1 2.0 - - - +
57A ARG* 1.3 106.0 + - - +
59A THR* 1.3 55.6 + - - +
61A GLU* 3.6 14.5 - - - +
62A GLU* 2.8 52.1 + - - +
110A GLU* 5.6 0.7 - - - +
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Residues in contact with THR 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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8A LEU* 3.4 22.6 + - - +
10A ILE* 4.1 20.4 - - + -
41A PRO* 3.8 28.2 + - + +
55A ALA 2.7 23.9 + - - -
56A LEU* 3.2 5.4 + - - -
58A GLU* 1.3 74.9 - - - +
60A GLN* 1.3 60.1 + - - +
63A ALA* 2.9 24.1 + - - +
64A GLY 3.3 4.2 + - - -
65A ILE* 3.7 22.1 + - + +
70A LEU* 4.3 6.3 - - + -
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Residues in contact with GLN 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 3.2 6.9 + - - +
57A ARG* 3.1 17.4 + - + +
59A THR* 1.3 77.9 - - - +
61A GLU* 1.3 89.4 + - - +
64A GLY* 2.9 25.6 + - - -
65A ILE 3.3 24.3 + - - +
66A GLU* 3.5 27.0 - - + +
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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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57A ARG* 3.0 48.7 + - - +
58A GLU* 3.6 18.1 - - - +
60A GLN* 1.3 98.5 + - - +
62A GLU* 1.3 68.9 + - - +
106A ARG 4.4 2.9 - - - +
108A SER* 3.7 19.5 + - - -
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Residues in contact with GLU 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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29A LEU* 3.8 13.1 - - + +
41A PRO* 3.9 13.0 - - + -
42A LYS 3.7 21.3 - - - +
58A GLU* 2.8 43.7 + - - +
61A GLU* 1.3 80.2 - - - +
63A ALA* 1.3 56.9 + - - +
106A ARG 3.7 6.7 - - - +
107A LEU* 3.7 13.9 - - - +
108A SER* 3.7 9.5 + - - -
110A GLU* 2.8 39.7 - - - +
111A HIS* 3.4 30.1 + - + -
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Residues in contact with ALA 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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27A LEU* 4.3 8.5 - - + -
29A LEU* 4.1 17.7 - - + -
41A PRO* 4.2 12.1 - - + -
59A THR 2.9 13.7 + - - +
62A GLU* 1.3 75.8 - - - +
64A GLY* 1.3 59.6 + - - +
65A ILE* 3.3 20.4 + - + +
105A ILE* 3.4 12.4 - - + -
106A ARG 2.7 30.6 + - - -
107A LEU* 4.8 0.2 - - - -
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Residues in contact with GLY 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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59A THR 3.3 0.2 + - - -
60A GLN* 2.9 26.2 + - - +
63A ALA* 1.3 76.8 - - - +
65A ILE* 1.3 60.6 + - - +
66A GLU* 3.7 9.4 + - - +
69A GLN* 3.8 6.8 + - - +
104A GLU 4.0 8.0 - - - +
106A ARG* 3.2 23.7 + - - +
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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