Contacts of the helix formed by residues 50 - 64 (chain A) in PDB entry 1UOU
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 SER 50 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42A MET* 5.4 0.2 - - - +
48A ARG* 3.8 11.6 + - - +
49A LEU* 1.3 70.7 - - - +
51A GLU* 1.3 60.2 + - - +
52A ALA* 3.5 6.9 + - - +
53A ASP* 3.0 36.0 + - - -
54A ILE* 2.8 28.1 + - - +
90A VAL* 5.5 1.3 - - - -
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Residues in contact with GLU 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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50A SER* 1.3 73.0 - - - +
52A ALA* 1.3 66.1 + - - +
53A ASP 3.2 0.2 - - - -
54A ILE* 3.5 1.6 + - - +
55A ARG* 3.1 53.6 + - - +
90A VAL* 3.7 36.6 - - + +
93A GLN* 5.3 4.7 + - - -
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Residues in contact with ALA 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 SER* 3.5 6.7 + - - +
51A GLU* 1.3 80.0 - - - +
53A ASP* 1.3 58.9 + - - +
55A ARG* 3.9 7.6 - - - +
56A GLY* 2.9 26.7 + - - -
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Residues in contact with ASP 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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34A LYS* 3.1 34.6 + - - +
39A LEU* 4.0 14.8 - - + +
42A MET* 3.6 25.6 - - - +
49A LEU* 3.8 19.6 - - + +
50A SER* 3.0 40.4 + - - +
51A GLU 3.2 0.2 - - - -
52A ALA* 1.3 74.7 - - - +
54A ILE* 1.3 65.8 + - - +
56A GLY* 3.3 2.0 + - - -
57A PHE* 3.1 23.7 + - - +
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Residues in contact with ILE 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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49A LEU* 3.6 27.4 - - + +
50A SER 2.8 25.3 + - - +
51A GLU 3.8 4.3 - - - +
53A ASP* 1.3 75.3 - - - +
55A ARG* 1.3 57.1 + - - +
57A PHE* 3.3 7.8 + - + +
58A VAL* 3.0 33.9 + - + +
83A MET* 3.4 33.0 - - + -
87A GLU* 4.4 7.6 - - + +
90A VAL* 4.0 16.4 - - + +
91A LEU* 3.8 37.0 - - + +
94A ALA* 4.4 6.5 - - + -
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Residues in contact with ARG 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* 3.1 49.3 + - + +
52A ALA* 3.9 6.5 - - - +
54A ILE* 1.3 74.2 - - - +
56A GLY* 1.3 59.3 + - - +
58A VAL* 3.9 5.9 - - - +
59A ALA* 2.9 34.8 + - - +
90A VAL* 5.1 3.9 - - + +
93A GLN* 4.4 12.5 + - - +
94A ALA* 4.2 24.1 + - + +
97A GLN* 3.0 44.6 + - - +
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Residues in contact with GLY 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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34A LYS 6.0 1.1 - - - -
36A LEU* 5.0 1.1 - - - +
39A LEU* 4.9 6.5 - - - -
52A ALA 2.9 17.9 + - - -
53A ASP* 3.7 1.8 - - - -
54A ILE 3.3 0.2 - - - -
55A ARG* 1.3 76.7 - - - +
57A PHE* 1.3 61.7 + - - +
59A ALA* 3.4 4.9 + - - +
60A ALA* 3.0 24.3 + - - +
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Residues in contact with PHE 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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36A LEU* 4.1 33.9 - - + -
39A LEU* 4.2 11.0 - - + +
40A ILE* 5.8 0.2 - - + -
49A LEU* 6.3 1.3 - - + -
53A ASP 3.1 12.6 + - - +
54A ILE* 3.5 9.4 - - + +
56A GLY* 1.3 73.1 - - - +
58A VAL* 1.3 72.0 + - + +
60A ALA* 3.1 5.9 + - - +
61A VAL* 2.9 49.7 + - + +
66A ALA* 4.8 0.4 - - + -
70A GLN 4.6 0.2 - - - -
71A ILE* 4.6 20.2 - - + -
74A MET* 3.7 48.7 - - + -
75A LEU* 5.5 4.5 - - + -
78A ILE* 5.4 4.7 - - + -
91A LEU* 6.0 2.5 - - + -
198A LEU* 4.6 18.8 - - + -
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Residues in contact with VAL 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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54A ILE* 3.0 18.2 + - + +
55A ARG* 3.9 3.6 - - - +
57A PHE* 1.3 91.6 - - + +
59A ALA* 1.3 58.7 + - - +
61A VAL* 3.1 10.7 + - - +
62A VAL* 3.1 25.5 + - + +
91A LEU* 4.3 11.7 - - + -
94A ALA* 3.7 38.4 - - + +
95A LEU* 4.1 17.3 - - + -
98A SER* 4.6 4.9 - - - -
194A ALA* 3.9 20.0 - - + -
198A LEU* 5.5 1.6 - - + -
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Residues in contact with ALA 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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55A ARG 2.9 21.3 + - - +
56A GLY* 3.8 5.6 - - - +
58A VAL* 1.3 77.6 - - - +
60A ALA* 1.3 52.6 + - - +
62A VAL* 3.5 10.6 + - - +
63A ASN* 2.4 41.3 + - - +
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Residues in contact with ALA 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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36A LEU* 4.0 21.8 - - + -
56A GLY 3.0 12.8 + - - +
57A PHE 3.1 8.7 + - - +
59A ALA* 1.3 75.3 - - - +
61A VAL* 1.3 65.4 + - - +
62A VAL 3.2 1.1 - - - -
63A ASN* 3.5 9.9 - - - +
64A GLY 3.3 4.0 + - - -
65A SER* 3.2 32.6 + - - -
66A ALA* 3.3 16.0 + - + +
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Residues in contact with VAL 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 PHE* 2.9 50.2 + - + +
58A VAL* 3.2 10.3 - - - +
60A ALA* 1.3 77.6 - - - +
62A VAL* 1.3 63.2 + - - +
64A GLY* 3.7 6.9 + - - -
66A ALA* 4.1 11.2 - - + +
71A ILE* 4.3 12.4 - - + +
194A ALA* 4.4 6.1 - - - +
197A ILE* 3.8 37.8 - - + +
198A LEU* 3.4 28.5 - - + -
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Residues in contact with VAL 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 VAL 3.1 15.4 + - - +
59A ALA* 3.6 11.4 - - - +
60A ALA 3.2 0.2 - - - -
61A VAL* 1.3 78.2 - - - +
63A ASN* 1.3 58.4 + - + +
64A GLY 3.7 0.3 + - - -
98A SER* 4.0 23.8 - - - +
193A PRO* 4.9 8.7 - - + -
194A ALA* 3.8 28.0 - - + +
197A ILE* 4.5 10.3 - - - +
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Residues in contact with ASN 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 ALA* 2.4 31.5 + - - +
60A ALA* 3.3 4.1 - - - +
61A VAL 3.4 0.2 - - - -
62A VAL* 1.3 77.2 - - + +
64A GLY* 1.3 57.0 + - - +
65A SER* 2.5 42.2 + - - +
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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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60A ALA 3.3 4.9 + - - -
61A VAL 3.7 5.4 + - - -
62A VAL 3.5 3.4 + - - -
63A ASN* 1.3 76.4 - - - +
65A SER* 1.3 61.1 + - - +
66A ALA 3.5 11.1 + - - +
67A GLN* 4.3 4.3 + - - +
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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