Contacts of the helix formed by residues 46 - 52 (chain A) in PDB entry 1UU1
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 46 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44A ARG 3.3 2.8 + - - +
45A LEU* 1.3 72.1 - - - +
47A SER* 1.3 58.4 + - - +
48A ASP* 2.9 28.9 + - - +
49A ALA* 2.9 33.9 + - + +
50A LEU* 3.6 5.2 + - - +
235A TYR* 2.9 24.1 + - - +
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Residues in contact with SER 47 (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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45A LEU* 3.6 5.8 + - - +
46A ASN* 1.3 74.4 + - - +
48A ASP* 1.3 59.6 + - - +
50A LEU* 3.4 19.8 + - - +
32B PRO* 3.5 7.5 - - - +
33B PHE 3.1 37.0 + - - -
35B GLU* 3.9 16.7 - - - +
38B VAL* 3.3 27.7 - - - +
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Residues in contact with ASP 48 (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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46A ASN* 2.9 18.6 + - - +
47A SER* 1.3 77.6 - - - +
49A ALA* 1.3 57.1 + - - +
50A LEU 3.3 0.2 - - - -
51A ARG* 2.8 66.0 + - - +
52A ILE* 4.1 4.3 - - - +
30B PRO 4.8 0.9 - - - +
32B PRO* 3.3 20.6 - - + +
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Residues in contact with ALA 49 (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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46A ASN* 2.9 23.6 + - + +
48A ASP* 1.3 79.1 - - - +
50A LEU* 1.3 63.4 + - - +
51A ARG 3.2 0.9 - - - -
52A ILE* 3.3 22.6 - - + +
54A TYR* 4.7 10.2 - - + -
235A TYR* 3.9 28.0 - - + +
208B ALA* 3.1 15.6 - - - +
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Residues in contact with LEU 50 (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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45A LEU* 5.6 3.1 - - + -
46A ASN 3.6 6.7 + - - +
47A SER* 3.4 12.3 + - - +
48A ASP 3.3 1.2 - - - -
49A ALA* 1.3 79.3 - - - +
51A ARG* 1.3 56.7 + - - +
235A TYR* 3.7 17.3 - - + -
236A VAL* 3.8 8.7 - - + -
33B PHE* 3.4 24.0 - - + -
38B VAL* 4.0 10.3 - - + -
205B SER 3.2 12.4 - - - +
206B LEU* 3.3 5.2 - - + -
207B ALA 3.1 6.6 + - - -
208B ALA* 2.9 25.5 + - - +
209B GLN* 3.6 37.0 + - + +
240B PHE* 3.5 28.5 - - + -
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Residues in contact with ARG 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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47A SER 4.3 0.8 + - - -
48A ASP* 2.8 40.8 + - - +
50A LEU* 1.3 79.7 - - - +
52A ILE* 1.3 75.2 + - - +
19B ARG* 4.5 7.3 - - - +
23B TYR 5.8 2.2 + - - -
28B GLU* 3.5 28.6 + - - +
29B ASN* 2.9 30.0 + - + +
30B PRO* 3.6 13.5 + - - +
31B PHE 3.3 32.3 - - - +
32B PRO* 3.8 2.5 - - + -
201B SER 4.5 1.4 - - - +
205B SER* 3.4 22.8 + - - -
207B ALA* 3.4 15.0 + - - +
320B LYS* 6.2 0.8 - - - +
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Residues in contact with ILE 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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48A ASP* 4.1 4.5 - - - +
49A ALA* 3.3 19.7 - - + +
51A ARG* 1.3 106.0 - - + +
53A TYR* 1.3 75.9 + - - +
54A TYR* 4.1 20.2 - - + +
19B ARG* 3.3 43.3 - - - +
28B GLU* 3.1 12.3 - - - +
207B ALA* 4.0 3.8 - - - -
208B ALA* 3.1 26.3 + - - +
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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