Contacts of the helix formed by residues 30 - 36 (chain E) in PDB entry 1U1C
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 ARG 30 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25E PRO* 3.5 18.8 - - + +
27E ASP* 3.0 39.0 + - + +
29E ASP* 1.3 78.1 - - - +
31E VAL* 1.3 64.8 + - - +
32E GLU 3.5 0.7 - - - -
33E LYS* 3.3 16.7 + - + +
34E ILE* 3.2 34.2 + - + +
92E ILE* 2.9 43.9 + - - +
93E GLY* 3.9 3.6 - - - -
94E THR* 4.2 10.8 - - - +
238E GLU* 4.0 34.2 + - + +
242E VAL* 4.9 2.2 - - + -
3042E PO4 2.8 36.6 + - - -
48F ARG* 3.7 3.0 - - - +
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Residues in contact with VAL 31 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25E PRO* 3.9 10.8 - - + -
28E PRO* 3.4 18.4 - - + +
29E ASP 3.4 1.4 - - - -
30E ARG* 1.3 78.5 - - - +
32E GLU* 1.3 62.6 + - - +
34E ILE 3.4 0.5 + - - -
35E ALA* 3.1 20.4 + - - +
51E THR* 3.4 32.3 - - + +
53E TRP* 3.6 26.7 - - + -
64E VAL* 3.6 29.4 - - + +
65E CYS 4.4 0.2 - - - -
66E SER* 3.7 25.6 - - - +
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Residues in contact with GLU 32 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28E PRO 4.8 0.8 + - - -
29E ASP 4.6 5.6 + - - +
30E ARG 3.5 0.2 - - - -
31E VAL* 1.3 75.9 - - - +
33E LYS* 1.3 61.4 + - + +
35E ALA* 3.3 1.5 + - - +
36E ALA* 2.9 33.3 + - + +
53E TRP* 3.5 51.3 + - + +
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Residues in contact with LYS 33 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29E ASP* 3.4 30.4 + - - +
30E ARG* 3.3 17.9 + - + +
31E VAL 3.3 0.4 - - - -
32E GLU* 1.3 80.5 - - + +
34E ILE* 1.3 61.4 - - + +
36E ALA* 3.6 13.2 + - - +
37E LEU* 3.8 13.3 + - - +
238E GLU* 4.0 28.2 + - - +
242E VAL* 5.0 2.4 - - - +
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Residues in contact with ILE 34 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23E ILE* 4.1 13.2 - - + -
25E PRO* 3.8 35.0 - - + -
30E ARG* 3.2 20.5 + - + +
31E VAL 3.8 5.6 - - - +
33E LYS* 1.3 77.0 - - + +
35E ALA* 1.3 61.2 + - - +
37E LEU* 3.2 19.4 + - - +
38E MET* 3.5 22.3 - - + +
64E VAL* 4.1 12.8 - - + -
92E ILE* 3.9 18.2 - - + -
242E VAL* 3.8 31.2 - - + -
245E VAL* 5.2 0.4 - - + -
246E VAL* 4.2 13.6 - - + +
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Residues in contact with ALA 35 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31E VAL 3.1 17.1 + - - +
32E GLU 3.3 4.0 + - - +
34E ILE* 1.3 76.1 - - - +
36E ALA* 1.3 61.3 + - - +
38E MET* 3.2 28.9 + - - +
41E PRO* 3.4 17.1 - - + +
53E TRP* 3.8 35.4 - - + -
55E ALA* 4.0 8.3 - - + +
64E VAL* 4.1 8.2 - - + +
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Residues in contact with ALA 36 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32E GLU* 2.9 21.0 + - + +
33E LYS* 3.8 9.4 - - - +
34E ILE 3.2 0.6 - - - -
35E ALA* 1.3 76.4 - - - +
37E LEU* 1.3 63.2 + - + +
38E MET 3.2 6.1 + - - +
41E PRO* 4.4 13.5 - - + +
53E TRP* 6.5 0.2 - - + -
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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