Contacts of the strand formed by residues 60 - 65 (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 LYS 60 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56E GLU* 3.4 5.6 - - - +
57E LEU 2.8 36.6 + - - +
58E ASP* 4.5 9.4 - - + +
59E GLY* 1.3 84.7 - - - +
61E PRO* 1.3 72.0 - - + +
62E VAL* 3.5 3.0 + - - +
253E LEU* 3.5 52.5 + - + +
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Residues in contact with PRO 61 (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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16E LEU 3.7 19.5 - - - +
17E GLN* 3.3 29.6 - - + +
18E GLY 4.0 4.5 - - - +
19E ALA* 3.4 22.9 - - + +
20E THR 4.6 2.3 + - - -
21E LEU 4.9 0.9 + - - +
54E ARG* 4.7 6.3 - - - +
55E ALA 3.4 8.7 - - - +
56E GLU* 4.3 6.5 - - + +
59E GLY 4.3 3.6 - - - +
60E LYS* 1.3 89.7 - - + +
62E VAL* 1.3 62.7 + - - +
253E LEU* 4.8 3.5 - - - +
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Residues in contact with VAL 62 (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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19E ALA* 4.4 0.2 - - - -
21E LEU* 3.9 19.1 - - + +
23E ILE* 4.2 13.9 - - + -
38E MET* 4.1 25.1 - - + -
54E ARG* 3.6 4.2 - - - +
55E ALA* 2.7 40.0 + - - +
57E LEU* 3.8 22.7 - - + -
60E LYS 3.8 9.2 - - - +
61E PRO* 1.3 79.7 - - - +
63E ILE* 1.3 76.6 + - - +
64E VAL* 5.0 0.2 - - - +
253E LEU* 3.9 20.6 - - + -
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Residues in contact with ILE 63 (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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16E LEU* 3.8 31.0 - - + -
19E ALA* 3.8 13.0 - - + -
21E LEU 3.0 14.1 + - - +
22E ALA* 3.1 18.4 - - + -
23E ILE 2.8 31.4 + - - -
44E LEU* 3.8 29.8 - - + -
52E THR* 4.1 8.1 - - + -
53E TRP 3.7 4.0 - - - +
54E ARG* 3.9 15.3 - - + -
62E VAL* 1.3 75.4 - - - +
64E VAL* 1.3 70.7 + - - +
65E CYS* 4.1 1.6 - - + -
81E LEU* 4.0 19.5 - - + -
86E ILE* 3.9 4.3 - - + -
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Residues in contact with VAL 64 (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* 3.3 13.5 - - + +
25E PRO* 4.0 13.5 - - + -
31E VAL* 3.6 33.7 - - + +
34E ILE* 4.1 18.2 - - + -
35E ALA* 4.1 13.5 - - + -
38E MET* 3.8 28.7 - - + -
52E THR* 3.3 4.9 - - - +
53E TRP* 2.8 44.1 + - + +
55E ALA* 5.2 1.3 - - + -
62E VAL* 5.0 2.7 - - + +
63E ILE* 1.3 75.5 - - - +
65E CYS* 1.3 64.4 + - - +
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Residues in contact with CYS 65 (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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9E LEU* 4.1 20.2 - - - -
23E ILE 3.1 7.3 + - - -
24E VAL* 3.2 29.4 - - + +
25E PRO* 3.4 3.8 - - - +
50E PHE* 4.9 1.6 - - - -
51E THR 3.4 6.1 - - - -
52E THR* 3.4 20.6 - - - +
63E ILE* 4.1 8.5 - - + -
64E VAL* 1.3 76.2 - - - +
66E SER* 1.3 77.0 + - - +
77E ALA* 4.6 3.1 - - - -
81E LEU* 3.9 33.7 - - + -
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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