Contacts of the strand formed by residues 24 - 29 (chain C) in PDB entry 1U4R
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 ILE 24 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C LEU* 3.9 20.6 - - + -
20C PRO 4.2 8.1 - - - +
21C ARG* 3.4 22.3 + - - +
22C ALA 3.3 5.1 - - - +
23C HIS* 1.3 84.2 - - + +
25C LYS* 1.3 63.2 + - - +
26C GLU 3.6 11.9 - - - +
41C PHE* 3.4 40.8 - - + -
42C VAL 4.0 3.1 - - - +
43C THR* 4.2 3.6 - - + +
61C TYR* 3.4 39.7 - - + -
65C LEU* 3.9 19.1 - - + +
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Residues in contact with LYS 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C HIS 3.8 0.2 + - - -
24C ILE* 1.3 75.3 - - - +
26C GLU* 1.3 89.2 + - + +
42C VAL* 2.9 31.3 + - - +
43C THR 3.3 18.6 - - - +
44C ALA* 4.0 19.9 + - + +
46C ASN* 2.7 28.9 + - - +
65C LEU* 4.3 12.5 - - - +
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Residues in contact with GLU 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C ILE* 3.6 9.9 - - - +
25C LYS* 1.3 110.2 + - + +
27C TYR* 1.3 72.2 - - - +
41C PHE* 3.6 2.9 - - - -
42C VAL* 2.9 35.7 + - + +
65C LEU* 4.7 2.7 - - - -
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Residues in contact with TYR 27 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C GLU* 1.3 83.5 - - - +
28C PHE* 1.3 76.0 - - - +
29C TYR* 3.5 31.2 - + - -
39C VAL* 4.4 4.9 - - + -
40C VAL 3.1 13.7 - - - +
41C PHE* 4.0 16.6 - - + -
42C VAL* 4.4 1.8 - - - +
62C ILE* 3.4 37.6 - - + +
65C LEU* 3.7 24.5 - - + -
66C GLU* 2.5 37.7 + - + +
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Residues in contact with PHE 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C PRO* 4.1 18.6 - - + -
27C TYR* 1.3 88.1 - - - +
29C TYR* 1.3 73.5 + - - +
30C THR* 4.1 11.7 - - + -
39C VAL* 4.6 0.7 - - - -
40C VAL* 2.9 76.5 + - + +
42C VAL* 4.1 16.4 - - + -
48C GLN* 3.7 20.6 - - - -
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Residues in contact with TYR 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C TYR* 3.5 27.6 - + - -
28C PHE* 1.3 81.3 - - - +
30C THR* 1.3 70.5 + - - +
31C SER 3.8 0.2 + - - -
38C ALA 3.3 12.3 - - - +
39C VAL* 3.6 23.1 - - + -
53C PRO* 4.5 11.7 - - + -
62C ILE* 3.4 25.4 - - + +
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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