Contacts of the strand formed by residues 20 - 24 (chain B) in PDB entry 1UUG
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 GLU 20 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66A TYR* 4.2 17.3 + - + +
67A HIS* 4.7 4.3 - - - -
86A PRO* 3.7 7.3 - - - +
87A PRO* 3.5 19.8 - - + +
88A SER* 2.9 48.5 + - - -
189A SER* 4.5 0.3 - - - -
190A PRO* 4.3 5.4 - - - +
18B ILE* 3.6 4.4 - - - +
19B GLN* 1.3 81.8 - - - +
21B SER* 1.3 66.0 + - - +
22B ILE* 3.8 19.1 - - + +
43B VAL 4.1 0.2 - - - -
44B HIS* 3.4 0.9 - - - -
45B THR* 2.8 46.4 + - - +
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Residues in contact with SER 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A GLN* 4.3 3.6 - - - +
64A ASP* 4.5 11.3 - - - +
67A HIS* 3.0 23.0 + - - -
133A ALA* 3.5 24.9 - - - +
18B ILE* 4.1 1.0 - - - +
20B GLU* 1.3 75.2 + - - +
22B ILE* 1.3 66.7 + - - +
23B LEU 4.3 0.7 + - - -
42B LEU* 4.9 6.8 - - - +
43B VAL 3.3 6.5 - - - -
44B HIS* 2.8 29.4 + - - -
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Residues in contact with ILE 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A GLN* 3.6 11.4 - - + +
77A PHE* 5.7 2.7 - - + -
88A SER* 4.4 2.0 - - - +
187A HIS* 3.7 51.4 - - + +
189A SER* 4.3 7.0 - - - +
20B GLU* 3.8 28.5 - - + +
21B SER* 1.3 81.6 - - - +
23B LEU* 1.3 72.2 + - - +
24B MET* 4.3 10.5 - - + -
42B LEU* 3.3 3.6 - - - -
43B VAL* 2.7 49.9 + - + +
45B THR* 5.7 0.2 - - - +
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Residues in contact with LEU 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A GLN* 2.8 37.3 + - - +
134A HIS* 4.4 22.0 - - + +
167A HIS* 4.0 36.9 - - + +
21B SER 4.3 0.2 + - - -
22B ILE* 1.3 71.5 - - - +
24B MET* 1.3 69.1 + - - +
25B LEU* 4.9 3.6 - - + -
28B GLU* 4.5 2.1 - - - +
40B ASP* 4.0 26.9 - - + +
41B ILE 3.5 12.3 - - - +
42B LEU* 3.8 24.2 - - + +
61B ASP* 4.1 19.1 - - - +
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Residues in contact with MET 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187A HIS* 3.9 18.4 - - + -
189A SER* 4.0 18.8 - - - +
191A LEU* 4.0 24.9 - - + -
192A SER* 3.4 29.4 - - - +
22B ILE* 4.3 8.5 - - + +
23B LEU* 1.3 80.7 - - - +
25B LEU* 1.3 66.8 + - - +
28B GLU* 3.4 26.5 - - - +
29B VAL* 3.9 16.6 - - + -
40B ASP* 3.6 4.0 - - - +
41B ILE* 2.8 37.7 + - + +
43B VAL* 4.1 12.3 - - + -
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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