Contacts of the strand formed by residues 43 - 47 (chain A) in PDB entry 1UMZ
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 THR 43 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A TRP* 2.7 26.4 + - - -
20A ALA 3.2 7.3 + - - -
23A HIS* 3.7 15.5 - - - +
24A ILE* 3.3 13.0 - - - +
35A LEU* 3.5 34.3 - - + -
36A HIS 3.6 17.3 - - - +
42A GLY* 1.3 75.3 - - - -
44A GLY* 1.3 59.9 + - - +
172A SER* 3.2 5.3 - - - -
173A LEU* 3.0 31.5 + - + +
174A TRP* 3.6 7.4 - - - -
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Residues in contact with GLY 44 (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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17A PRO* 3.8 2.6 - - - +
18A THR* 2.9 28.7 + - - -
19A TRP* 3.5 9.7 + - - +
24A ILE* 3.9 7.0 - - - +
35A LEU* 4.6 4.5 - - - -
43A THR* 1.3 80.5 + - - +
45A PHE* 1.3 65.4 + - - +
171A SER 3.1 13.2 - - - -
172A SER* 4.0 5.2 - - - -
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Residues in contact with PHE 45 (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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11A PHE* 3.5 27.1 - + + -
15A TYR* 3.5 37.2 - + - -
16A VAL 3.3 14.8 - - - +
17A PRO* 3.8 2.9 - - + -
18A THR* 3.9 6.2 + - - +
24A ILE* 4.4 1.8 - - + -
33A ILE* 3.6 21.3 - - + -
35A LEU* 3.9 25.6 - - + -
44A GLY* 1.3 75.7 - - - +
46A GLN* 1.3 64.4 + - - +
58A MET* 4.0 12.1 - - + -
170A TYR* 3.5 5.1 - - - +
171A SER* 2.9 57.4 + - - +
199A TYR* 3.9 18.2 - + - -
202A PHE* 4.4 3.1 - + - -
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Residues in contact with GLN 46 (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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15A TYR* 3.3 8.1 - - - -
16A VAL* 2.8 44.1 + - + +
18A THR* 3.1 29.3 + - + +
45A PHE* 1.3 76.7 - - - +
47A SER* 1.3 66.3 + - - +
168A LYS* 3.8 25.0 + - + +
169A ILE 3.1 7.6 - - - +
170A TYR* 3.3 36.8 + - + -
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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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14A ASN 3.3 11.9 - - - -
15A TYR* 3.4 9.8 - - - -
16A VAL* 4.8 1.1 - - - +
46A GLN* 1.3 82.8 - - - +
48A LYS* 1.3 64.7 + - - +
49A GLY 2.7 25.4 + - - -
51A TYR* 4.5 0.4 - - - -
168A LYS* 3.5 15.6 - - - +
169A ILE* 2.7 47.9 + - - +
204A ILE* 4.0 6.3 - - - -
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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