Contacts of the strand formed by residues 110 - 113 (chain H) in PDB entry 3UAJ
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 PHE 110 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35H SER* 3.9 6.5 - - - -
37H LEU* 3.9 14.1 - - + -
47H TRP* 3.5 22.9 - + - -
96H ALA* 3.8 21.1 - - + -
97H ARG 3.4 5.6 - - - -
98H GLN* 3.5 37.9 - - + -
108H ASP 5.0 1.6 - - - -
109H SER* 1.3 67.2 - - - +
111H ASP* 1.3 60.2 + - - +
112H LEU 3.8 0.7 - - - -
113H TRP* 2.9 49.2 + + + +
37L TYR* 2.8 30.7 + - - -
47L LEU* 3.9 5.3 - - - +
90L GLN* 3.4 17.9 - - - -
97L LEU* 3.8 13.9 - - + -
99L PHE* 3.7 20.2 - + - -
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Residues in contact with ASP 111 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97H ARG* 2.8 40.6 + - - +
99H GLY 4.6 0.2 + - - -
104H GLY* 3.2 31.7 - - - +
105H VAL* 3.8 24.6 - - + +
109H SER 3.2 5.9 + - - +
110H PHE* 1.3 73.4 - - - +
112H LEU* 1.3 71.5 + - - +
113H TRP* 3.9 9.1 + - - -
46L LYS* 6.0 0.7 - - - -
47L LEU* 4.8 14.1 + - + -
56L GLU* 5.8 2.7 - - - -
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Residues in contact with LEU 112 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1H GLU 6.3 0.2 - - - +
2H VAL* 3.4 52.3 - - + +
3H GLN* 5.6 0.7 - - - +
4H LEU* 3.5 27.6 - - + +
34H TRP* 4.7 0.9 - - + -
96H ALA* 3.3 6.6 - - - +
97H ARG* 2.9 55.2 + - + +
111H ASP* 1.3 85.9 + - - +
113H TRP* 1.3 62.7 + - - +
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Residues in contact with TRP 113 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4H LEU* 3.7 10.8 + - - +
37H LEU* 4.0 32.1 - - + -
45H LEU* 4.1 9.2 - - + -
94H TYR* 3.8 36.6 - + + -
95H CYS 4.0 2.5 - - - -
96H ALA* 4.0 7.4 - - + -
110H PHE* 2.9 49.9 + + + +
111H ASP 3.9 8.6 + - - -
112H LEU* 1.3 79.5 - - - +
114H GLY* 1.3 63.6 - - - +
37L TYR* 3.6 15.4 - + - -
44L ALA* 4.0 16.1 - - + +
45L PRO* 3.3 53.7 + - + +
46L LYS* 5.2 1.3 - - - -
99L PHE* 4.7 5.2 - + - -
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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