Contacts of the strand formed by residues 88 - 91 (chain A) in PDB entry 3UMZ
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 88 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77A GLU 3.5 1.7 - - - +
78A ILE* 3.3 4.4 - - - +
79A GLU* 2.7 59.9 + - + +
81A LEU* 4.0 14.1 - - + -
87A PRO* 1.3 75.1 - - - +
89A LEU* 1.3 64.3 + - - +
90A ARG* 3.4 33.2 + - + +
112A SER* 3.6 23.6 - - - -
113A HIS 3.4 3.6 - - - +
114A ARG* 3.5 45.3 - - - +
115A LEU* 4.9 0.2 - - - -
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Residues in contact with LEU 89 (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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76A ALA* 4.3 1.6 - - + -
77A GLU 3.4 14.4 - - - +
78A ILE* 3.8 17.5 - - + +
87A PRO 4.1 0.6 + - - -
88A ILE* 1.3 73.0 - - - +
90A ARG* 1.3 69.2 - - - +
98A THR* 4.3 3.6 - - + -
100A ILE* 3.5 32.1 - - + -
107A LEU* 3.7 18.9 - - + +
111A VAL 3.7 1.4 - - - +
113A HIS* 2.8 43.0 + - + +
115A LEU* 3.9 17.7 - - + +
121A ILE* 3.9 21.5 - - + -
123A PHE* 4.0 22.2 - - + -
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Residues in contact with ARG 90 (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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53A LYS* 5.2 5.7 - - - +
76A ALA* 3.2 6.8 - - - +
77A GLU* 2.9 54.1 + - + +
79A GLU* 2.5 41.0 + - - +
88A ILE* 3.4 21.3 + - + +
89A LEU* 1.3 77.4 - - - +
91A ASP* 1.3 65.0 + - - +
92A CYS* 3.9 2.6 + - - -
98A THR* 5.8 0.2 - - - -
107A LEU* 4.5 2.2 - - - -
110A GLY* 5.5 7.6 - - - +
111A VAL 3.4 23.1 - - - +
112A SER* 3.0 23.7 + - - -
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Residues in contact with ASP 91 (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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75A HIS 3.6 5.0 - - - +
90A ARG* 1.3 76.3 - - - +
92A CYS* 1.3 59.6 + - - +
93A GLY* 2.8 30.1 + - - -
94A SER* 2.7 30.3 + - - +
97A GLY* 4.6 2.2 - - - -
98A THR* 2.7 35.1 + - - +
107A LEU* 3.7 28.3 - - + +
108A SER 4.6 3.3 + - - +
109A PRO* 3.6 27.0 - - - +
110A GLY 4.2 3.8 + - - +
111A VAL 4.8 1.6 + - - -
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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