Contacts of the strand formed by residues 107 - 111 (chain E) in PDB entry 6UWZ
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 ASN 107 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89D ASP* 4.2 13.1 + - - +
150D THR* 3.4 41.5 + - + +
151D TYR* 4.4 8.3 + - - -
79E ARG* 4.2 16.0 - - + +
80E ILE 3.5 9.6 - - - +
81E PRO* 3.4 28.1 - - - +
104E TYR* 5.1 2.5 + - - -
105E TYR 4.9 1.9 - - - +
106E ALA* 1.3 81.6 - - - +
108E VAL* 1.3 61.2 + - - +
109E LEU* 3.9 3.6 + - - +
117E TYR 4.3 1.2 - - - +
118E TRP* 3.5 10.0 - - - -
119E LEU 4.8 1.6 + - - -
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Residues in contact with VAL 108 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60E TRP* 4.1 7.2 - - + -
79E ARG* 4.4 0.9 - - - -
80E ILE 2.8 29.1 + - - +
82E SER* 3.9 16.4 - - - -
85E LEU* 3.5 23.1 - - + -
87E LEU* 4.2 6.7 - - + -
107E ASN* 1.3 72.4 - - - +
109E LEU* 1.3 66.2 + - - +
110E VAL* 3.2 6.9 + - - +
116E MET* 3.8 42.6 - - + -
117E TYR 3.8 9.9 - - - +
118E TRP* 3.6 25.1 - - + -
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Residues in contact with LEU 109 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150D THR* 4.0 37.5 - - + +
77E LEU* 3.7 20.2 - - + -
78E VAL 3.5 5.2 - - - -
79E ARG* 4.0 24.2 - - + +
107E ASN 4.3 1.3 - - - +
108E VAL* 1.3 70.0 - - - +
110E VAL* 1.3 60.0 + - - +
111E TYR* 4.0 15.6 - - + +
115E SER 3.5 1.0 - - - +
116E MET* 3.3 7.1 - - - -
117E TYR* 2.9 63.3 + - + +
119E LEU 6.1 0.2 - - - +
35G SER* 5.6 2.2 - - - +
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Residues in contact with VAL 110 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11E LEU* 5.2 0.2 - - + -
65E LEU* 3.7 31.4 - - + +
67E TRP* 3.4 12.9 - - + -
77E LEU* 3.3 3.5 - - - -
78E VAL* 2.6 42.7 + - + +
80E ILE* 3.8 28.0 - - + -
85E LEU* 4.6 0.2 - - + -
108E VAL* 3.3 16.4 - - + +
109E LEU* 1.3 71.8 - - - +
111E TYR* 1.3 63.6 + - - +
115E SER 3.5 2.7 - - - -
116E MET* 3.5 37.2 - - + -
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Residues in contact with TYR 111 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65E LEU 3.6 8.8 - - - +
67E TRP* 3.6 3.9 - - - -
76E ASP* 3.3 22.7 - - - -
77E LEU* 3.8 31.1 - - + +
109E LEU* 4.0 26.6 - - + +
110E VAL* 1.3 75.8 - - - +
112E ASN* 1.3 63.0 + - - +
113E ASP* 3.1 18.8 - - - +
114E GLY* 2.8 22.0 + - - -
115E SER* 2.9 28.0 + - - +
116E MET 5.4 0.2 - - - -
117E TYR* 4.4 12.4 - - + +
35G SER* 4.6 10.0 + - - -
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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