Contacts of the strand formed by residues 111 - 116 (chain E) in PDB entry 2ZUQ
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 VAL 111 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63E GLN* 3.6 1.4 - - - -
64E GLN* 3.0 37.6 + - + +
110E ALA* 1.3 73.3 - - - +
112E TYR* 1.3 63.6 + - - +
113E TYR* 3.8 29.3 - - + +
125E GLY 4.9 1.3 - - - +
126E GLY* 3.9 25.1 - - - -
127E THR 3.6 11.9 - - - +
128E LYS* 3.8 23.6 - - + +
43F LYS* 6.5 0.4 - - + -
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Residues in contact with TYR 112 (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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26E GLN* 2.4 24.6 - - - +
41E MET* 3.7 31.0 - - + -
61E TRP* 4.7 2.0 - - + -
62E TYR 3.6 4.5 - - - +
63E GLN* 2.9 42.1 + - + -
73E LEU* 4.7 4.7 - - + -
88E PHE* 4.0 17.2 - + - -
99E LEU* 3.6 22.9 - - + -
101E ILE* 3.5 18.6 - - + +
108E ASP* 2.7 32.9 + - - +
110E ALA 3.8 14.6 - - - -
111E VAL* 1.3 72.7 - - - +
113E TYR* 1.3 55.0 + - - +
126E GLY* 3.3 1.6 - - - -
127E THR 2.9 24.1 + - - +
129E LEU* 3.7 16.8 - - + -
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Residues in contact with TYR 113 (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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26E GLN* 3.6 4.0 - - - +
61E TRP* 2.9 19.6 - - - -
62E TYR* 3.0 36.4 + - + +
64E GLN* 3.7 24.6 + - + -
70E PRO* 5.4 1.6 - - + -
111E VAL* 3.8 34.2 - - + +
112E TYR* 1.3 74.8 - - - +
114E CYS* 1.3 64.0 + - - +
123E PHE* 4.9 5.4 - - + -
124E GLY 3.8 18.8 - - - -
125E GLY 3.5 22.3 + - - -
126E GLY* 4.4 0.9 - - - -
39F GLN* 2.9 13.7 + - - -
43F LYS* 2.7 34.3 + - - +
44F ARG* 4.7 2.2 - - - -
45F LEU* 4.1 27.6 - - + -
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Residues in contact with CYS 114 (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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24E MET* 4.3 5.6 - - - +
26E GLN* 3.4 22.9 - - - +
43E CYS* 2.0 49.8 - - + -
59E LEU* 4.5 2.5 - - + -
60E ALA 3.5 14.1 - - - +
61E TRP* 3.7 12.3 - - + -
62E TYR* 5.6 0.2 - - - -
113E TYR* 1.3 76.5 - - - +
115E LYS* 1.3 59.7 - - - +
116E GLN 4.2 0.4 + - - -
122E THR 4.1 0.7 - - - +
123E PHE* 3.3 3.6 - - - -
124E GLY* 2.6 36.2 + - - -
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Residues in contact with LYS 115 (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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59E LEU* 3.0 5.4 - - - -
60E ALA* 2.5 48.3 + - + -
62E TYR* 2.9 39.7 - - + +
114E CYS* 1.3 73.2 - - - +
116E GLN* 1.3 71.4 + - - +
117E SER* 4.4 7.2 - - - +
121E TYR* 3.1 41.2 - - + +
122E THR 3.7 7.6 - - - +
123E PHE* 3.5 28.7 - - + -
105F ALA* 4.5 5.6 - - - +
106F MET* 3.6 23.9 - - - +
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Residues in contact with GLN 116 (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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22E ILE* 3.3 26.7 - - + +
24E MET* 3.6 19.5 - - + +
49E LEU* 3.6 26.2 - - + +
58E TYR 3.6 5.4 - - - +
59E LEU* 3.9 1.1 - - - +
114E CYS 4.2 0.8 - - - -
115E LYS* 1.3 80.7 - - - +
117E SER* 1.3 59.1 + - - +
118E TYR* 3.2 11.1 - - - +
119E ASN 2.8 43.7 - - - +
120E LEU 3.5 2.4 - - - +
121E TYR* 3.7 0.7 - - - -
122E THR* 3.1 47.9 + - - +
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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