Contacts of the strand formed by residues 107 - 112 (chain E) in PDB entry 4QY2
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 GLY 107 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72E GLY 3.1 15.0 - - - -
73E MET* 4.0 4.3 - - - -
74E TRP* 3.5 15.5 - - - -
105E SER* 3.4 6.5 + - - -
106E GLY* 1.3 80.7 - - - +
108E ILE* 1.3 68.5 + - - +
253E LEU* 3.6 2.3 - - - -
254E ILE* 2.9 27.9 + - - -
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Residues in contact with ILE 108 (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 MET* 3.7 38.4 - - + -
60E LEU* 4.0 18.8 - - + -
70E LEU 3.7 19.3 - - - +
71E THR* 3.2 9.7 - - - -
72E GLY 2.9 28.1 + - - -
74E TRP* 3.6 12.8 - - + -
102E ILE* 4.6 7.0 - - + -
105E SER* 4.6 1.1 - - - +
107E GLY* 1.3 79.3 - - - +
109E ASN* 1.3 79.7 + - - +
110E LYS* 4.3 11.0 - - - -
251E SER* 4.3 9.4 - - - +
252E LYS 3.5 5.8 - - - +
253E LEU* 3.8 14.6 - - + -
254E ILE* 4.7 0.2 - - - -
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Residues in contact with ASN 109 (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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71E THR* 4.5 2.9 - - - -
72E GLY 4.9 0.7 + - - +
73E MET* 4.8 9.0 - - - +
108E ILE* 1.3 83.5 - - - +
110E LYS* 1.3 63.9 + - - +
111E ILE* 4.9 4.4 - - + +
251E SER* 3.5 4.3 - - - -
252E LYS* 2.9 52.0 + - + +
254E ILE* 3.9 24.3 - - - +
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Residues in contact with LYS 110 (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 MET 2.7 28.1 + - - -
60E LEU* 3.8 9.6 - - - +
70E LEU* 3.0 26.8 + - - +
71E THR* 3.8 8.0 - - + +
108E ILE* 4.3 4.0 - - - -
109E ASN* 1.3 74.4 - - - +
111E ILE* 1.3 64.3 + - - +
141E GLU* 2.5 31.9 + - - +
249E ARG* 3.3 42.9 + - + +
250E VAL 3.3 15.3 - - - +
251E SER* 3.1 24.2 - - - +
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Residues in contact with ILE 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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109E ASN* 4.9 6.3 - - + +
110E LYS* 1.3 79.9 - - - +
112E SER* 1.3 73.7 + - - +
161E TYR* 3.3 26.2 - - + +
162E ARG 5.6 1.6 - - - +
164E THR* 5.6 6.1 - - - +
165E ASP* 5.9 1.3 - - + +
169E HIS* 4.0 25.8 - - + +
249E ARG* 4.1 2.9 - - - +
250E VAL* 2.7 48.0 + - + +
252E LYS* 5.1 6.5 - - + -
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Residues in contact with SER 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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111E ILE* 1.3 87.3 - - - +
113E THR* 1.3 63.4 + - - +
114E GLY* 3.3 13.6 + - - -
161E TYR* 4.0 4.6 - - - -
248E SER 3.3 12.2 + - - -
249E ARG* 4.0 11.1 - - - +
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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