Contacts of the strand formed by residues 106 - 111 (chain E) in PDB entry 1NQ3
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 ALA 106 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77E VAL 2.8 16.7 + - - +
78E LYS* 3.3 12.1 - - + -
79E ALA* 3.0 22.3 + - - +
105E PRO* 1.3 78.2 - - - +
107E ARG* 1.3 61.6 + - - +
22F SER 3.7 6.3 - - - +
24F ALA* 4.5 0.2 - - - -
25F VAL* 3.6 8.4 - - + +
32F TYR* 3.4 29.4 - - + +
34F SER* 3.4 19.5 - - - +
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Residues in contact with ARG 107 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78E LYS* 4.4 2.9 - - - +
79E ALA 3.3 14.4 - - - +
81E VAL* 4.3 13.1 - - + +
89E PHE* 3.5 28.2 - - - -
93E ASN* 2.9 30.3 + - - +
96E TYR* 3.6 44.5 - - - +
105E PRO 3.7 0.8 + - - +
106E ALA* 1.3 77.4 - - - +
108E ALA* 1.3 79.8 + - - +
109E ALA* 4.9 3.2 - - - +
18F ILE 5.3 1.2 + - - -
20F PRO* 4.0 4.8 - - - +
21F TYR* 3.7 48.0 - - + +
22F SER 4.4 0.2 + - - -
34F SER* 2.8 18.6 + - - +
35F GLY 3.0 22.3 + - - +
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Residues in contact with ALA 108 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78E LYS* 4.4 6.3 - - - -
79E ALA 3.2 3.7 + - - +
80E THR* 3.4 7.4 - - + +
81E VAL 2.8 25.8 + - - -
107E ARG* 1.3 78.3 - - - +
109E ALA* 1.3 60.7 + - - +
110E TYR* 4.3 11.4 - - + -
35F GLY* 4.4 4.5 - - - +
82F LEU* 5.7 0.2 - - + -
122F GLU* 4.2 14.4 - - - +
124F GLU* 3.6 30.7 - - - +
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Residues in contact with ALA 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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81E VAL* 3.3 22.4 - - + +
83E LEU* 5.2 1.1 - - + -
86E ILE* 5.1 2.0 - - - -
89E PHE* 3.6 34.5 - - + -
107E ARG* 4.9 6.1 - - + +
108E ALA* 1.3 75.6 - - - +
110E TYR* 1.3 67.5 + - - +
116F PRO* 3.3 26.0 - - + +
122F GLU* 4.0 5.9 + - - +
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Residues in contact with TYR 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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110D TYR* 3.8 7.3 + + - -
80E THR* 3.8 20.1 - - + +
81E VAL 3.2 5.8 + - - +
82E LEU* 3.5 30.5 - - + +
83E LEU* 3.1 25.7 + - - +
86E ILE* 4.2 11.2 - - - -
108E ALA* 4.3 8.7 - - + -
109E ALA* 1.3 81.7 - - - +
111E GLN* 1.3 61.7 + - - +
112E VAL* 4.0 10.3 - - + -
124E GLU* 5.4 0.2 + - - -
82F LEU* 3.3 31.0 - - + -
110F TYR* 3.8 16.0 + - - -
112F VAL* 3.7 26.5 - - + -
114F ALA 3.6 12.6 - - - +
115F LEU* 3.7 14.1 - - + -
122F GLU* 4.6 3.8 - - - -
124F GLU* 4.3 6.8 + - - -
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Residues in contact with GLN 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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83E LEU* 3.2 16.2 - - - +
84E ALA 3.5 24.0 + - - +
85E ASP* 3.5 3.9 - - - +
86E ILE* 2.8 40.6 + - + +
110E TYR* 1.3 71.9 - - - +
112E VAL* 1.3 59.8 + - - +
112F VAL* 3.4 6.9 - - - +
113F ALA* 2.7 48.8 + - - +
114F ALA* 2.9 31.6 + - + +
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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