Contacts of the strand formed by residues 127 - 134 (chain N) in PDB entry 2FBW
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 GLN 127 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66N ALA 2.8 28.7 + - - -
68N LEU* 3.8 13.3 - - - +
69N GLY* 3.8 2.5 + - - +
70N ASN* 2.8 38.6 + - - +
71N MET* 3.5 24.9 + - + +
125N ILE 3.8 7.6 - - - +
126N TYR* 1.3 92.9 - - - +
128N ARG* 1.3 60.6 + - - +
144N HIS* 3.1 24.7 - - - +
145N ARG* 3.3 16.6 + - - +
146N CYS 3.3 4.5 - - - +
147N CYS* 3.7 20.3 - - - -
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Residues in contact with ARG 128 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62N GLY* 3.0 30.3 + - - -
126N TYR* 4.0 23.4 + - + +
127N GLN* 1.3 73.8 - - - +
129N ALA* 1.3 76.2 + - - +
130N PHE* 3.9 12.5 + - - -
133N GLN* 5.5 0.2 + - - -
144N HIS* 3.9 6.1 - - - -
145N ARG 3.4 5.5 + - - -
146N CYS* 2.8 49.0 + - + +
148N CYS* 3.6 13.8 - - - +
150N ALA* 3.0 32.3 + - - +
151N ASP* 4.5 6.8 - - - +
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Residues in contact with ALA 129 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128N ARG* 1.3 84.0 - - - +
130N PHE* 1.3 70.2 + - - +
142N GLN* 3.6 28.7 - - + +
143N ALA 3.6 10.3 - - - -
144N HIS* 3.7 18.9 - - + +
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Residues in contact with PHE 130 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62N GLY* 3.8 29.2 - - - -
63N GLY 4.6 2.2 - - - -
65N ASN* 5.4 4.0 - - - -
128N ARG* 3.9 10.3 + - - -
129N ALA* 1.3 82.6 - - - +
131N GLY* 1.3 74.7 + - - +
132N GLY 3.3 1.4 + - - -
133N GLN* 3.6 26.4 + - - +
142N GLN* 3.0 22.5 + - - +
143N ALA 4.5 0.6 + - - -
146N CYS* 3.5 30.5 - - + -
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Residues in contact with GLY 131 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130N PHE* 1.3 84.8 - - - +
132N GLY* 1.3 61.0 + - - -
133N GLN* 3.7 5.5 + - - +
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Residues in contact with GLY 132 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82N ASP* 3.8 21.7 - - - +
130N PHE 3.3 1.4 + - - -
131N GLY* 1.3 73.3 - - - -
133N GLN* 1.3 59.9 + - - +
134N SER* 5.7 0.2 - - - -
142N GLN* 5.3 2.0 + - - -
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Residues in contact with GLN 133 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65N ASN* 2.9 38.6 + - - +
79N HIS* 3.8 6.3 - - + -
82N ASP* 3.3 8.3 - - + +
130N PHE* 3.6 29.9 + - - +
131N GLY 3.5 7.1 + - - +
132N GLY* 1.3 82.5 - - - +
134N SER* 1.3 59.9 + - - +
142N GLN* 3.0 29.8 + - - +
143N ALA* 3.1 12.8 + - + +
145N ARG* 3.0 47.3 + - - +
146N CYS* 4.7 2.2 - - - +
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Residues in contact with SER 134 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78N TRP* 4.0 4.0 - - - +
82N ASP* 2.7 34.1 + - - +
133N GLN* 1.3 75.2 - - - +
135N LEU* 1.3 60.9 + - - +
138N GLY* 3.0 34.0 + - - -
141N GLY 3.2 15.0 - - - -
143N ALA* 3.7 6.3 - - - +
145N ARG* 2.9 20.6 + - - -
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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