Contacts of the strand formed by residues 127 - 134 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66A ALA 2.9 28.5 + - - -
68A LEU* 3.8 13.2 - - - +
69A GLY* 3.8 2.7 + - - +
70A ASN* 2.9 36.9 + - - +
71A MET* 3.6 23.9 + - + +
74A ASP* 5.3 0.2 + - - -
125A ILE 3.8 7.0 - - - +
126A TYR* 1.3 93.4 - - - +
128A ARG* 1.3 59.5 + - - +
144A HIS* 3.1 26.8 - - - +
145A ARG* 3.4 15.6 + - - +
146A CYS 3.3 5.2 - - - +
147A CYS* 3.8 19.3 - - - -
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Residues in contact with ARG 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A GLY* 3.0 30.4 + - - -
126A TYR* 4.0 8.2 - - + +
127A GLN* 1.3 74.2 - - - +
129A ALA* 1.3 75.6 + - - +
130A PHE* 3.8 3.1 + - - -
133A GLN* 5.4 0.2 + - - -
144A HIS* 3.9 6.1 - - - -
145A ARG 3.4 5.7 + - - -
146A CYS* 2.8 48.4 + - + +
148A CYS* 3.6 13.9 - - - -
150A ALA* 3.0 21.2 + - - +
151A ASP* 4.6 3.6 - - - +
265A THR* 5.2 0.2 + - - -
267A GLY* 3.9 22.5 - - - -
270A GLY 5.4 1.6 - - - +
271A GLU* 2.9 46.5 + - - +
336A ARG* 3.1 32.7 + - - +
337A LEU* 4.1 2.7 - - - +
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Residues in contact with ALA 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A ARG* 1.3 81.2 - - - +
130A PHE* 1.3 71.0 + - - +
142A GLN* 3.6 28.7 - - + +
143A ALA 3.5 9.4 - - - -
144A HIS* 3.6 18.7 - - + +
270A GLY* 3.4 33.0 + - - +
294A LEU* 4.2 7.6 - - + -
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Residues in contact with PHE 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A GLY* 3.8 24.5 - - - -
63A GLY 4.7 0.7 - - - -
128A ARG* 3.8 3.5 + - - -
129A ALA* 1.3 83.0 - - - +
131A GLY* 1.3 64.1 + - - +
132A GLY 3.3 1.7 + - - -
133A GLN* 3.6 26.6 + - - +
142A GLN* 3.0 22.1 + - - +
143A ALA 4.5 0.4 + - - -
146A CYS* 3.5 28.5 - - + -
265A THR* 4.1 1.6 - - - -
266A GLU* 3.5 31.4 - - + -
267A GLY* 3.5 24.0 - - - -
270A GLY* 5.0 0.2 - - - -
294A LEU* 3.9 11.0 - - - -
297A ARG* 3.6 14.4 - - - -
410A GLY* 3.5 37.9 - - - +
411A ALA* 3.9 4.0 - - + -
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Residues in contact with GLY 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A PHE* 1.3 72.9 - - - +
132A GLY* 1.3 60.8 + - - -
133A GLN* 3.8 4.3 + - - +
266A GLU* 2.7 32.4 + - - +
294A LEU* 3.5 22.7 - - - +
295A ALA 4.0 7.2 - - - -
296A SER* 5.0 2.3 - - - -
297A ARG* 6.3 0.2 - - - -
409A LEU* 4.1 12.6 - - - +
410A GLY* 4.4 8.5 + - - +
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Residues in contact with GLY 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A ASP* 3.8 19.2 - - - +
130A PHE 3.3 1.2 + - - -
131A GLY* 1.3 73.6 - - - -
133A GLN* 1.3 60.2 + - - +
134A SER* 5.6 0.8 - - - -
142A GLN* 5.3 0.6 + - - -
294A LEU 2.9 17.8 + - - -
295A ALA 4.2 0.2 + - - -
296A SER* 4.6 4.0 - - - -
409A LEU* 4.0 14.8 - - - +
621A TYR* 4.1 28.2 + - - -
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Residues in contact with GLN 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A ASN* 2.9 37.6 + - - +
79A HIS* 3.7 5.6 - - - -
82A ASP* 3.4 4.0 - - + +
130A PHE* 3.6 30.0 + - - +
131A GLY 3.5 5.6 - - - +
132A GLY* 1.3 81.6 - - - +
134A SER* 1.3 61.2 + - - +
142A GLN* 3.1 28.5 + - - +
143A ALA* 3.2 13.4 + - + +
145A ARG* 3.0 47.3 + - - +
146A CYS* 4.8 2.2 - - - +
409A LEU* 4.3 14.1 - - + -
410A GLY 4.4 1.2 + - - -
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Residues in contact with SER 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A TRP* 3.9 4.0 - - - +
82A ASP* 2.7 34.7 + - - +
132A GLY 5.6 0.9 - - - -
133A GLN* 1.3 73.3 - - - +
135A LEU* 1.3 60.9 + - - +
137A PHE* 4.8 0.2 - - - -
138A GLY* 3.0 34.4 + - - -
141A GLY 3.2 14.8 - - - -
143A ALA* 3.8 8.2 - - - +
145A ARG* 2.9 20.3 + - - -
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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