Contacts of the strand formed by residues 127 - 133 (chain B) in PDB entry 2A8I
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 PHE 127 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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298A VAL* 6.1 0.7 - - + -
299A ARG* 4.0 9.6 - - - +
118B SER* 3.8 21.8 - - - -
119B ILE 3.4 17.9 - - - -
120B MSE 4.2 11.7 - - + -
125B LEU 4.8 0.4 - - - +
126B ASN* 1.3 86.6 + - - +
128B GLY* 1.3 58.8 + - - +
129B ALA* 3.5 29.6 - - + -
146B LEU 4.9 0.3 - - - +
147B LEU* 4.0 12.1 - - - -
163B CYS* 3.3 38.0 - - - +
164B PHE* 5.3 3.8 - + + -
267B ALA 4.1 1.6 - - - -
268B LEU 4.3 1.3 - - - -
269B TYR* 3.6 65.7 - + + -
270B GLY 5.2 1.6 - - - -
273B CYS* 4.6 7.9 - - - -
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Residues in contact with GLY 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118B SER* 3.2 3.6 - - - -
119B ILE* 2.9 35.5 + - - +
127B PHE* 1.3 76.8 - - - +
129B ALA* 1.3 63.0 + - - +
143B ALA* 3.5 25.4 - - - +
146B LEU* 4.3 2.2 - - - -
147B LEU* 4.1 7.5 - - - +
163B CYS 3.4 5.8 - - - -
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Residues in contact with ALA 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B ALA 3.3 10.3 - - - +
118B SER* 3.7 1.8 - - - -
127B PHE* 3.5 19.3 - - + -
128B GLY* 1.3 75.1 - - - +
130B VAL* 1.3 70.4 + - - +
143B ALA* 4.0 3.4 - - - +
146B LEU* 3.3 7.4 - - - +
163B CYS 2.7 11.0 + - - +
164B PHE* 3.4 9.3 - - + -
165B LEU 3.2 21.3 + - - -
267B ALA 3.4 24.9 - - - +
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Residues in contact with VAL 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115B CYS 4.3 1.3 - - - +
116B ASP* 3.3 1.7 - - - -
117B ALA* 2.9 47.9 + - + +
129B ALA* 1.3 80.3 - - - +
131B GLY* 1.3 59.0 + - - +
133B LEU* 4.0 23.1 - - + -
139B PRO* 3.9 20.9 - - + +
142B VAL* 3.6 30.3 - - + -
143B ALA* 4.3 3.8 - - + +
146B LEU* 3.8 10.1 - - + -
164B PHE* 4.0 4.9 - - - -
165B LEU 3.2 11.2 - - - +
170B ALA* 4.4 10.1 - - + -
267B ALA* 3.4 4.2 - - - +
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Residues in contact with GLY 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115B CYS 3.8 0.7 - - - -
116B ASP* 3.4 10.3 - - - -
130B VAL* 1.3 75.4 - - - +
132B ALA* 1.3 70.1 + - - +
133B LEU* 3.2 4.4 + - - +
164B PHE* 3.7 2.2 - - - -
165B LEU 3.1 8.5 + - - -
166B VAL* 3.1 16.8 - - - -
167B GLY 3.1 18.5 + - - -
263B VAL* 4.3 5.2 - - - -
267B ALA* 4.1 9.2 - - - -
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Residues in contact with ALA 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A VAL* 3.9 25.1 - - + -
114B GLU* 4.0 30.0 - - - +
115B CYS 3.1 1.7 + - - -
116B ASP* 3.0 15.6 + - - -
131B GLY* 1.3 73.0 - - - +
133B LEU* 1.3 62.0 + - - +
134B SER* 3.9 2.8 + - - -
167B GLY* 3.4 18.0 - - - +
258B LYS* 5.9 0.2 - - - +
261B GLY* 4.2 15.9 - - - -
262B ARG 5.0 2.5 - - - +
263B VAL* 4.1 6.4 - - + +
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Residues in contact with LEU 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B ILE 3.7 0.7 - - - +
114B GLU* 3.3 2.4 - - - -
115B CYS* 2.8 44.5 + - + +
130B VAL* 4.0 27.6 - - + -
131B GLY 3.2 5.3 + - - +
132B ALA* 1.3 75.8 - - - +
134B SER* 1.3 74.1 + - - +
136B ILE* 3.8 28.2 - - + +
139B PRO* 4.2 11.0 - - + -
142B VAL* 4.1 16.8 - - + -
167B GLY 4.2 3.1 - - - +
170B ALA* 3.8 9.0 - - + -
171B TYR* 3.5 38.1 - - + +
187B MSE 6.1 0.2 - - - +
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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