Contacts of the strand formed by residues 115 - 121 (chain A) 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 CYS 115 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A GLY* 3.9 16.4 - - - +
105A SER* 3.5 24.2 - - - -
113A ILE* 3.8 15.0 - - - -
114A GLU* 1.3 77.0 - - - +
116A ASP* 1.3 66.2 + - - +
130A VAL* 4.0 1.0 - - - +
131A GLY* 3.6 1.9 - - - -
132A ALA 3.2 5.7 + - - -
133A LEU* 2.8 41.3 + - + +
136A ILE 5.3 0.2 - - - -
139A PRO* 3.4 29.6 - - + -
187A MSE 4.4 5.2 - - - -
251A SER* 5.5 0.7 - - - +
252A SER 3.5 9.0 - - - +
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Residues in contact with ASP 116 (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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115A CYS* 1.3 75.6 - - - +
117A ALA* 1.3 64.2 + - - +
130A VAL 3.4 4.0 - - - -
131A GLY* 3.3 3.6 - - - -
132A ALA* 3.0 27.2 + - - -
251A SER* 3.4 1.6 + - - -
252A SER* 2.8 38.2 + - - +
254A GLY* 4.9 6.2 - - - -
258A LYS* 4.5 10.1 + - - -
262A ARG 4.3 3.9 - - - +
263A VAL* 3.8 6.2 - - - +
264A GLY* 2.9 31.6 + - - -
266A ALA* 3.6 18.4 - - + +
267A ALA* 3.9 13.0 - - + +
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Residues in contact with ALA 117 (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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116A ASP* 1.3 76.9 - - - +
118A SER* 1.3 63.6 + - - +
129A ALA* 3.2 2.8 - - - +
130A VAL* 2.9 36.1 + - + +
139A PRO* 3.7 29.2 - - + +
140A VAL* 3.8 16.4 - - - +
143A ALA* 4.2 2.0 - - - -
250A VAL 3.3 12.6 - - - +
251A SER* 3.7 7.4 - - - +
266A ALA 3.2 5.8 + - - +
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Residues in contact with SER 118 (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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117A ALA* 1.3 75.3 - - - +
119A ILE* 1.3 64.9 + - - +
127A PHE* 3.7 13.8 - - - -
128A GLY 3.2 7.6 - - - -
129A ALA* 3.5 17.5 - - - -
140A VAL* 5.0 2.4 - - - +
143A ALA* 4.1 3.5 - - - +
249A ALA* 3.3 4.2 - - - +
250A VAL* 3.0 42.3 + - - +
266A ALA 2.7 21.2 + - - -
267A ALA* 4.4 1.4 - - - -
268A LEU 5.1 1.2 + - - -
272A GLY* 4.8 0.9 - - - -
273A CYS* 3.5 11.6 + - - -
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Residues in contact with ILE 119 (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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83A THR* 3.8 12.8 - - - +
86A VAL* 3.8 18.4 - - + -
87A THR* 3.4 25.1 - - - +
118A SER* 1.3 78.9 - - - +
120A MSE 1.3 68.7 + - - +
127A PHE* 3.3 6.2 - - - -
128A GLY 2.9 29.0 + - - +
140A VAL* 4.9 4.3 - - + +
143A ALA* 3.6 34.5 - - + +
144A ASN* 3.8 12.6 - - + +
147A LEU* 3.8 14.3 - - + +
248A ALA 3.2 15.9 - - - +
249A ALA* 4.0 7.0 - - + -
273A CYS* 3.9 3.8 - - - -
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Residues in contact with MSE 120 (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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83A THR* 4.4 0.2 - - - +
119A ILE* 1.3 78.3 - - - +
121A ASP* 1.3 59.4 + - - +
125A LEU* 4.0 11.4 - - - +
126A ASN 3.4 17.7 - - - +
127A PHE* 4.4 9.0 - - + -
147A LEU* 4.2 4.5 - - - -
247A ALA* 3.3 8.1 - - - +
248A ALA 2.9 29.9 + - - +
269A TYR* 4.0 13.7 - - + +
270A GLY 5.8 0.2 - - - -
273A CYS* 4.1 9.6 - - - +
274A TRP* 3.5 55.9 - - + -
275A ALA* 3.3 40.2 - - + +
332B PHE* 3.7 17.3 - - + -
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Residues in contact with ASP 121 (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 ALA* 5.1 3.8 + - - +
83A THR* 3.3 30.9 + - + +
120A MSE 1.3 72.9 - - - +
122A GLY* 1.3 57.2 + - - +
123A LYS* 3.6 11.8 + - - +
124A SER* 2.7 41.5 + - - +
125A LEU* 2.7 35.9 + - - -
126A ASN 3.0 10.1 + - - +
147A LEU* 4.1 9.8 - - + +
151A GLN* 5.0 0.7 + - - +
245A ASN* 5.6 1.7 - - - +
246A VAL 4.1 5.9 - - - +
275A ALA* 4.0 3.1 - - - +
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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