Contacts of the strand formed by residues 142 - 150 (chain A) in PDB entry 2G9Y
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 142 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141A LEU* 1.3 76.8 - - - +
143A THR* 1.3 61.9 + - - +
201A ASP* 3.0 16.2 - - + +
309A LEU 5.7 0.2 - - - +
310A LEU* 3.8 17.3 - - + +
313A ASN* 3.7 29.4 + - + +
316A GLY 3.0 7.7 + - - -
317A PHE* 3.2 13.8 - - + -
318A PHE 3.1 22.9 + - - -
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Residues in contact with THR 143 (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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133A LEU* 3.6 41.1 - - + +
136A ALA* 3.8 15.0 - - + -
137A LYS* 3.7 19.3 - - + +
141A LEU 3.8 1.8 - - - +
142A ALA* 1.3 82.2 - - - +
144A GLY* 1.3 58.5 + - - +
200A ALA* 3.3 10.8 - - - +
201A ASP* 2.8 28.9 + - - -
202A VAL 3.0 23.8 + - - +
310A LEU* 3.3 8.0 - - - +
318A PHE* 3.3 6.7 - - + +
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Residues in contact with GLY 144 (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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133A LEU* 4.2 9.1 - - - +
143A THR* 1.3 76.2 - - - +
145A ASN* 1.3 60.6 + - - +
200A ALA* 5.3 0.2 - - - -
202A VAL* 3.2 9.9 - - - -
310A LEU* 3.8 9.1 - - - +
318A PHE* 2.9 13.2 + - - +
319A LEU* 3.4 20.0 - - - -
320A GLN* 3.0 23.4 + - - +
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Residues in contact with ASN 145 (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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133A LEU* 4.3 10.3 - - + -
144A GLY* 1.3 73.3 - - - +
146A VAL* 1.3 64.8 + - - +
151A LEU* 4.5 1.7 - - - +
156A PRO* 2.8 48.2 + - - +
159A LEU* 3.6 22.4 - - - +
160A VAL* 4.4 12.9 - - + +
195A LEU* 5.3 2.4 - - - +
200A ALA* 5.0 2.2 - - + -
202A VAL 2.8 10.6 + - - +
203A THR* 3.2 20.8 - - + +
204A LEU 3.0 24.1 + - - +
319A LEU* 4.2 0.8 - - - +
320A GLN* 3.7 6.5 + - - +
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Residues in contact with VAL 146 (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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145A ASN* 1.3 83.2 + - - +
147A SER* 1.3 67.6 + - - +
151A LEU* 5.4 0.2 - - - -
156A PRO* 5.2 0.2 - - - +
202A VAL* 4.9 1.6 - - + -
204A LEU* 3.4 28.9 - - + +
299A LEU* 3.9 18.6 - - + -
302A MET* 3.9 30.3 - - + +
306A ALA* 4.2 9.2 - - + -
319A LEU* 3.9 20.2 - - + -
320A GLN* 2.8 18.1 + - - +
321A VAL* 4.2 11.9 - - + -
322A GLU* 2.9 22.4 + - - +
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Residues in contact with SER 147 (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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146A VAL* 1.3 80.4 - - - +
148A THR* 1.3 63.1 + - - +
149A ALA* 3.0 19.1 + - - +
151A LEU* 4.7 2.2 - - - -
156A PRO* 4.0 22.0 - - - +
204A LEU 2.9 8.6 + - - +
205A GLY* 3.0 26.7 - - - -
264A MET* 3.9 2.9 - - - +
302A MET* 4.0 5.0 - - - +
322A GLU* 2.7 38.5 + - - -
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Residues in contact with THR 148 (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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147A SER* 1.3 73.4 + - - +
149A ALA* 1.3 60.6 + - - +
263A ASN* 3.9 1.7 - - - +
264A MET* 3.0 47.3 + - + +
299A LEU* 4.0 20.2 - - + +
302A MET* 4.5 5.8 - - + -
322A GLU 3.3 11.1 + - - +
323A GLY* 3.9 2.1 - - - -
324A ALA* 3.0 24.8 + - - +
325A SER* 3.7 11.2 + - - -
341A GLU* 4.6 8.6 + - - +
344A ASP* 4.0 21.1 - - - +
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Residues in contact with ALA 149 (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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147A SER* 3.0 15.0 + - - +
148A THR* 1.3 82.1 + - - +
150A GLU* 1.3 70.2 + - - +
151A LEU* 3.3 1.4 + - - -
153A ASP* 3.6 21.5 - - + +
205A GLY* 4.0 0.9 - - - -
206A GLY* 3.0 20.5 + - - -
263A ASN* 3.2 16.4 - - - +
322A GLU* 4.2 1.6 - - - +
324A ALA* 3.3 24.7 - - + +
325A SER* 5.8 0.2 - - - -
328A LYS* 3.9 1.3 - - - -
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Residues in contact with GLU 150 (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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149A ALA* 1.3 72.9 - - - +
151A LEU* 1.3 57.6 + - - +
152A GLN* 3.1 6.3 - - - +
153A ASP* 2.8 38.6 + - + +
156A PRO* 4.1 1.4 - - - +
169A TYR* 2.6 40.1 + - + +
206A GLY 3.4 11.2 - - - -
207A GLY* 3.4 19.0 - - - +
262A GLY* 3.8 19.7 - - - -
263A ASN* 2.9 24.1 + - - +
328A LYS* 5.2 1.9 + - - -
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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