Contacts of the strand formed by residues 142 - 150 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141B LEU* 1.3 74.2 - - - +
143B THR* 1.3 61.5 + - - +
201B ASP* 2.9 15.7 - - - +
309B LEU 5.5 0.2 - - - +
310B LEU* 3.6 18.4 - - + +
313B ASN* 3.1 23.6 - - + +
316B GLY 2.9 7.5 + - - -
317B PHE* 3.1 19.4 - - + -
318B PHE 2.8 26.5 + - - -
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Residues in contact with THR 143 (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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133B LEU* 3.6 43.5 - - + +
136B ALA* 3.9 9.4 - - + -
137B LYS* 3.7 25.1 - - + +
141B LEU 3.9 3.4 - - - +
142B ALA* 1.3 79.7 - - - +
144B GLY* 1.3 59.3 + - - +
200B ALA* 3.4 11.5 - - - +
201B ASP* 3.0 26.7 + - - +
202B VAL 3.0 23.6 + - - +
310B LEU* 3.6 5.2 - - - +
318B PHE* 3.4 3.6 - - + +
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Residues in contact with GLY 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B LEU* 4.3 2.8 - - - +
143B THR* 1.3 75.5 - - - +
145B ASN* 1.3 59.5 + - - +
202B VAL* 3.3 10.1 - - - -
310B LEU* 3.8 8.9 - - - +
318B PHE* 2.8 18.6 + - - +
319B LEU* 3.4 22.0 - - - -
320B GLN* 3.1 24.1 + - - +
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Residues in contact with ASN 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B LEU* 4.2 11.9 - - + -
144B GLY* 1.3 73.6 - - - +
146B VAL* 1.3 63.6 + - - +
151B LEU* 4.4 2.2 - - - +
156B PRO* 2.9 50.7 + - - +
159B LEU* 3.6 19.9 - - - +
160B VAL* 4.6 11.3 - - - +
195B LEU* 5.4 2.8 - - - +
200B ALA* 5.1 2.9 - - + -
202B VAL 2.8 11.0 + - - +
203B THR* 3.4 20.2 + - - +
204B LEU 3.1 23.4 + - - +
319B LEU* 4.2 0.4 - - - +
320B GLN* 3.8 7.6 + - - +
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Residues in contact with VAL 146 (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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145B ASN* 1.3 81.3 + - - +
147B SER* 1.3 67.3 + - - +
151B LEU* 5.3 0.4 - - - -
156B PRO* 5.5 0.2 - - - +
202B VAL* 4.9 1.8 - - + -
204B LEU* 3.4 23.6 - - + +
299B LEU* 4.2 11.2 - - + -
302B MET* 3.9 37.5 - - + +
303B THR 4.9 0.2 - - - +
306B ALA* 4.2 15.9 - - + -
319B LEU* 3.9 18.8 - - + -
320B GLN* 2.8 16.4 + - - +
321B VAL* 3.4 13.2 - - + -
322B GLU* 2.8 25.5 + - - +
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Residues in contact with SER 147 (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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146B VAL* 1.3 79.1 - - - +
148B THR* 1.3 63.7 + - - +
149B ALA* 2.9 22.4 + - - +
151B LEU* 4.6 2.7 - - - +
156B PRO* 4.1 21.7 - - - +
204B LEU 3.0 7.8 + - - +
205B GLY* 3.0 26.3 - - - -
264B MET* 3.8 3.3 - - - +
302B MET* 3.9 5.2 - - - +
322B GLU* 2.7 35.3 + - - -
324B ALA* 3.8 0.3 - - - +
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Residues in contact with THR 148 (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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147B SER* 1.3 73.0 + - - +
149B ALA* 1.3 60.4 + - - +
263B ASN* 3.8 2.1 - - - +
264B MET* 2.8 46.2 + - + +
265B PRO 6.2 0.4 - - - -
299B LEU* 3.8 37.7 - - + +
302B MET* 4.4 7.0 - - + -
322B GLU 3.4 4.6 + - - +
323B GLY* 4.1 1.4 - - - -
324B ALA* 3.1 25.3 + - - +
325B SER* 3.7 10.1 + - - -
341B GLU* 4.7 9.2 + - - +
344B ASP* 4.2 10.1 - - - +
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Residues in contact with ALA 149 (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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147B SER* 2.9 14.5 + - - +
148B THR* 1.3 81.8 + - - +
150B GLU* 1.3 69.7 + - - +
151B LEU* 3.2 2.1 + - - -
153B ASP* 3.9 13.9 - - + +
205B GLY* 4.1 0.7 - - - -
206B GLY 3.1 18.4 + - - -
263B ASN* 3.0 17.3 - - - +
322B GLU* 4.4 0.9 - - - +
324B ALA* 3.3 22.9 - - + -
325B SER* 5.9 0.2 - - - -
328B LYS* 3.8 10.1 - - - -
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Residues in contact with GLU 150 (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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149B ALA* 1.3 70.2 - - - +
151B LEU* 1.3 52.6 + - - +
152B GLN* 3.0 7.2 - - - +
153B ASP* 2.7 41.5 + - + +
156B PRO* 4.3 1.4 - - - +
169B TYR* 2.6 41.8 + - + +
206B GLY 3.4 11.2 - - - -
207B GLY* 3.6 19.0 - - - +
262B GLY* 3.8 18.8 - - - -
263B ASN* 2.8 26.8 + - - +
328B LYS* 5.3 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