Contacts of the strand formed by residues 328 - 334 (chain B) in PDB entry 2G1Y
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 ARG 328 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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187B TYR* 3.3 56.5 - - + +
188B ILE 3.4 9.0 - - - +
189B ASN* 3.5 26.6 - - - +
190B LEU* 4.1 2.4 - - - +
196B TRP* 3.6 3.6 - - - -
323B ASP* 2.9 55.5 + - + +
326B ASN* 3.3 26.6 + - - +
327B ASN* 1.3 77.5 - - - +
329B ILE* 1.3 67.9 + - - +
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Residues in contact with ILE 329 (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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187B TYR* 3.2 5.1 - - - -
188B ILE* 2.9 43.0 + - + +
190B LEU* 4.0 14.1 - - + -
196B TRP* 3.8 30.1 - - + +
198B ILE* 4.2 7.6 - - + -
220B VAL* 3.3 33.0 - - + -
320B THR* 3.7 26.9 - - + -
321B GLU 3.4 3.8 - - - +
322B PHE* 4.0 7.4 - - + -
328B ARG* 1.3 80.3 - - - +
330B GLY* 1.3 65.3 + - - +
331B PHE* 3.8 18.8 - - + -
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Residues in contact with GLY 330 (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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185B PHE* 3.7 11.7 - - - -
186B HIS 3.5 4.5 - - - -
187B TYR* 3.5 26.4 - - - -
320B THR* 3.4 2.8 - - - +
321B GLU* 2.8 35.0 + - - -
329B ILE* 1.3 73.7 - - - +
331B PHE* 1.3 70.9 + - - -
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Residues in contact with PHE 331 (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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184B ASN 4.0 1.4 - - - +
185B PHE* 3.2 7.8 - - - -
186B HIS* 3.0 28.4 + - - +
188B ILE* 3.6 27.1 - - + -
198B ILE* 4.5 5.2 - - + -
220B VAL* 4.2 18.6 - - + -
267B LEU* 3.9 22.2 - - + -
272B TYR* 3.4 37.0 + + + +
310B LEU* 4.9 0.7 - - + -
314B PHE* 3.6 22.9 - + - -
318B PHE* 4.1 10.1 - - + -
319B TYR 3.5 4.7 - - - -
320B THR* 3.1 32.5 - - + -
329B ILE* 3.8 16.2 - - + -
330B GLY* 1.3 79.7 - - - -
332B ALA* 1.3 61.6 + - - +
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Residues in contact with ALA 332 (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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181B TYR* 3.8 24.7 - - + -
182B GLU 4.1 6.1 - - - +
184B ASN 4.4 5.2 - - - +
185B PHE* 3.6 27.6 - - + +
272B TYR* 5.8 0.4 - - - -
318B PHE* 3.2 8.7 - - - -
319B TYR* 2.7 36.6 + - - -
331B PHE* 1.3 78.9 - - - +
333B LEU* 1.3 60.3 + - - +
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Residues in contact with LEU 333 (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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159B ARG* 5.9 1.8 - - - +
181B TYR* 3.1 2.5 - - - -
182B GLU* 2.8 70.1 + - + +
317B LYS* 3.7 37.0 - - + +
318B PHE* 4.2 15.5 - - + -
332B ALA* 1.3 70.8 - - - +
334B ALA* 1.3 87.2 + - - +
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Residues in contact with ALA 334 (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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156B TYR* 4.5 13.2 - - + -
159B ARG* 4.5 9.6 + - - +
180B HIS 3.3 13.2 - - - +
181B TYR* 3.9 1.1 - - - +
315B ILE 4.6 1.6 - - - +
316B ARG 4.1 10.8 - - - +
317B LYS 3.1 19.1 + - - +
318B PHE 4.1 0.7 - - - -
319B TYR* 3.5 22.4 - - + +
332B ALA 3.1 3.6 + - - -
333B LEU* 1.3 91.7 - - - +
335B ARG* 1.3 61.2 + - - +
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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