Contacts of the strand formed by residues 241 - 245 (chain B) in PDB entry 3GSB
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 LEU 241 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134B MET* 3.8 36.2 - - + +
137B TYR* 3.9 31.9 - - + -
138B THR* 3.9 15.9 - - + -
207B ALA 3.0 12.0 + - - +
208B GLY* 3.0 2.4 - - - -
209B VAL 2.8 27.7 + - - +
235B THR* 4.3 4.1 - - - +
239B ASP 5.8 0.7 - - - +
240B ALA* 1.3 78.1 - - - +
242B LEU* 1.3 59.7 + - - +
243B VAL* 4.0 6.7 - - + -
267B ASP* 3.3 28.5 - - + +
268B LEU* 5.2 4.7 - - + -
290B ILE* 4.0 18.8 - - + -
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Residues in contact with LEU 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B VAL* 3.6 20.0 - - + +
211B LEU* 4.1 11.0 - - + -
228B LEU* 5.2 0.9 - - + +
231B LEU* 4.7 10.8 - - + +
232B ARG* 3.6 45.5 - - + +
235B THR* 4.0 15.9 - - + +
240B ALA 4.0 0.6 + - - -
241B LEU* 1.3 72.3 - - - +
243B VAL* 1.3 64.4 + - - +
244B PHE* 3.6 35.7 - - + -
264B VAL* 4.7 4.5 - - + -
266B PRO* 3.3 14.0 - - + +
267B ASP* 2.8 36.3 + - - +
268B LEU 3.6 3.3 + - - -
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Residues in contact with VAL 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B VAL* 3.6 29.8 - - + -
134B MET* 3.5 34.3 - - + -
209B VAL 2.8 15.1 + - - +
210B ILE* 4.2 17.5 - - + -
211B LEU* 3.3 24.1 + - - +
241B LEU* 4.5 6.7 - - + -
242B LEU* 1.3 80.5 - - - +
244B PHE* 1.3 73.1 + - - +
268B LEU* 3.6 25.1 - - + +
269B THR* 4.4 2.0 - - - +
270B THR* 4.9 2.7 - - + -
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Residues in contact with PHE 244 (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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211B LEU* 3.7 22.2 - - + -
213B PRO* 3.5 24.2 - - + -
228B LEU* 4.1 24.0 - - + -
242B LEU* 3.6 27.1 - - + -
243B VAL* 1.3 83.7 - - - +
245B ASP* 1.3 59.0 + - - +
246B GLU* 3.1 26.9 + - + -
258B VAL 5.3 0.4 - - - -
259B GLN* 4.0 8.1 - - + -
264B VAL* 4.0 22.0 - - + -
266B PRO* 3.7 34.1 - - + -
268B LEU 3.3 7.4 + - - +
269B THR* 3.2 6.0 - - - -
270B THR 3.1 22.9 + - - -
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Residues in contact with ASP 245 (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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127B CYS* 3.3 12.5 - - - -
151B HIS* 3.2 36.1 - - + -
210B ILE* 4.7 6.9 - - + +
211B LEU 2.9 12.2 + - - +
212B GLU* 3.9 5.9 - - - +
213B PRO* 3.4 15.6 - - - +
243B VAL 4.1 1.0 + - - -
244B PHE* 1.3 69.2 - - - +
246B GLU* 1.3 57.3 + - - +
247B VAL* 3.3 11.3 + - - +
248B MET* 5.0 0.5 + - - +
249B THR* 4.2 1.4 + - - +
270B THR* 3.3 16.8 - - - +
601B PMP 2.8 47.6 + - - +
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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
------------------------------------------------------------
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