Contacts of the strand formed by residues 247 - 252 (chain B) in PDB entry 2IGT
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 GLY 247 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122B TRP* 3.9 16.8 - - - -
206B ASP 3.5 2.4 + - - -
207B ILE* 3.4 5.4 - - - +
208B ILE 3.1 23.6 + - - -
241B LEU* 3.9 6.4 - - - +
245B ALA* 3.6 1.8 - - - +
246B LEU* 1.3 82.4 - - - +
248B LEU* 1.3 60.1 + - - +
249B VAL 4.2 0.2 - - - -
306B TRP* 3.1 20.9 - - - -
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Residues in contact with LEU 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B ILE* 3.4 35.7 - - + +
210B THR* 4.7 7.4 - - + -
234B LEU* 4.6 11.7 - - + +
237B CYS* 3.9 26.9 - - + -
238B ARG 4.8 0.4 - - - +
241B LEU* 4.5 16.8 - - + -
247B GLY* 1.3 75.0 - - - +
249B VAL* 1.3 66.9 + - - +
266B MSE 3.7 30.7 - - + +
270B MSE 4.2 16.2 - - - -
304B SER 3.8 1.9 - - - +
305B ARG* 3.3 3.5 - - - -
306B TRP* 2.9 39.4 + - + +
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Residues in contact with VAL 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B HIS* 3.9 32.3 - - + +
122B TRP* 3.7 34.8 - - + -
208B ILE 2.8 10.3 + - - +
209B LEU* 3.4 18.1 - - + +
210B THR* 2.9 31.3 + - - +
248B LEU* 1.3 76.3 - - - +
250B LEU* 1.3 62.7 + - - +
251B THR* 4.2 14.9 - - + +
303B PHE* 5.4 0.4 - - + -
304B SER 3.7 4.5 - - - +
305B ARG* 3.9 22.0 - - + +
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Residues in contact with LEU 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B THR* 3.6 14.4 - - + -
212B PRO* 3.7 32.1 - - + -
230B LEU* 4.0 29.2 - - + -
234B LEU* 4.4 14.8 - - + -
248B LEU 4.1 0.8 + - - -
249B VAL* 1.3 73.3 - - - +
251B THR* 1.3 69.0 + - - +
252B ALA* 5.0 3.1 - - + -
262B MSE 4.1 29.2 - - + +
266B MSE 3.6 14.8 - - + -
303B PHE* 3.1 8.2 - - - +
304B SER* 2.8 43.6 + - - +
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Residues in contact with THR 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B GLN* 3.6 23.4 + - - +
119B HIS* 3.6 32.5 - - + +
210B THR 2.9 6.6 + - - +
211B ASP* 2.8 43.1 + - - +
212B PRO* 3.4 21.0 - - - +
249B VAL* 4.1 10.7 + - + -
250B LEU* 1.3 80.1 - - - +
252B ALA* 1.3 62.0 + - - +
253B TYR* 5.1 0.7 - - - -
301B SER* 5.5 0.2 - - - -
302B LEU 3.4 5.8 - - - +
303B PHE* 4.4 1.6 - - + -
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Residues in contact with ALA 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B ASP* 4.3 0.2 + - - -
212B PRO 4.4 5.4 - - - -
226B LEU* 4.5 15.5 - - + -
250B LEU* 5.0 4.7 - - + -
251B THR* 1.3 75.4 - - - +
253B TYR* 1.3 68.0 + - - +
255B ILE* 3.5 3.3 - - - +
262B MSE 4.4 22.0 - - + -
301B SER* 3.5 1.6 - - - -
302B LEU* 2.8 52.0 + - + +
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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