Contacts of the strand formed by residues 242 - 250 (chain C) in PDB entry 2G1T
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 ILE 242 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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237C MET* 4.0 24.7 - - + -
238C GLU 3.9 7.2 - - - +
239C ARG* 3.1 17.8 + - - +
240C THR* 3.1 5.9 - - - +
241C ASP* 1.3 100.1 - - + +
243C THR* 1.3 71.1 + - - +
244C MET* 3.7 13.0 + - - +
259C GLY* 4.0 8.5 - - - -
260C VAL 3.3 23.6 - - - +
261C TRP* 4.0 17.7 - - + -
262C LYS* 4.3 1.5 - - - -
268C VAL* 4.5 4.0 - - + -
270C VAL* 4.0 15.7 - - + -
305C CYS* 5.2 4.0 - - - -
314C ILE* 4.7 14.4 - - + -
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Residues in contact with THR 243 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242C ILE* 1.3 71.8 - - - +
244C MET* 1.3 70.3 + - - +
245C LYS* 4.2 14.4 - - + +
259C GLY* 3.2 5.2 - - - -
260C VAL* 2.9 42.5 + - - +
262C LYS* 3.3 26.2 - - - +
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Residues in contact with MET 244 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239C ARG 5.7 2.0 - - - +
242C ILE* 3.7 15.0 + - - +
243C THR* 1.3 79.4 - - - +
245C LYS* 1.3 67.3 + - - +
257C TYR* 3.8 30.5 - - + -
258C GLU 4.1 1.3 - - - -
259C GLY* 5.2 0.2 - - - -
270C VAL* 3.6 43.3 - - + -
272C THR* 3.9 15.3 - - + -
312C TYR* 4.3 15.3 - - + +
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Residues in contact with LYS 245 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243C THR* 4.2 14.6 - - + +
244C MET* 1.3 80.8 - - - +
246C HIS* 1.3 78.4 + - + +
257C TYR* 3.6 15.1 - - - +
258C GLU* 2.8 41.4 + - + +
260C VAL* 3.5 31.7 - - + +
267C THR* 5.5 1.4 + - - -
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Residues in contact with HIS 246 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245C LYS* 1.3 85.0 - - + +
247C LYS* 1.3 68.5 + - - +
248C LEU* 3.5 10.3 + - + +
257C TYR* 4.0 0.2 - - - -
258C GLU* 2.6 68.1 + - + +
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Residues in contact with LYS 247 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245C LYS 3.8 0.2 + - - -
246C HIS* 1.3 78.5 + - - +
248C LEU* 1.3 64.7 + - - +
249C GLY* 3.1 35.0 - - - +
250C GLY* 4.3 1.6 - - - +
255C GLU* 2.6 38.5 + - + +
256C VAL 3.6 4.5 - - - +
257C TYR* 3.5 29.3 - - + +
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Residues in contact with LEU 248 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246C HIS* 4.1 18.6 - - + +
247C LYS* 1.3 74.9 - - - +
249C GLY* 1.3 57.9 + - - +
256C VAL* 2.7 17.6 + - + +
257C TYR 4.1 4.0 - - - +
258C GLU* 3.7 37.2 - - + +
269C ALA* 5.2 0.7 - - + -
317C PHE* 3.7 22.4 - - + -
1301G 112 3.5 53.1 + - + +
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Residues in contact with GLY 249 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247C LYS* 3.1 28.2 - - - +
248C LEU* 1.3 81.9 - - - +
250C GLY* 1.3 59.3 + - - -
255C GLU* 3.5 0.2 - - - -
256C VAL 2.9 21.2 + - - -
1301G 112 4.4 9.3 + - - -
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Residues in contact with GLY 250 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247C LYS* 4.3 3.3 - - - +
249C GLY* 1.3 74.4 - - - -
251C GLY* 1.3 57.8 + - - -
254C GLY 3.3 12.3 - - - -
255C GLU* 3.9 4.7 - - - -
256C VAL 4.3 0.2 - - - -
1301G 112 3.3 24.8 + - - +
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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