Contacts of the strand formed by residues 297 - 307 (chain C) 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 VAL 297 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15C ILE* 6.0 0.4 - - + -
17C GLU* 4.8 0.2 - - - +
52C TRP* 3.8 19.2 - - - -
283C VAL* 3.5 39.7 - - + -
284C ILE 3.5 4.0 - - - +
285C ARG* 3.4 37.0 - - + +
296C ARG* 1.3 74.0 - - - +
298C LEU* 1.3 65.2 + - - +
299C SER* 4.1 3.9 + - - +
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Residues in contact with LEU 298 (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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26C LEU* 4.1 27.4 - - + -
29C SER* 5.5 2.5 - - - +
34C LYS* 4.2 19.3 - - + +
47C GLU* 3.7 40.8 - - + +
49C GLN* 3.9 18.8 - - + -
50C ALA* 4.9 0.4 - - + -
52C TRP* 4.4 20.0 - - + -
283C VAL* 3.5 0.2 - - - -
284C ILE* 2.8 42.1 + - + +
286C GLU* 6.1 0.2 - - + -
296C ARG 3.8 0.6 + - - -
297C VAL* 1.3 75.8 - - - +
299C SER* 1.3 66.1 + - - +
300C THR* 3.6 11.5 + - + +
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Residues in contact with SER 299 (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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47C GLU* 5.7 0.3 - - - -
49C GLN* 3.0 35.1 + - - +
281C GLU* 2.6 42.3 + - - +
282C LEU 4.0 0.2 + - - -
283C VAL* 3.7 15.5 - - - +
297C VAL* 4.0 5.8 + - - +
298C LEU* 1.3 77.4 - - - +
300C THR* 1.3 60.8 + - - +
301C SER 4.3 3.1 + - - -
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Residues in contact with THR 300 (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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34C LYS* 6.4 0.4 - - - +
49C GLN* 5.1 1.9 + - - +
115C GLU* 3.3 31.4 - - + +
253C TYR* 3.3 19.6 - - - -
254C SER 5.0 2.4 + - - -
282C LEU 2.9 19.2 + - - +
284C ILE* 3.7 31.6 - - + -
298C LEU* 3.9 14.1 - - + +
299C SER* 1.3 76.7 - - - +
301C SER* 1.3 76.2 + - - +
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Residues in contact with SER 301 (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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116C GLN* 3.8 2.5 + - - -
252C ALA 3.5 13.5 - - - -
253C TYR* 3.5 30.5 + - - +
254C SER 5.7 0.2 - - - +
281C GLU* 3.4 8.8 - - - +
282C LEU* 3.0 40.3 + - - +
299C SER* 3.9 2.2 + - - -
300C THR* 1.3 92.7 + - - +
302C LEU* 1.3 71.1 + - - +
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Residues in contact with LEU 302 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251C THR* 3.4 5.4 - - - +
252C ALA* 2.9 39.0 + - + +
255C ILE* 3.5 21.8 - - + -
257C ALA* 3.3 24.9 - - + +
258C SER 3.9 7.0 - - - +
259C PHE* 3.9 17.0 - - - +
262C MSE 3.8 30.1 - - + -
280C GLY 3.4 6.5 - - - +
281C GLU* 4.1 22.7 - - + +
282C LEU* 5.1 0.6 - - - +
301C SER* 1.3 81.3 + - - +
303C PHE* 1.3 65.3 + - - +
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Residues in contact with PHE 303 (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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14C VAL* 3.3 35.9 - - + -
16C LEU* 3.6 29.2 - - + -
119C HIS* 3.6 32.5 - + + +
249C VAL* 5.5 0.4 - - + -
250C LEU* 3.1 13.0 - - - +
251C THR* 4.4 0.2 - - + -
259C PHE* 4.8 2.4 - - - +
262C MSE 4.8 5.4 - - - +
278C ALA* 3.4 26.9 - - + -
279C SER* 3.3 8.8 - - - -
280C GLY 2.9 49.0 + - - +
281C GLU 3.6 16.2 - - - -
282C LEU* 4.2 3.1 - - + -
302C LEU* 1.3 77.4 - - - +
304C SER* 1.3 67.1 + - - +
305C ARG* 4.3 11.4 - - + -
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Residues in contact with SER 304 (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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249C VAL* 3.6 0.5 - - - +
250C LEU* 2.8 36.2 + - - +
262C MSE 3.9 17.8 + - - -
266C MSE 3.1 41.3 - - - +
277C VAL* 3.4 3.8 - - - +
278C ALA 3.4 5.8 - - - -
279C SER* 2.8 20.5 + - - -
303C PHE* 1.3 75.8 - - - +
305C ARG* 1.3 60.7 + - - +
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Residues in contact with ARG 305 (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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14C VAL* 6.2 2.2 - - - +
16C LEU* 4.6 17.6 - - - +
118C VAL* 5.9 0.8 + - - +
119C HIS* 4.6 14.1 + - + +
122C TRP* 3.9 44.9 - - + +
248C LEU 3.3 3.1 - - - +
249C VAL* 3.8 26.5 - - + -
276C VAL 3.5 1.7 - - - +
277C VAL* 3.3 6.1 - - - -
278C ALA* 2.8 55.4 + - - +
303C PHE* 4.7 9.3 - - + -
304C SER* 1.3 77.4 + - - +
306C TRP* 1.3 69.1 + - - +
307C GLU* 3.1 25.8 + - + +
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Residues in contact with TRP 306 (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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8C PRO* 4.4 1.1 - - + -
241C LEU* 4.3 13.5 - - + -
245C ALA* 4.3 14.6 - - + -
247C GLY* 3.1 9.7 - - - -
248C LEU* 2.9 45.7 + - + +
266C MSE 4.3 7.6 - - - +
270C MSE 3.6 55.8 - - + +
273C ALA* 3.9 19.5 - - + +
274C GLY 2.9 22.1 + - - -
276C VAL 3.4 15.7 - - - +
277C VAL* 3.9 13.5 - - + -
304C SER 4.3 0.2 - - - -
305C ARG* 1.3 74.0 - - - +
307C GLU* 1.3 67.8 + - - +
308C PRO* 3.8 38.6 - - + -
1006C ACY 4.1 19.3 - - + -
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Residues in contact with GLU 307 (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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122C TRP* 3.0 30.5 + - + -
246C LEU 3.6 10.1 - - - +
275C GLY* 3.3 1.9 - - - -
276C VAL* 3.0 41.8 + - + +
278C ALA* 6.0 0.5 - - - +
305C ARG* 3.1 33.3 + - + +
306C TRP* 1.3 87.2 - - - +
308C PRO* 1.4 70.3 - - + +
309C LYS* 3.1 8.7 + - - +
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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