Contacts of the strand formed by residues 297 - 307 (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 VAL 297 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15B ILE* 5.8 1.3 - - + -
17B GLU* 4.4 2.9 - - - +
52B TRP* 3.7 19.0 - - - -
283B VAL* 3.5 37.2 - - + -
284B ILE 3.6 3.6 - - - -
285B ARG* 3.5 38.6 - - + +
296B ARG* 1.3 74.9 - - - +
298B LEU* 1.3 62.5 + - - +
299B SER* 4.1 4.0 + - - +
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Residues in contact with LEU 298 (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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26B LEU* 4.1 25.6 - - + -
29B SER* 5.4 2.5 - - - -
34B LYS* 4.1 17.9 - - + +
47B GLU* 3.7 42.6 - - + +
49B GLN* 3.9 22.0 - - + +
50B ALA* 4.8 0.7 - - + -
52B TRP* 4.2 20.4 - - + -
284B ILE* 2.7 46.2 + - + +
296B ARG 3.8 1.0 + - - -
297B VAL* 1.3 73.2 - - - +
299B SER* 1.3 64.5 + - - +
300B THR* 3.6 11.3 + - + +
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Residues in contact with SER 299 (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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49B GLN* 2.8 37.1 + - - +
255B ILE* 5.3 7.3 - - - +
281B GLU* 2.6 41.3 + - - +
282B LEU 4.0 0.3 + - - -
283B VAL* 3.7 16.8 - - - +
297B VAL* 4.0 5.8 - - - +
298B LEU* 1.3 75.5 - - - +
300B THR* 1.3 61.4 + - - +
301B SER 4.3 2.9 + - - -
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Residues in contact with THR 300 (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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34B LYS* 6.3 1.6 - - - +
49B GLN* 5.0 1.1 - - - +
115B GLU* 3.2 29.7 + - + +
253B TYR* 3.2 17.2 - - - -
254B SER 5.0 0.5 + - - -
255B ILE* 3.4 11.8 - - - +
282B LEU 2.9 13.5 + - - +
284B ILE* 3.6 33.2 - - + -
298B LEU* 3.8 14.4 - - + +
299B SER* 1.3 78.4 - - - +
301B SER* 1.3 78.2 + - - +
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Residues in contact with SER 301 (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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116B GLN* 3.8 6.9 + - - -
252B ALA 3.5 9.9 - - - -
253B TYR* 3.7 21.5 - - - -
255B ILE* 3.2 14.1 - - - +
281B GLU* 3.3 9.2 - - - +
282B LEU* 3.0 41.8 + - - +
299B SER* 3.8 1.3 + - - -
300B THR* 1.3 92.9 + - - +
302B LEU* 1.3 68.3 + - - +
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Residues in contact with LEU 302 (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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119B HIS* 5.4 0.2 - - - -
251B THR* 3.4 6.4 - - - +
252B ALA* 2.8 46.6 + - + +
254B SER 5.1 3.4 - - - +
255B ILE* 3.6 26.5 - - + -
257B ALA* 3.5 26.9 - - + +
258B SER* 3.9 1.8 - - - +
259B PHE* 3.9 22.2 - - + +
262B MSE 3.8 29.2 - - + -
280B GLY 3.4 6.1 - - - +
281B GLU* 4.0 22.7 - - + +
282B LEU* 5.6 0.4 - - - -
301B SER* 1.3 80.1 + - - +
303B PHE* 1.3 65.7 + - - +
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Residues in contact with PHE 303 (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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14B VAL* 3.3 35.2 - - + -
16B LEU* 3.5 30.3 - - + -
119B HIS* 3.6 32.1 - + + +
249B VAL* 5.4 0.9 - - + -
250B LEU* 3.1 13.5 - - - +
251B THR* 4.4 0.4 - - + -
259B PHE* 4.7 2.6 - - - +
262B MSE 5.0 4.4 - - - +
278B ALA* 3.5 27.8 - - + -
279B SER* 3.3 7.8 - - - -
280B GLY 3.1 50.4 + - - +
281B GLU 3.6 15.0 - - - -
282B LEU* 4.2 2.2 - - + -
302B LEU* 1.3 77.2 - - - +
304B SER* 1.3 69.9 + - - +
305B ARG* 4.2 12.1 - - + -
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Residues in contact with SER 304 (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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249B VAL* 5.2 0.2 - - - -
250B LEU* 2.8 39.2 + - - +
262B MSE 4.2 17.0 - - - -
263B HIS* 4.0 0.7 - - - -
266B MSE 3.1 40.3 - - - +
277B VAL* 3.4 1.9 - - - +
278B ALA 3.4 6.5 - - - -
279B SER* 2.8 20.3 + - - -
303B PHE* 1.3 76.6 - - - +
305B ARG* 1.3 58.1 + - - +
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Residues in contact with ARG 305 (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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14B VAL* 6.0 1.8 - - - +
16B LEU* 4.7 18.2 - - - +
118B VAL* 5.8 1.8 + - - +
119B HIS* 4.6 13.3 - - - -
122B TRP* 3.9 46.0 - - + +
248B LEU 3.3 4.7 - - - +
249B VAL* 3.9 26.7 - - + -
276B VAL 3.5 1.7 - - - +
277B VAL* 3.3 5.3 - - - -
278B ALA* 2.8 55.5 + - - +
303B PHE* 4.6 10.8 - - + -
304B SER* 1.3 74.4 + - - +
306B TRP* 1.3 70.9 + - - +
307B GLU* 3.3 24.8 + - + +
309B LYS* 5.3 2.8 - - - +
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Residues in contact with TRP 306 (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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8B PRO* 4.3 1.1 - - + -
241B LEU* 4.2 18.2 - - + -
245B ALA* 4.3 13.7 - - + -
247B GLY* 3.1 15.1 - - - -
248B LEU* 2.9 46.0 + - + +
266B MSE 4.4 8.5 - - - +
270B MSE 3.6 54.0 - - + +
273B ALA* 3.9 19.0 - - + +
274B GLY 2.8 23.6 + - - -
276B VAL 3.4 14.6 - - - -
277B VAL* 4.0 11.9 - - + -
304B SER 4.3 0.2 - - - -
305B ARG* 1.3 73.6 - - - +
307B GLU* 1.3 71.1 + - - +
308B PRO* 3.9 36.6 - - + -
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Residues in contact with GLU 307 (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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122B TRP* 2.8 30.8 + - + +
246B LEU 3.7 10.9 - - - +
275B GLY* 3.2 2.6 - - - -
276B VAL* 2.8 37.9 + - + +
305B ARG* 3.3 31.3 + - + +
306B TRP* 1.3 86.6 + - - +
308B PRO* 1.3 70.6 - - + +
309B LYS* 3.2 51.3 + - + +
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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