Contacts of the helix formed by residues 298 - 312 (chain B) in PDB entry 1G9Y
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 LYS 298 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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217B VAL* 3.1 36.6 - - + +
218B ASP* 2.9 28.1 + - - +
219B GLY 5.0 0.9 + - - -
221B GLY 2.9 24.5 + - - +
222B SER* 4.6 4.7 - - - +
223B ILE* 3.6 14.6 - - + +
295B LEU* 4.1 6.7 - - + -
297B LEU* 1.3 87.0 - - + +
299B GLN* 1.3 63.5 + - - +
300B LYS 3.3 2.2 - - - -
301B GLN* 3.3 24.6 - - + +
302B ALA* 3.1 22.7 + - - +
336B ASN* 5.1 1.6 + - - +
415C G 4.2 4.6 + - - -
416C A 3.0 25.1 + - - -
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Residues in contact with GLN 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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292B GLN* 3.0 48.3 + - + +
293B PRO* 3.6 12.5 + - - +
295B LEU* 3.5 35.1 + - + +
296B LYS* 4.5 4.2 + - - +
297B LEU 3.6 2.2 - - - +
298B LYS* 1.3 77.8 - - - +
300B LYS* 1.3 65.4 + - + +
302B ALA* 3.2 2.1 + - - +
303B ASN* 3.0 34.6 + - - +
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Residues in contact with LYS 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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297B LEU 5.4 0.2 + - - -
298B LYS 3.3 0.6 - - - -
299B GLN* 1.3 79.8 - - + +
301B GLN* 1.3 66.7 + - - +
302B ALA 3.2 0.3 + - - -
303B ASN* 3.3 6.8 + - - +
304B LEU* 3.0 28.1 + - + +
335B LEU* 3.4 36.3 - - + -
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Residues in contact with GLN 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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223B ILE* 3.8 15.5 - - + -
297B LEU 3.7 13.2 + - - +
298B LYS* 3.3 40.9 - - + +
300B LYS* 1.3 80.5 + - - +
302B ALA* 1.3 61.5 + - - +
304B LEU* 3.3 11.6 + - - +
305B VAL* 3.0 29.1 + - - +
332B ILE* 3.9 24.1 - - + +
335B LEU* 3.5 34.3 + - + +
336B ASN* 2.9 25.9 + - - +
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Residues in contact with ALA 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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223B ILE* 3.5 23.3 - - + +
288B LEU* 4.4 10.4 - - + +
292B GLN* 4.2 13.2 - - + -
295B LEU* 3.7 14.6 - - + -
298B LYS 3.1 15.0 + - - +
299B GLN 3.4 8.5 - - - +
300B LYS 3.1 0.2 - - - -
301B GLN* 1.3 77.5 - - - +
303B ASN* 1.3 58.0 + - - +
305B VAL* 3.2 5.6 + - - +
306B LEU* 3.0 32.9 + - - +
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Residues in contact with ASN 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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292B GLN* 2.8 43.1 - - - +
299B GLN* 3.0 31.0 + - - +
300B LYS* 3.9 6.2 - - - +
302B ALA* 1.3 75.5 - - - +
304B LEU* 1.3 57.4 + - + +
306B LEU* 3.4 15.8 - - - +
307B LYS* 3.0 27.0 + - - +
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Residues in contact with LEU 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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300B LYS* 3.0 22.7 + - + +
301B GLN 3.6 4.3 - - - +
303B ASN* 1.3 75.6 - - + +
305B VAL* 1.3 59.9 + - - +
307B LYS* 3.2 20.5 + - + +
308B ILE* 2.8 34.3 + - - +
328B TRP* 4.4 13.7 - - + +
331B GLN* 4.0 37.7 - - + +
332B ILE* 3.7 22.9 - - + -
335B LEU* 3.8 24.0 - - + -
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Residues in contact with VAL 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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223B ILE* 3.5 20.9 - - + -
224B ILE 4.5 11.7 - - - +
225B ALA* 5.0 0.7 - - + -
241B LEU* 3.4 27.1 - - + -
242B THR 5.8 0.4 - - - +
284B LEU* 4.4 3.1 - - + -
288B LEU* 3.7 22.2 - - + -
301B GLN 3.0 19.1 + - - +
302B ALA 3.5 6.7 - - - +
304B LEU* 1.3 74.8 - - - +
306B LEU* 1.3 65.5 + - - +
308B ILE* 3.0 7.0 + - - +
309B ILE* 2.9 31.2 + - + +
332B ILE* 3.7 17.9 - - + -
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Residues in contact with LEU 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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285B HIS* 3.6 44.5 - - + +
288B LEU* 3.6 33.2 - - + +
289B THR* 3.9 24.0 - - + +
292B GLN* 4.9 3.1 - - + +
302B ALA 3.0 11.0 + - - +
303B ASN* 3.4 28.3 - - - +
305B VAL* 1.3 79.2 - - - +
307B LYS* 1.3 55.1 + - - +
309B ILE* 3.4 4.1 + - + +
310B GLU* 2.9 39.1 + - - +
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Residues in contact with LYS 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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303B ASN 3.0 15.0 + - - +
304B LEU* 3.4 21.7 - - + +
305B VAL 3.1 0.2 - - - -
306B LEU* 1.3 75.0 - - - +
308B ILE* 1.3 65.8 + - - +
310B GLU* 3.3 15.3 + - - +
311B GLN* 3.1 30.4 + - + +
328B TRP* 3.4 50.4 - - + +
331B GLN* 5.5 1.0 - - - +
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Residues in contact with ILE 308 (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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225B ALA* 4.3 8.1 - - + -
239B LEU* 4.5 9.6 - - + -
241B LEU* 4.0 23.8 - - + -
304B LEU 2.8 16.8 + - - +
305B VAL* 3.5 8.1 - - - +
307B LYS* 1.3 72.8 - - - +
309B ILE* 1.3 58.0 + - - +
311B GLN* 3.1 4.4 + - - +
312B LEU* 2.9 29.9 + - + +
325B VAL* 3.8 20.8 - - + +
328B TRP* 3.4 38.4 - - + -
329B VAL* 4.0 13.0 - - + +
332B ILE* 3.7 27.8 - - + -
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Residues in contact with ILE 309 (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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241B LEU* 3.3 27.4 - - + -
281B ILE* 3.4 51.6 - - + +
282B LYS* 4.7 7.6 - - - +
284B LEU* 4.3 9.2 - - + -
285B HIS* 3.6 36.6 - - + +
305B VAL* 2.9 21.3 + - + +
306B LEU* 3.5 7.6 - - + +
308B ILE* 1.3 77.4 - - - +
310B GLU* 1.3 64.1 + - - +
311B GLN 3.2 0.5 + - - -
312B LEU* 3.2 18.2 + - - +
313B PRO* 3.8 4.7 - - - +
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Residues in contact with GLU 310 (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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285B HIS* 3.2 28.7 + - + +
306B LEU* 2.9 22.8 + - - +
307B LYS* 3.3 17.6 + - - +
309B ILE* 1.3 76.5 - - + +
311B GLN* 1.3 74.5 + - - +
313B PRO* 3.8 13.6 - - - +
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Residues in contact with GLN 311 (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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307B LYS* 3.1 24.1 + - + +
308B ILE* 3.5 4.5 - - - +
310B GLU* 1.3 98.0 + - + +
312B LEU* 1.3 66.8 + - - +
313B PRO* 3.3 3.1 - - - -
314B SER* 3.0 12.0 + - - -
315B ALA* 3.0 22.0 + - - +
321B LYS* 2.6 39.3 + - - +
325B VAL* 4.4 8.7 - - + -
328B TRP* 4.7 9.2 - - - +
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Residues in contact with LEU 312 (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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239B LEU* 4.1 32.8 - - + +
241B LEU* 4.9 15.3 - - + -
281B ILE* 3.4 30.3 - - + -
308B ILE* 2.9 12.3 + - + +
309B ILE* 3.2 12.1 + - - +
311B GLN* 1.3 77.1 - - - +
313B PRO* 1.3 72.7 - - + +
315B ALA* 2.9 20.5 + - + +
316B LYS* 3.2 44.6 + - + +
322B PHE* 6.2 0.2 - - + -
325B VAL* 5.7 0.2 - - - -
503D A 3.7 17.0 - - - +
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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
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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