Contacts of the helix formed by residues 289 - 302 (chain A) in PDB entry 6GXV
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 ASP 289 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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287A LEU 3.5 0.8 + - - -
288A PHE* 1.3 67.5 - - - +
290A VAL* 1.3 63.2 + - - +
291A PRO* 3.6 7.1 - - - +
292A LEU* 3.3 27.6 + - + +
293A HIS 3.3 14.9 + - - -
315A THR* 3.5 0.9 - - - -
316A MET* 3.0 35.5 + - + -
317A MET* 2.7 35.9 + - - +
324A ALA* 4.8 0.2 - - + -
325A VAL 2.8 18.1 + - - +
326A THR* 4.0 12.9 - - + +
327A PHE* 3.6 12.1 - - - +
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Residues in contact with VAL 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265A GLU* 6.0 0.4 - - + -
266A TYR 3.7 18.8 - - - +
267A TRP* 3.6 55.2 - - + -
268A ASN 3.4 22.0 - - - +
269A THR* 4.4 1.8 - - + -
274A LEU* 5.1 0.4 - - + -
288A PHE* 2.9 25.2 + - + +
289A ASP* 1.3 71.7 - - - +
291A PRO* 1.4 70.5 - - + +
293A HIS* 3.1 13.0 + - - +
294A MET* 3.1 20.4 + - + +
327A PHE* 4.1 8.7 - - + -
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Residues in contact with PRO 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268A ASN 4.2 2.2 - - - +
269A THR 3.8 26.5 - - - +
270A SER 4.5 0.4 - - - -
271A LEU* 4.2 17.5 - - + +
274A LEU* 4.0 14.6 - - + -
289A ASP* 3.5 11.2 - - - +
290A VAL* 1.4 95.5 - - + +
292A LEU* 1.3 54.6 + - - +
294A MET* 3.3 8.6 + - + +
295A ASN* 2.9 33.2 + - - +
313A ASN 5.3 0.7 - - - +
314A ASN* 3.2 29.6 - - + +
315A THR* 4.2 3.1 - - + -
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Residues in contact with LEU 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289A ASP* 3.3 33.9 + - + +
290A VAL 3.3 0.8 - - - -
291A PRO* 1.3 74.4 - - - +
293A HIS* 1.3 60.6 + - - +
295A ASN* 3.1 4.9 + - - +
296A PHE* 2.9 64.5 + - + -
311A LEU 3.7 20.6 - - - +
312A LEU* 4.1 15.0 - - + -
315A THR* 3.6 15.2 - - + +
317A MET* 3.8 21.1 - - - -
326A THR* 3.9 15.9 - - + -
327A PHE 5.0 1.8 - - - +
355A ILE* 3.9 4.9 - - + -
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Residues in contact with HIS 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A TRP* 4.1 15.3 - + - -
289A ASP 3.3 2.8 + - - -
290A VAL 3.1 8.9 + - - +
292A LEU* 1.3 77.7 - - - +
294A MET* 1.3 74.4 + - + +
296A PHE* 3.2 13.4 + - - +
297A GLN* 3.0 24.3 + - - +
327A PHE* 3.6 31.4 + + + +
328A VAL 2.6 20.5 + - - -
329A ASP* 3.0 20.6 - - - -
333A THR* 3.5 8.2 - - + +
341A SER* 2.8 45.7 + - - -
343A VAL* 4.1 3.5 - - + +
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Residues in contact with MET 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267A TRP* 3.3 36.8 - - + +
269A THR* 3.3 41.3 - - + +
290A VAL* 3.1 13.3 + - + +
291A PRO* 3.3 9.2 + - + +
293A HIS* 1.3 86.9 - - + +
295A ASN* 1.3 63.2 + - - +
297A GLN* 3.2 19.2 + - - +
298A ALA* 2.9 30.1 + - - +
341A SER* 4.5 3.1 - - - -
301B ASN* 5.4 0.4 - - - +
504B GLC 4.3 15.9 - - - +
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Residues in contact with ASN 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291A PRO* 2.9 17.2 + - - +
292A LEU* 3.1 8.0 + - + +
294A MET* 1.3 75.5 - - - +
296A PHE* 1.3 65.1 + - - +
298A ALA* 3.2 6.1 + - - +
299A ALA* 3.0 24.4 + - - +
306A TYR* 4.0 16.2 + - - +
310A ASN 3.8 3.4 + - - -
311A LEU* 2.8 36.5 + - + +
313A ASN 3.0 27.1 + - - +
315A THR* 3.5 10.1 - - - +
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Residues in contact with PHE 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292A LEU* 2.9 52.7 + - + -
293A HIS* 3.5 8.5 - - - +
295A ASN* 1.3 74.3 - - - +
297A GLN* 1.3 62.5 + - - +
300A ALA* 3.0 25.5 + - - +
311A LEU* 4.2 12.6 - - + -
327A PHE 3.6 24.7 - - - -
328A VAL* 4.1 8.1 - - + -
343A VAL* 4.0 14.4 - - + -
347A PHE* 3.7 21.2 - + + -
351A ALA* 3.5 45.3 - - + -
354A THR* 4.0 16.2 - - + -
355A ILE* 3.6 13.0 - - + -
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Residues in contact with GLN 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293A HIS* 3.0 14.6 + - - +
294A MET* 3.6 19.1 + - - +
295A ASN 3.2 0.2 - - - -
296A PHE* 1.3 77.0 - - - +
298A ALA* 1.3 52.7 + - - +
300A ALA* 3.3 4.0 + - - +
301A ASN* 2.8 58.8 + - - +
341A SER* 3.4 45.2 - - - +
342A TRP 4.5 5.2 - - - +
343A VAL* 4.2 7.6 - - + +
511A GLC 2.8 36.7 + - - +
294B MET* 4.5 12.0 - - - +
297B GLN* 5.3 2.0 - - - +
504B GLC 4.9 3.0 + - - -
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Residues in contact with ALA 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294A MET 2.9 17.1 + - - +
295A ASN* 3.7 6.5 - - - +
297A GLN* 1.3 75.8 - - - +
299A ALA* 1.3 56.6 + - - +
301A ASN* 3.2 1.5 + - - -
302A GLY* 2.9 26.3 + - - -
306A TYR* 3.7 23.6 - - + -
269B THR* 3.6 16.7 + - - +
270B SER* 4.8 0.3 + - - -
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Residues in contact with ALA 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295A ASN 3.0 15.2 + - - +
296A PHE 3.9 0.2 - - - +
298A ALA* 1.3 72.4 - - - +
300A ALA* 1.3 66.6 + - - +
302A GLY* 3.2 11.6 + - - -
303A GLY 3.9 3.5 + - - -
306A TYR* 3.4 37.1 - - + +
308A MET* 4.1 3.8 - - - -
311A LEU* 3.9 3.8 - - + -
346A TRP* 4.1 6.8 - - - -
347A PHE* 3.5 32.1 - - + -
431A ASP* 4.6 4.3 - - - +
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Residues in contact with ALA 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296A PHE 3.0 18.2 + - - +
297A GLN* 3.7 4.9 - - - +
299A ALA* 1.3 76.9 - - - +
301A ASN* 1.3 66.6 + - - +
302A GLY 3.3 1.2 + - - -
303A GLY 3.6 4.2 + - - -
342A TRP 5.8 0.4 - - - +
343A VAL* 4.3 2.7 - - + -
344A SER* 4.2 19.3 - - - +
346A TRP* 3.5 33.3 + - - +
347A PHE* 3.5 23.6 - - + -
192B GLU* 3.6 8.1 - - - +
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Residues in contact with ASN 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297A GLN* 2.8 45.1 + - - +
298A ALA* 4.6 0.6 - - - +
300A ALA* 1.3 79.7 - - - +
302A GLY* 1.3 57.9 + - - +
303A GLY 3.3 0.7 - - - -
342A TRP 4.9 1.6 - - - +
344A SER* 4.2 6.2 + - - -
511A GLC 3.2 23.4 + - - -
192B GLU* 4.6 1.3 - - - +
267B TRP* 5.6 3.0 - - + +
268B ASN* 3.4 23.1 + - - -
269B THR* 3.4 34.2 + - + +
294B MET* 5.5 1.0 - - - +
1F GLC 3.2 35.4 + - - +
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Residues in contact with GLY 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298A ALA 2.9 12.7 + - - -
299A ALA 3.2 4.0 + - - -
300A ALA 3.2 1.2 - - - -
301A ASN* 1.3 76.4 - - - +
303A GLY* 1.3 64.8 + - - +
304A GLY 3.2 2.9 - - - -
305A TYR* 3.0 20.2 + - - +
306A TYR 4.3 4.0 - - - -
268B ASN* 3.2 19.8 + - - +
269B THR* 4.1 1.3 - - - -
270B SER* 3.6 21.3 - - - -
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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