Contacts of the helix formed by residues 285 - 299 (chain A) in PDB entry 3H13
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 SER 285 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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283A HIS 4.2 0.6 + - - -
284A LEU* 1.3 75.9 - - - +
286A MET* 1.3 59.2 + - - +
287A HIS* 3.6 10.5 + - - +
288A GLY* 3.0 17.4 + - - +
289A ILE* 2.8 29.4 + - - +
323A GLY* 4.4 1.1 - - - -
324A VAL* 3.9 15.7 - - - +
325A ASP* 3.5 20.9 - - - -
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Residues in contact with MET 286 (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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285A SER* 1.3 70.4 - - - +
287A HIS* 1.3 61.8 + - - +
289A ILE* 3.2 11.7 + - - +
290A SER* 3.0 26.7 + - - -
321A VAL 3.5 14.1 - - - +
322A TYR* 3.5 16.6 + - - +
325A ASP* 2.9 17.7 + - - +
327A THR* 3.9 16.6 - - - -
329A SER 3.6 12.1 - - - +
330A GLY* 3.5 26.2 - - - +
331A LEU* 3.4 30.6 - - + +
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Residues in contact with HIS 287 (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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285A SER* 3.2 8.6 + - - +
286A MET* 1.3 76.8 - - - +
288A GLY* 1.3 67.7 + - - +
290A SER* 3.4 7.5 + - - -
291A GLN* 3.0 37.3 + - + +
325A ASP* 4.6 0.4 + - - -
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Residues in contact with GLY 288 (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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284A LEU* 4.1 15.5 - - - -
285A SER* 3.0 22.0 + - - -
287A HIS* 1.3 80.0 - - - +
289A ILE* 1.3 62.3 + - - +
291A GLN* 3.3 7.4 + - - +
292A ILE* 3.0 28.7 + - - +
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Residues in contact with ILE 289 (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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257A ILE* 4.2 14.4 - - + +
259A CYS* 4.1 6.7 - - - -
284A LEU* 3.9 21.3 - - + +
285A SER 2.8 14.4 + - - +
286A MET* 3.4 11.7 - - - +
288A GLY* 1.3 76.2 - - - +
290A SER* 1.3 57.5 + - - +
292A ILE* 3.4 1.2 + - - +
293A LEU* 2.8 47.0 + - + +
312A LEU* 4.6 10.5 - - + -
314A SER* 5.0 0.2 - - - +
321A VAL* 4.2 19.1 - - + -
323A GLY* 3.7 33.7 - - - +
331A LEU* 3.5 17.5 - - + -
336A ILE* 5.1 1.8 - - + -
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Residues in contact with SER 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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286A MET 3.0 16.4 + - - -
287A HIS* 3.8 8.2 - - - -
289A ILE* 1.3 73.8 - - - +
291A GLN* 1.3 62.4 + - - +
293A LEU* 4.0 7.7 - - - +
294A GLY* 2.8 28.1 + - - -
331A LEU* 3.6 23.9 - - - +
339A MET* 4.0 9.3 - - - +
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Residues in contact with GLN 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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287A HIS* 3.0 31.5 + - + +
288A GLY* 3.3 8.3 + - - +
290A SER* 1.3 77.1 - - - +
292A ILE* 1.3 67.2 + - + +
294A GLY* 3.4 1.2 + - - -
295A GLN* 3.1 52.4 + - - +
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Residues in contact with ILE 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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255A LEU* 4.0 17.5 - - + -
257A ILE* 4.3 8.7 - - + -
281A PHE* 3.7 31.6 - - + -
284A LEU* 3.4 37.0 - - + -
288A GLY* 3.0 14.7 + - - +
289A ILE 4.0 2.2 - - - +
291A GLN* 1.3 79.2 - - + +
293A LEU* 1.3 65.4 + - - +
295A GLN* 3.1 15.0 + - - +
296A PHE* 3.0 48.2 + - + -
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Residues in contact with LEU 293 (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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255A LEU* 3.8 25.6 - - + -
257A ILE* 4.2 9.0 - - + -
289A ILE* 2.8 48.6 + - + +
290A SER* 4.0 1.8 - - - +
292A ILE* 1.3 72.1 - - - +
294A GLY* 1.3 63.1 + - - +
296A PHE* 3.1 2.5 + - - +
297A ALA* 2.9 24.4 + - - +
310A CYS* 4.3 13.2 - - - -
312A LEU* 5.9 1.8 - - + -
331A LEU* 4.6 3.4 - - + -
336A ILE* 3.8 35.9 - - + -
339A MET* 3.3 21.7 - - + +
340A PHE* 3.8 19.1 - - + -
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Residues in contact with GLY 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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290A SER 2.8 16.3 + - - -
291A GLN 3.8 1.3 - - - -
293A LEU* 1.3 77.1 - - - +
295A GLN* 1.3 60.7 + - - +
297A ALA* 3.5 3.4 + - - +
298A CYS* 3.3 29.0 + - - -
339A MET* 3.0 18.6 - - - +
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Residues in contact with GLN 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 GLN* 3.1 46.0 + - + +
292A ILE* 3.1 17.6 + - - +
294A GLY* 1.3 78.6 - - - +
296A PHE* 1.3 70.3 + - + +
298A CYS* 3.3 12.6 + - - +
299A MET* 3.2 23.4 + - + +
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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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253A ILE* 3.8 24.5 - - + -
255A LEU* 3.9 25.4 - - + -
279A GLN* 3.4 43.7 - - + -
281A PHE* 3.8 20.6 - + - -
292A ILE* 3.0 47.5 + - + +
293A LEU 3.9 2.9 - - - +
295A GLN* 1.3 82.2 - - + +
297A ALA* 1.3 59.8 + - - +
298A CYS 3.4 0.5 + - - -
299A MET* 3.6 28.7 + - + +
302A HIS* 2.6 33.9 + + - -
308A PHE* 4.8 4.5 - + + -
340A PHE* 4.2 7.6 - - + -
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Residues in contact with ALA 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 LEU 2.9 16.4 + - - +
294A GLY* 3.8 7.2 - - - +
295A GLN 3.3 0.4 - - - -
296A PHE* 1.3 77.3 - - - +
298A CYS* 1.3 61.2 + - - +
299A MET 3.5 0.7 + - - +
302A HIS* 4.3 2.3 - - - -
339A MET* 3.5 30.1 - - + +
340A PHE* 3.6 21.7 - - + -
344A SER 4.6 4.8 - - - +
345A CYS* 3.2 27.2 - - + +
347A TYR* 5.7 1.0 - - - +
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Residues in contact with CYS 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 GLY 3.3 18.1 + - - +
295A GLN* 3.3 7.7 + - - +
296A PHE 3.2 0.6 - - - -
297A ALA* 1.3 78.3 - - - +
299A MET* 1.3 66.8 + - - +
300A PRO* 3.2 9.0 - - - +
347A TYR* 6.1 0.3 - - - -
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Residues in contact with MET 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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253A ILE* 3.7 20.2 - - - -
279A GLN* 4.5 7.6 - - - +
295A GLN* 3.2 17.3 - - + +
296A PHE* 3.6 59.0 + - + +
297A ALA 3.5 2.0 - - - +
298A CYS* 1.3 76.7 - - - +
300A PRO* 1.3 67.8 - - - +
301A GLU* 3.3 20.9 - - + +
302A HIS* 3.2 25.2 + - + +
347A TYR* 4.1 6.6 - - - +
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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