Contacts of the helix formed by residues 283 - 292 (chain A) in PDB entry 1HMU
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 PHE 283 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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281A MET 3.3 4.0 + - - -
282A ASP* 1.3 74.4 + - - +
284A ASN* 1.3 80.9 + - - +
285A VAL 3.2 1.1 + - - -
286A GLU 3.8 6.7 + - - +
287A GLY 5.2 0.5 + - - -
290A VAL* 3.6 29.6 - - + +
296A LEU* 3.9 23.1 - - + +
361A ARG* 5.6 0.3 + - - -
383A LEU* 4.6 13.1 - - + +
387A ALA* 4.2 11.0 - - + -
388A THR 4.3 5.6 - - - -
389A ASN* 3.2 40.4 + - - -
397A TYR* 3.8 35.9 - + + -
401A MET* 4.6 3.4 - - + -
404A TRP* 3.9 28.5 - + - -
409A ILE* 4.3 5.8 - - + -
410A PRO* 4.2 13.0 - - + -
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Residues in contact with ASN 284 (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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229A LEU* 3.7 5.5 - - - +
282A ASP* 2.8 28.6 + - - +
283A PHE* 1.3 97.3 - - - +
285A VAL* 1.3 57.6 - - - +
286A GLU 3.7 0.6 + - - -
348A TYR* 3.9 12.0 - - + -
359A ASN 3.3 27.5 + - - -
361A ARG* 3.2 57.9 + - + +
383A LEU* 4.4 1.0 - - - +
387A ALA* 3.5 14.2 + - - +
389A ASN* 3.4 7.1 - - - +
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Residues in contact with VAL 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A LEU* 4.3 6.5 - - + -
230A GLN* 4.2 1.4 - - - -
231A ILE* 3.6 34.0 + - + +
232A SER* 3.0 31.7 + - - +
233A SER* 4.0 0.9 - - - -
275A ALA* 4.3 4.5 - - + -
281A MET* 3.5 28.0 - - + -
282A ASP* 3.4 14.6 - - - +
283A PHE 3.2 0.4 - - - -
284A ASN* 1.3 82.6 - - + +
286A GLU* 1.3 58.1 + - - +
287A GLY 3.4 3.5 + - - -
348A TYR* 3.4 37.7 - - + +
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Residues in contact with GLU 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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232A SER* 2.6 31.5 + - - -
233A SER* 3.3 27.1 + - - -
281A MET* 3.6 7.4 - - + +
282A ASP 4.4 1.6 - - - +
283A PHE 3.8 4.3 + - - +
284A ASN 3.7 1.2 - - - -
285A VAL* 1.3 77.8 - - - +
287A GLY* 1.3 66.3 + - - +
288A ARG 3.5 0.2 + - - -
289A GLY* 3.0 16.4 + - - -
290A VAL* 3.9 23.3 - - + +
295A ILE* 3.5 24.0 - - + +
296A LEU* 3.9 23.6 - - + -
298A LYS* 2.9 25.3 + - - -
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Residues in contact with GLY 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A GLN* 4.9 5.4 - - - -
229A LEU 4.7 5.6 + - - -
230A GLN* 3.5 24.4 + - - -
233A SER* 4.3 0.4 - - - -
283A PHE 5.2 0.4 + - - -
284A ASN 4.8 3.2 + - - -
285A VAL* 3.4 4.2 + - - +
286A GLU* 1.3 79.8 - - - +
288A ARG* 1.3 62.3 + - - -
289A GLY 3.2 0.3 + - - -
290A VAL* 3.2 19.1 + - - +
361A ARG* 5.0 7.0 + - - +
370A SER* 4.3 11.6 + - - -
377A ASN* 4.1 1.9 + - - -
383A LEU* 5.1 0.2 - - - +
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Residues in contact with ARG 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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230A GLN* 5.3 0.4 - - - +
233A SER* 5.1 1.0 + - - -
234A TYR* 3.1 22.4 + - - -
286A GLU 3.5 0.2 + - - -
287A GLY* 1.3 71.3 - - - -
289A GLY* 1.3 60.7 + - - +
290A VAL 3.1 2.3 + - - -
291A SER* 2.8 25.3 + - - -
292A ARG* 3.5 18.2 - - - +
371A GLU* 3.0 52.3 + - + +
373A GLY* 3.5 29.9 + - - +
374A ASN* 4.0 12.3 - - - +
376A GLU* 2.7 27.3 + - + +
377A ASN* 3.5 21.0 + - + +
427A TRP* 3.7 13.6 - - - -
1D ASG 3.0 34.9 + - - +
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Residues in contact with GLY 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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233A SER* 5.3 0.8 + - - -
286A GLU* 3.0 15.8 + - - -
288A ARG* 1.3 78.5 - - - +
290A VAL* 1.3 60.4 + - - +
291A SER 2.9 6.7 - - - -
292A ARG* 2.9 55.1 + - - +
295A ILE* 3.6 13.1 - - - +
1D ASG 5.4 0.4 + - - -
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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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283A PHE* 3.6 40.8 - - + +
286A GLU* 3.5 16.5 + - + -
287A GLY 3.2 18.2 + - - +
288A ARG 3.1 0.2 - - - -
289A GLY* 1.3 77.8 - - - +
291A SER* 1.3 58.5 + - - +
292A ARG 3.2 4.7 + - - +
295A ILE* 4.0 9.3 - - - +
296A LEU* 5.0 3.1 - - + -
377A ASN* 3.9 20.6 - - - +
383A LEU* 3.9 17.5 - - + -
401A MET* 3.2 31.0 - - + +
404A TRP* 5.6 2.9 - - + -
406A TRP* 4.9 5.6 - - + -
546A TRP* 4.7 0.2 - - - -
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Residues in contact with SER 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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288A ARG 2.8 19.3 + - - -
289A GLY 2.9 0.6 - - - -
290A VAL* 1.3 80.8 - - - +
292A ARG* 1.3 57.1 + - - +
293A PRO* 4.2 0.3 - - - +
377A ASN* 3.0 21.7 + - - -
401A MET* 4.8 1.3 - - - -
406A TRP* 5.3 1.8 - - - -
546A TRP* 3.4 18.7 - - - -
549A ILE* 3.6 35.5 - - - +
550A ASN* 3.0 31.3 + - - +
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Residues in contact with ARG 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A SER* 5.7 1.4 + - - +
288A ARG* 3.5 15.6 - - - +
289A GLY* 2.9 31.3 + - - +
290A VAL 4.1 0.3 - - - +
291A SER* 1.3 80.0 - - - +
293A PRO* 1.3 73.6 - - + +
294A ASP 3.5 0.5 + - - -
295A ILE* 3.4 31.7 + - + +
376A GLU* 2.7 34.5 + - - +
399A ASN* 4.5 0.2 - - - +
546A TRP* 3.4 8.9 - - - -
550A ASN* 3.5 15.9 - - - +
553A HIS* 4.3 8.5 - - + +
1D ASG 3.0 64.3 + - - +
2D GCD 4.0 13.8 + - - -
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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