Contacts of the helix formed by residues 285 - 300 (chain A) in PDB entry 4GHI
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 285 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281A TYR* 4.8 2.0 - - + -
282A HIS* 2.9 14.4 + - + +
284A LEU* 1.3 80.7 - - - +
286A SER* 1.3 63.8 + - - +
287A GLU 3.4 2.0 - - - -
288A ASN* 3.2 14.8 + - + +
289A MET* 2.9 29.2 + - + +
306A GLN 4.4 4.2 - - - +
307A TYR* 3.9 21.7 - - + -
308A ARG* 2.9 65.8 + - - +
318A TRP* 4.7 2.3 - - - -
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Residues in contact with SER 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A TYR* 4.7 7.9 + - - -
281A TYR* 4.1 16.0 + - - +
282A HIS 3.2 13.8 + - - -
283A ALA* 3.2 19.5 + - - -
284A LEU 3.5 0.4 - - - -
285A ASP* 1.3 77.3 - - - +
287A GLU* 1.3 69.7 + - - +
289A MET* 3.3 6.3 + - - +
290A THR* 3.0 27.4 + - - -
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Residues in contact with GLU 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A ALA 4.8 1.5 + - - +
284A LEU 5.4 0.8 - - - -
285A ASP 3.4 0.2 - - - -
286A SER* 1.3 82.7 - - - +
288A ASN* 1.3 64.0 + - - +
290A THR* 3.3 13.8 + - - +
291A LYS* 3.2 36.7 + - - +
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Residues in contact with ASN 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A LEU 4.5 12.0 + - - -
285A ASP* 3.2 14.9 + - - +
287A GLU* 1.3 80.3 - - - +
289A MET* 1.3 68.8 + - + +
291A LYS* 3.3 18.3 + - - +
292A SER* 3.0 29.3 + - - -
306A GLN 5.9 1.2 + - - -
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Residues in contact with MET 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A MET* 4.4 3.5 - - - +
278A TYR* 4.0 2.8 + - - -
281A TYR* 3.5 43.1 - - + +
285A ASP* 2.9 21.0 + - + +
286A SER 3.9 1.8 - - - +
288A ASN* 1.3 89.8 - - + +
290A THR* 1.3 61.2 + - - +
292A SER* 3.8 3.7 - - - +
293A HIS* 2.9 30.0 + - - +
304A SER* 3.5 24.2 - - - +
305A GLY* 5.3 0.2 - - - -
306A GLN 4.6 5.8 - - - +
307A TYR* 3.7 39.5 - - + -
401A 0X3 4.0 21.5 - - - +
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Residues in contact with THR 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A TYR* 3.5 27.0 + - + +
286A SER 3.0 15.2 + - - -
287A GLU* 3.6 19.2 + - - +
288A ASN 3.3 0.2 - - - -
289A MET* 1.3 76.3 - - - +
291A LYS* 1.3 59.1 + - + +
293A HIS* 3.4 2.6 + - - +
294A GLN* 3.0 52.1 + - + +
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Residues in contact with LYS 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A GLU* 3.2 25.5 + - - +
288A ASN* 3.5 18.9 + - - +
289A MET 3.2 0.2 - - - -
290A THR* 1.3 75.2 - - + +
292A SER* 1.3 59.7 + - - +
294A GLN* 3.2 18.4 + - - +
295A ASN* 2.9 39.3 + - - +
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Residues in contact with SER 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A ASN 3.0 18.0 + - - -
289A MET* 3.4 5.8 + - - +
291A LYS* 1.3 76.0 - - - +
293A HIS* 1.3 56.3 + - - +
295A ASN* 3.1 11.7 + - - +
296A LEU* 2.8 29.3 + - - +
302A VAL* 3.8 9.8 - - - +
303A VAL 4.6 0.3 + - - -
304A SER* 3.1 27.8 + - - -
401A 0X3 3.4 26.3 - - - +
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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
----------------------------------------------------------
250A MET 3.2 25.9 + - - -
251A ASP* 4.8 3.4 - - - -
252A MET* 3.6 28.6 - - + +
278A TYR* 2.9 29.8 + + - +
289A MET 2.9 18.5 + - - +
290A THR 3.6 2.0 - - - +
292A SER* 1.3 77.0 - - - +
294A GLN* 1.3 63.9 + - + +
296A LEU* 3.3 3.8 + - + +
297A CYS* 3.0 39.1 + - - -
337A ILE* 4.3 13.4 - - + +
401A 0X3 3.5 8.9 + - - -
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Residues in contact with GLN 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A THR* 3.0 36.4 + - + +
291A LYS* 3.2 21.1 + - - +
293A HIS* 1.3 76.2 - - + +
295A ASN* 1.3 65.3 + - - +
297A CYS* 3.3 5.1 + - - +
298A THR* 3.0 33.4 + - + +
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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
----------------------------------------------------------
291A LYS* 2.9 25.1 + - - +
292A SER* 3.5 9.6 + - - +
294A GLN* 1.3 79.4 - - - +
296A LEU* 1.3 56.5 + - - +
298A THR* 3.1 8.2 + - - -
299A LYS* 2.8 56.6 + - + +
301A GLN 4.6 1.6 - - - -
302A VAL* 4.2 13.8 - - + +
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Residues in contact with LEU 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 SER 2.8 16.3 + - - +
293A HIS* 3.5 8.5 - - + +
294A GLN 3.3 0.2 - - - -
295A ASN* 1.3 76.7 - - - +
297A CYS* 1.3 58.4 + - - +
300A GLY* 2.8 31.9 + - - +
301A GLN* 3.6 21.1 - - - -
302A VAL* 3.8 10.4 - - + +
323A GLY* 3.6 30.7 - - - +
324A THR 3.9 0.4 - - - +
325A VAL* 3.5 19.1 - - + +
337A ILE* 3.7 26.5 - - + -
401A 0X3 3.3 35.0 - - - +
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Residues in contact with CYS 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A MET* 4.0 25.8 - - + -
293A HIS* 3.0 45.3 + - - +
294A GLN* 3.8 6.1 - - - +
295A ASN 3.3 0.2 - - - -
296A LEU* 1.3 79.5 - - - +
298A THR* 1.3 64.0 + - + +
325A VAL* 4.6 5.2 - - - -
327A TYR* 3.8 12.8 + - - -
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Residues in contact with THR 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A GLN* 3.0 19.2 + - + +
295A ASN* 3.1 13.3 + - - -
297A CYS* 1.3 82.2 - - + +
299A LYS* 1.3 73.4 + - - +
327A TYR* 5.5 0.4 - - - -
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Residues in contact with LYS 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A ASN* 2.8 42.7 + - + +
298A THR* 1.3 85.8 + - - +
300A GLY* 1.3 59.2 + - - +
301A GLN* 3.3 15.3 + - - +
302A VAL* 6.4 0.2 - - + -
327A TYR* 4.9 0.4 - - - -
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Residues in contact with GLY 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A LEU* 2.8 22.8 + - - -
298A THR 3.7 1.2 - - - -
299A LYS* 1.3 73.5 - - - +
301A GLN* 1.3 68.0 + - - +
324A THR* 4.0 1.0 - - - +
325A VAL* 2.8 28.3 + - - +
327A TYR* 3.5 26.1 + - - -
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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