Contacts of the helix formed by residues 358 - 373 (chain A) in PDB entry 4QA7
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 GLU 358 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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232A GLN* 5.2 3.3 - - - +
356A ARG 3.3 16.2 + - - +
357A ASN* 1.3 73.0 - - - +
359A PRO* 1.3 68.0 - - + +
360A HIS* 3.0 42.6 + - + +
361A ARG* 3.0 38.0 + - + +
362A ILE* 3.3 10.4 + - - +
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Residues in contact with PRO 359 (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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357A ASN 3.5 6.5 - - - +
358A GLU* 1.3 85.8 - - + +
360A HIS* 1.3 57.0 + - + +
362A ILE* 3.9 9.1 - - + +
363A GLN* 3.2 26.9 + - - +
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Residues in contact with HIS 360 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358A GLU* 3.0 37.3 + - + +
359A PRO* 1.3 77.4 - - + +
361A ARG* 1.3 70.0 + - + +
362A ILE 3.3 0.4 - - - -
363A GLN* 3.2 7.9 + - - +
364A GLN* 3.0 52.5 + - - +
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Residues in contact with ARG 361 (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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213A ASP* 5.9 1.0 + - - -
214A VAL* 4.9 12.1 - - - +
230A PRO* 5.7 4.6 - - - +
232A GLN* 6.1 5.7 - - + +
358A GLU* 3.0 35.7 + - + +
360A HIS* 1.3 82.9 - - + +
362A ILE* 1.3 69.1 + - + +
364A GLN* 2.7 38.9 + - - +
365A ILE* 3.1 60.0 + - + +
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Residues in contact with ILE 362 (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 VAL* 6.1 1.6 - - + -
230A PRO 4.9 4.7 - - - +
231A ILE* 5.1 4.0 - - + -
243A ILE* 3.7 43.1 - - + -
357A ASN* 3.9 32.5 - - + +
358A GLU 3.7 13.2 - - - +
359A PRO* 3.9 10.3 - - + +
360A HIS 3.3 0.2 - - - -
361A ARG* 1.3 79.4 - - + +
363A GLN* 1.3 62.8 + - - +
365A ILE* 3.3 17.4 + - + +
366A LEU* 3.0 36.0 + - + +
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Residues in contact with GLN 363 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359A PRO 3.2 14.3 + - - +
360A HIS* 3.5 11.7 - - - +
361A ARG 3.2 0.6 - - - -
362A ILE* 1.3 81.1 - - - +
364A GLN* 1.3 59.2 + - + +
366A LEU* 3.5 18.7 + - - +
367A ASN* 3.0 53.6 + - - +
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Residues in contact with GLN 364 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360A HIS* 3.0 41.7 + - - +
361A ARG* 2.7 46.2 + - - +
363A GLN* 1.3 77.0 - - - +
365A ILE* 1.3 56.7 + - - +
367A ASN* 3.2 11.3 + - - +
368A TYR* 2.9 29.4 + - - +
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Residues in contact with ILE 365 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A VAL* 3.7 23.6 - - + -
229A VAL* 4.1 15.9 - - + -
230A PRO* 3.3 37.2 - - + +
361A ARG* 3.1 48.1 + - + +
362A ILE* 3.3 15.5 + - + +
364A GLN* 1.3 75.5 - - - +
366A LEU* 1.3 60.3 + - + +
368A TYR* 3.3 6.8 + - - +
369A ILE* 2.9 42.0 + - + +
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Residues in contact with LEU 366 (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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242A GLN 5.3 1.1 - - - +
243A ILE* 4.0 23.1 - - + +
246A SER* 3.9 28.7 - - - +
247A VAL* 3.9 24.9 - - + -
362A ILE* 3.0 34.7 + - + +
363A GLN* 3.8 20.9 - - - +
365A ILE* 1.3 78.3 - - + +
367A ASN* 1.3 59.5 + - - +
369A ILE* 3.6 7.3 + - + +
370A LYS* 3.1 28.4 + - - +
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Residues in contact with ASN 367 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363A GLN* 3.0 44.3 + - - +
364A GLN* 3.2 9.8 + - - +
366A LEU* 1.3 76.5 - - - +
368A TYR* 1.3 60.8 + - - +
370A LYS* 3.4 5.8 + - - +
371A GLY* 3.0 25.8 + - - -
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Residues in contact with TYR 368 (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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214A VAL* 3.6 38.1 - - + -
215A SER* 3.9 22.2 + - - -
217A VAL* 5.0 2.0 - - + -
364A GLN 2.9 13.2 + - - +
365A ILE* 3.5 9.9 - - - +
367A ASN* 1.3 77.1 - - - +
369A ILE* 1.3 61.3 + - - +
371A GLY* 3.2 3.2 + - - -
372A ASN* 3.1 62.5 + - - +
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Residues in contact with ILE 369 (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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214A VAL* 4.1 13.0 - - + +
227A VAL* 3.9 24.7 - - + -
228A ASN 4.1 3.6 - - - +
229A VAL* 3.7 31.0 - - + -
247A VAL* 4.0 20.9 - - + -
250A GLU* 5.9 0.4 - - + -
365A ILE* 2.9 32.0 + - + +
366A LEU* 3.9 7.0 - - + +
368A TYR* 1.3 73.9 - - - +
370A LYS* 1.3 61.2 + - - +
372A ASN* 3.0 13.8 + - - +
373A LEU* 2.9 47.9 + - + +
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Residues in contact with LYS 370 (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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250A GLU* 4.8 20.4 - - + +
366A LEU 3.1 20.1 + - - +
367A ASN* 3.7 6.7 - - - +
368A TYR 3.4 0.2 - - - -
369A ILE* 1.3 77.9 - - - +
371A GLY* 1.3 61.1 + - - +
373A LEU* 3.4 9.2 + - - +
374A LYS* 3.4 21.3 + - - +
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Residues in contact with GLY 371 (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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367A ASN 3.0 14.1 + - - -
368A TYR 3.6 4.5 - - - -
369A ILE 3.2 0.4 - - - -
370A LYS* 1.3 78.0 - - - +
372A ASN* 1.3 63.3 + - - +
374A LYS* 3.7 10.8 + - - +
375A HIS* 3.3 20.4 + - - -
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Residues in contact with ASN 372 (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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214A VAL 4.2 3.2 + - - -
217A VAL* 3.5 22.9 - - + +
224A TYR* 3.5 47.8 - - + +
227A VAL* 6.1 2.9 - - + -
368A TYR* 3.1 46.1 + - - +
369A ILE* 3.0 13.6 + - + +
371A GLY* 1.3 76.4 - - - +
373A LEU* 1.3 59.6 + - + +
374A LYS 3.1 9.7 + - - -
375A HIS* 3.2 14.3 + - - -
376A VAL 4.1 0.3 + - - -
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Residues in contact with LEU 373 (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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196A MET* 4.1 21.3 - - + -
224A TYR 4.3 4.9 - - - +
227A VAL* 4.0 21.5 - - + -
247A VAL 4.4 0.9 - - - +
250A GLU* 3.6 32.1 - - + +
251A VAL* 3.7 27.6 - - + +
254A ALA* 3.7 15.3 - - + +
369A ILE* 2.9 35.0 + - + +
370A LYS* 3.4 6.4 + - - +
372A ASN* 1.3 75.6 - - + +
374A LYS* 1.3 61.1 + - - +
375A HIS 3.2 0.9 - - - -
376A VAL* 3.4 26.0 + - + +
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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