Contacts of the helix formed by residues 385 - 394 (chain A) in PDB entry 4XZC
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 ARG 385 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303A ALA* 4.1 12.3 - - - +
305A ILE* 3.6 29.6 - - + +
314A TRP* 3.9 11.3 - - + -
373A LYS 4.6 5.3 + - - -
374A LEU 5.1 0.2 + - - -
376A MET* 3.1 40.9 + - - +
377A HIS 2.9 21.0 + - - -
378A PRO* 3.9 4.4 - - - +
380A VAL 2.8 36.4 + - - -
381A LEU* 4.0 7.6 - - + -
382A THR* 2.9 33.5 + - - +
384A GLY* 1.3 73.3 - - - +
386A MET* 1.3 56.5 + - - +
387A SER* 3.0 8.3 - - - -
388A GLU* 3.0 30.4 + - + +
389A MET 3.9 0.3 + - - -
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Residues in contact with MET 386 (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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328A LEU* 5.4 3.6 - - + -
331A PHE* 4.8 3.6 - - + -
332A LEU* 3.9 23.5 - - + +
335A MET* 3.6 14.1 - - - +
345A MET* 3.8 25.6 - - - -
349A LEU* 4.8 10.1 - - + -
356A TRP* 5.8 0.2 - - + -
360A ILE* 4.2 17.5 - - + -
364A PHE* 3.9 10.8 - - + -
381A LEU* 3.8 19.5 - - - -
382A THR 3.4 7.2 + - - +
383A ALA 3.3 18.6 - - - +
384A GLY 3.0 1.4 - - - -
385A ARG* 1.3 76.6 - - - +
387A SER* 1.3 59.5 + - - +
388A GLU 3.1 0.2 - - - -
389A MET* 3.2 30.4 + - + +
390A GLY 2.9 23.2 + - - -
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Residues in contact with SER 387 (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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335A MET* 4.6 8.0 - - - +
383A ALA 4.9 0.2 + - - -
384A GLY 3.0 17.8 + - - -
385A ARG* 4.2 1.6 - - - -
386A MET* 1.3 79.3 - - - +
388A GLU* 1.3 68.0 + - - +
390A GLY* 3.7 1.5 - - - +
391A ALA* 3.0 25.1 + - - +
410A HIS* 4.0 7.7 - - - +
411A SER* 4.3 23.6 + - - -
412A LYS* 5.7 2.2 + - - +
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Residues in contact with GLU 388 (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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305A ILE* 3.5 37.1 - - + +
307A SER* 2.5 35.8 + - - +
311A SER* 3.4 9.4 + - - +
314A TRP* 3.9 14.6 - - + -
385A ARG* 3.0 22.1 + - + +
387A SER* 1.3 84.7 + - - +
389A MET* 1.3 61.8 + - - +
391A ALA* 3.4 4.3 + - - +
392A CYS* 3.4 21.7 + - - -
412A LYS* 2.4 34.7 + - - +
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Residues in contact with MET 389 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A SER* 3.2 33.7 - - - +
314A TRP* 3.6 37.5 - - + -
315A ALA* 3.9 12.6 - - - +
328A LEU* 4.0 31.0 - - + -
332A LEU* 3.4 12.7 - - + +
360A ILE* 4.0 8.5 - - + -
381A LEU* 4.4 0.2 - - - -
385A ARG 4.6 0.9 - - - +
386A MET* 3.2 35.3 + - - +
388A GLU* 1.3 75.7 - - - +
390A GLY* 1.3 53.4 + - - +
393A PHE* 2.7 42.8 + - + +
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Residues in contact with GLY 390 (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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332A LEU* 3.9 11.1 - - - +
335A MET* 4.3 0.4 - - - -
386A MET 2.9 14.6 + - - -
387A SER 3.7 1.3 - - - -
388A GLU 3.2 0.2 - - - -
389A MET* 1.3 72.1 - - - +
391A ALA* 1.3 62.8 + - - +
392A CYS 3.1 1.6 - - - -
394A GLY* 2.8 31.2 + - - -
395A VAL 3.8 0.3 + - - -
410A HIS* 3.3 32.6 - - - -
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Residues in contact with ALA 391 (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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80A CYS* 3.7 13.7 - - - -
307A SER* 5.8 0.7 - - - +
387A SER 3.0 16.9 + - - +
388A GLU* 3.4 4.9 + - - +
390A GLY* 1.3 72.9 - - - +
392A CYS* 1.3 57.9 + - - +
395A VAL* 3.8 6.1 - - - +
410A HIS* 3.4 21.1 - - + -
412A LYS* 4.3 17.3 - - + -
413A SER* 4.5 6.5 + - - +
466A HIS* 3.1 37.3 + - + +
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Residues in contact with CYS 392 (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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80A CYS* 4.3 12.8 - - - +
83A ALA* 4.6 0.7 - - - +
84A CYS* 3.3 16.6 - - - -
307A SER* 3.6 12.6 - - - -
308A ILE* 3.4 52.9 - - + -
311A SER* 3.6 10.1 - - - +
388A GLU 3.4 14.4 + - - +
390A GLY 3.1 0.6 - - - -
391A ALA* 1.3 79.8 - - - +
393A PHE* 1.3 66.4 + - + +
394A GLY 3.6 0.4 - - - -
395A VAL 4.8 1.1 + - - -
396A VAL 5.7 0.2 + - - -
466A HIS* 4.0 3.8 - - - -
467A PHE* 3.8 20.5 - - + -
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Residues in contact with PHE 393 (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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83A ALA 4.4 2.0 - - - -
84A CYS* 3.7 11.5 - - - -
308A ILE* 3.8 10.5 - - + -
311A SER* 3.5 38.6 - - - -
312A TYR* 3.6 40.8 - + - -
315A ALA* 4.3 2.2 - - + -
325A PHE* 3.6 33.2 - + + -
328A LEU* 3.9 20.0 - - + -
329A SER* 2.9 31.5 + - - +
332A LEU* 3.7 9.9 - - + -
389A MET* 2.7 33.1 + - + +
392A CYS* 1.3 78.3 - - + +
394A GLY* 1.3 55.7 + - - +
395A VAL 3.5 2.9 + - - -
396A VAL 3.8 4.0 - - - +
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Residues in contact with GLY 394 (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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329A SER 4.0 2.0 - - - -
332A LEU* 3.8 8.1 - - - -
333A PHE* 3.4 30.3 - - - -
389A MET 3.7 1.4 + - - -
390A GLY 2.8 22.0 + - - -
393A PHE* 1.3 73.7 - - - +
395A VAL* 1.3 58.0 + - - +
396A VAL 3.9 0.7 - - - -
408A SER* 3.2 14.7 + - - -
410A HIS* 3.1 16.4 + - - -
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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