Contacts of the helix formed by residues 390 - 400 (chain l) in PDB entry 6QX2
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 HIS 390 (chain l).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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386l ILE* 2.9 44.3 + - + +
387l ALA 3.4 3.8 - - - -
388l LEU 3.3 0.2 - - - -
389l ASP* 1.3 91.6 + - + +
391l ILE* 1.3 62.9 + - - +
392l ASP* 3.3 3.1 - - - -
393l GLU* 3.1 28.8 + - - +
394l ILE* 3.1 19.2 + - + +
415l PHE* 4.1 20.0 - + + -
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Residues in contact with ILE 391 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395j ILE* 4.8 3.8 - - + -
399j ARG* 3.3 45.1 - - - +
430j LEU* 4.8 7.4 - - + -
387l ALA 3.0 17.9 + - - +
388l LEU* 3.6 13.4 + - - +
389l ASP 3.7 0.6 - - - -
390l HIS* 1.3 75.7 - - - +
392l ASP* 1.3 63.7 + - - +
394l ILE* 3.3 11.5 + - + -
395l ILE* 3.0 49.7 + - + +
428l MET* 4.9 2.5 - - + -
433l LEU* 3.5 39.0 - - + -
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Residues in contact with ASP 392 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395j ILE* 5.6 4.8 - - - +
399j ARG* 2.9 29.9 + - - -
390l HIS 3.3 0.6 - - - -
391l ILE* 1.3 81.9 - - - +
393l GLU* 1.3 63.3 + - + +
395l ILE* 3.6 7.7 + - - +
396l SER* 3.1 26.1 + - - -
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Residues in contact with GLU 393 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390l HIS* 3.1 33.7 + - - +
392l ASP* 1.3 77.7 - - + +
394l ILE* 1.3 59.1 + - - +
396l SER* 3.3 7.8 + - - -
397l THR* 2.8 33.0 + - - +
415l PHE* 3.9 19.7 - - + -
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Residues in contact with ILE 394 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430j LEU* 4.7 2.2 - - + -
386l ILE* 5.0 0.7 - - + +
387l ALA* 3.6 32.8 - - + +
390l HIS* 3.1 16.2 + - + +
391l ILE* 3.3 18.1 + - + +
393l GLU* 1.3 75.1 - - - +
395l ILE* 1.3 62.6 - - - +
397l THR* 3.4 8.4 - - - -
398l ILE* 3.1 41.4 + - + +
411l LEU* 3.9 11.9 - - + -
415l PHE* 3.8 35.2 - - + -
417l LEU* 5.0 6.1 - - + -
425l ILE* 4.0 17.7 - - + -
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Residues in contact with ILE 395 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391j ILE* 5.1 4.0 - - + -
392j ASP* 6.0 2.9 - - + -
395j ILE* 4.1 33.2 - - + -
430j LEU* 3.9 29.2 - - + -
433j LEU* 4.2 13.5 - - + -
391l ILE* 3.0 34.4 + - + +
392l ASP* 3.8 7.6 - - - +
393l GLU 3.3 0.2 - - - -
394l ILE* 1.3 74.8 - - - +
396l SER* 1.3 52.0 + - - +
398l ILE* 3.1 8.9 + - + +
399l ARG* 2.8 59.3 + - + +
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Residues in contact with SER 396 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392l ASP 3.1 13.9 + - - -
393l GLU* 3.3 8.9 + - - -
395l ILE* 1.3 76.9 - - - +
397l THR* 1.3 56.2 + - - +
399l ARG* 3.1 12.3 + - - +
400l GLU* 2.9 41.5 + - - +
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Residues in contact with THR 397 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393l GLU* 2.8 22.1 + - - +
394l ILE 3.4 8.7 - - - -
396l SER* 1.3 74.1 - - - +
398l ILE* 1.3 54.5 + - - +
400l GLU* 3.5 17.8 - - - +
401l SER* 2.6 32.4 + - - -
407l ALA 4.8 0.4 - - - +
410l SER* 3.6 33.8 - - - +
411l LEU* 3.9 22.4 - - + -
414l ARG* 4.9 5.8 - - + +
415l PHE* 3.8 12.8 - - + -
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Residues in contact with ILE 398 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430j LEU* 3.7 42.0 - - + +
433j LEU* 3.9 21.1 - - + +
434j THR* 3.9 8.7 - - + +
394l ILE* 3.1 39.2 + - + +
395l ILE* 3.5 9.2 - - + +
397l THR* 1.3 73.6 - - - +
399l ARG* 1.3 64.5 + - - +
401l SER* 3.3 24.7 + - - +
407l ALA* 4.5 2.9 - - + -
411l LEU* 4.1 15.5 - - + -
425l ILE* 4.8 1.1 - - + -
426l LEU* 4.0 28.0 - - + -
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Residues in contact with ARG 399 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388j LEU 5.3 1.6 + - - -
391j ILE* 3.5 34.3 - - - +
392j ASP* 4.8 14.4 - - - +
433j LEU* 3.8 25.4 - - + +
435j GLY* 4.9 4.3 + - - -
395l ILE* 2.8 32.4 + - + +
396l SER* 3.1 11.4 + - - +
398l ILE* 1.3 73.4 - - - +
400l GLU* 1.3 59.9 + - - +
401l SER 3.1 13.1 + - - +
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Residues in contact with GLU 400 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396l SER* 2.9 21.3 + - - +
397l THR* 3.5 25.2 + - - +
399l ARG* 1.3 74.9 - - - +
401l SER* 1.3 61.2 + - - +
402l ASP* 3.5 12.5 - - - +
406l VAL* 5.6 0.3 - - - +
410l SER* 5.6 3.2 - - - +
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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