Contacts of the helix formed by residues 397 - 411 (chain A) in PDB entry 6N8Q
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 PRO 397 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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395A ASN 3.8 1.3 - - - +
396A ILE* 1.3 92.3 - - + +
398A LEU* 1.3 66.0 + - - +
399A LYS* 3.0 6.0 + - + +
400A LEU* 3.2 7.2 + - + +
401A TRP 3.0 18.9 + - - -
435A ARG* 4.5 0.9 - - - +
514A LYS* 3.5 46.9 - - + +
515A TYR* 4.7 13.7 - - + -
797A HIS* 6.4 0.4 - - + -
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Residues in contact with LEU 398 (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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396A ILE 3.3 2.4 + - - -
397A PRO* 1.3 73.4 - - - +
399A LYS* 1.3 62.9 + - - +
401A TRP* 3.5 2.6 - - + +
402A GLU* 3.1 54.1 + - + +
435A ARG* 3.4 45.6 - - - +
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Residues in contact with LYS 399 (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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397A PRO* 3.0 4.5 + - + +
398A LEU* 1.3 76.8 - - - +
400A LEU* 1.3 59.7 + - - +
402A GLU* 3.2 12.8 + - - +
403A ARG* 2.9 39.2 + - - +
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Residues in contact with LEU 400 (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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396A ILE* 4.6 7.4 - - + -
397A PRO* 3.2 11.2 + - + +
399A LYS* 1.3 77.9 - - - +
401A TRP* 1.3 57.5 + - - +
403A ARG* 3.7 18.3 - - - +
404A ILE* 2.9 52.9 + - + +
512A LEU* 5.0 8.7 - - + -
513A CYS 4.5 0.7 - - - +
514A LYS* 3.5 38.8 - - + +
515A TYR 5.3 2.7 - - - +
516A SER 4.8 1.1 - - - -
517A GLY* 3.7 27.1 - - - +
533A LEU* 3.7 23.6 - - + -
577A PHE* 5.2 0.2 - - + -
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Residues in contact with TRP 401 (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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396A ILE* 3.6 34.4 - - + +
397A PRO 3.0 12.8 + - - +
398A LEU* 3.5 10.8 - - + +
400A LEU* 1.3 76.5 - - - +
402A GLU* 1.3 63.5 + - + +
404A ILE* 3.4 5.3 + - + +
405A ILE* 3.0 62.7 + - + +
435A ARG* 3.4 37.0 - - + +
436A ASP 3.4 16.2 - - - -
437A LEU* 3.6 24.7 - - + -
451A ASP* 3.2 37.5 - - - -
453A SER* 3.9 3.6 - - - -
458A ARG* 5.8 0.4 - - - -
460A LEU* 3.7 18.6 - - + +
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Residues in contact with GLU 402 (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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398A LEU* 3.1 44.7 + - + +
399A LYS* 3.7 8.3 - - - +
401A TRP* 1.3 84.3 - - + +
403A ARG* 1.3 59.1 + - + +
405A ILE* 3.4 7.6 + - + +
406A ALA* 2.7 31.9 + - - +
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Residues in contact with ARG 403 (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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399A LYS* 2.9 28.9 + - + +
400A LEU* 3.7 18.0 - - - +
402A GLU* 1.3 78.1 - - + +
404A ILE* 1.3 58.1 + - - +
406A ALA* 3.4 6.1 + - - +
407A ALA* 3.0 28.9 + - - +
516A SER 5.8 0.8 + - - -
517A GLY* 5.4 1.6 - - - -
533A LEU* 3.0 62.8 + - + +
534A ASN* 4.2 0.2 - - - +
535A ASP* 3.0 42.5 + - - +
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Residues in contact with ILE 404 (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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396A ILE* 5.8 1.3 - - + -
400A LEU* 2.9 37.2 + - + +
401A TRP* 3.9 5.6 - - + +
403A ARG* 1.3 71.5 - - - +
405A ILE* 1.3 66.6 + - + +
407A ALA* 3.4 6.1 + - - +
408A GLY* 3.0 17.2 + - - -
437A LEU* 4.5 12.3 - - + -
449A PHE* 4.0 26.5 - - + -
460A LEU* 4.9 8.7 - - + -
461A TYR* 3.7 31.0 - - + +
512A LEU* 5.2 1.1 - - + -
533A LEU* 3.8 17.3 - - + -
577A PHE* 3.7 27.4 - - + -
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Residues in contact with ILE 405 (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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401A TRP* 3.0 52.7 + - + +
402A GLU* 3.7 7.9 - - + +
404A ILE* 1.3 75.5 - - - +
406A ALA* 1.3 63.2 + - - +
408A GLY* 3.0 11.1 + - - -
409A SER* 3.0 17.9 + - - +
458A ARG* 4.4 17.7 - - - +
460A LEU* 3.7 39.0 - - + +
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Residues in contact with ALA 406 (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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402A GLU 2.7 22.3 + - - +
403A ARG* 3.7 7.0 - - - +
405A ILE* 1.3 74.5 - - - +
407A ALA* 1.3 62.4 + - - +
409A SER* 3.0 20.5 + - - -
410A ARG* 3.2 17.1 + - - +
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Residues in contact with ALA 407 (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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403A ARG 3.0 16.9 + - - +
404A ILE* 3.8 7.0 - - - +
406A ALA* 1.3 75.9 - - - +
408A GLY* 1.3 61.7 + - - +
410A ARG* 3.3 22.5 + - - +
411A GLN* 3.6 11.4 + - - +
461A TYR* 4.2 7.9 - - + -
533A LEU* 5.1 3.4 - - + -
534A ASN 5.2 1.3 - - - +
535A ASP* 6.1 1.3 - - - -
574A GLU* 4.5 0.2 - - - +
575A PRO* 4.0 14.9 - - + +
576A GLY* 3.9 29.6 - - - +
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Residues in contact with GLY 408 (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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404A ILE 3.0 7.0 + - - -
405A ILE 3.0 5.7 + - - -
407A ALA* 1.3 75.9 - - - +
409A SER* 1.3 59.4 + - - +
411A GLN* 3.2 22.4 - - - +
412A ASN* 2.6 32.4 + - - -
460A LEU 3.2 24.9 - - - -
461A TYR* 4.1 1.7 - - - -
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Residues in contact with SER 409 (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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405A ILE* 3.0 18.4 + - - +
406A ALA* 3.0 13.0 + - - -
408A GLY* 1.3 76.5 - - - +
410A ARG* 1.3 63.6 + - - +
412A ASN* 3.3 23.0 + - - +
413A ALA* 4.0 3.1 + - - +
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Residues in contact with ARG 410 (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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406A ALA* 3.2 17.3 - - - +
407A ALA* 3.5 15.0 - - - +
408A GLY 3.2 0.8 - - - -
409A SER* 1.3 80.3 - - - +
411A GLN* 1.3 57.7 + - - +
412A ASN 3.6 0.3 + - - -
413A ALA* 4.2 12.3 + - - +
535A ASP 4.9 3.2 + - - -
536A GLU* 3.5 24.9 + - - +
537A ALA* 5.5 0.6 - - - +
574A GLU* 3.8 12.9 + - - +
575A PRO* 3.8 29.8 - - + +
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Residues in contact with GLN 411 (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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407A ALA 3.6 2.4 + - - -
408A GLY* 3.2 21.3 - - - +
410A ARG* 1.3 77.0 - - - +
412A ASN* 1.3 66.6 + - - +
413A ALA* 3.5 1.6 - - - -
414A HIS* 3.4 18.4 + - - -
461A TYR* 3.1 21.5 - - - -
462A LYS* 3.0 52.4 + - - +
574A GLU* 3.5 28.5 + - - +
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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