Contacts of the helix formed by residues 426 - 442 (chain A) in PDB entry 6CIM
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 426 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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419A ALA* 4.1 5.5 - - - +
423A GLU* 3.8 18.0 + - + +
424A GLY 3.5 2.3 - - - +
425A GLY* 1.3 73.2 - - - +
427A VAL* 1.3 65.2 + - - +
428A LYS* 3.4 17.2 + - - +
429A ALA* 2.9 40.6 + - + +
430A VAL* 3.1 23.2 + - - +
442C ARG* 3.6 14.9 + - - +
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Residues in contact with VAL 427 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415A VAL* 4.7 6.5 - - + +
416A LYS* 4.2 21.3 - - + -
419A ALA* 4.2 15.9 - - + -
420A ASP* 5.7 1.3 - - - +
425A GLY* 3.1 9.7 + - - +
426A ASP* 1.3 70.4 - - - +
428A LYS* 1.3 66.3 + - - +
430A VAL* 3.1 7.9 - - - +
431A CYS* 3.0 39.9 + - - -
438C ALA* 4.4 14.1 - - + -
442C ARG* 4.2 5.1 - - - +
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Residues in contact with LYS 428 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426A ASP* 3.2 12.9 + - - +
427A VAL* 1.3 80.7 - - - +
429A ALA* 1.3 70.2 + - - +
431A CYS* 3.9 1.3 - - - -
432A LEU* 3.0 35.4 + - + +
455A MET* 6.2 4.0 - - - -
435C PHE* 3.8 22.1 - - + -
438C ALA* 5.1 7.6 - - + +
439C LEU* 4.9 6.1 - - + +
442C ARG* 3.5 39.9 - - - +
444C GLU* 4.3 17.7 - - - +
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Residues in contact with ALA 429 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426A ASP* 2.9 32.6 + - + +
428A LYS* 1.3 85.0 - - - +
430A VAL* 1.3 58.3 + - - +
432A LEU* 3.4 9.8 + - + +
433A THR* 2.8 36.5 + - - +
396C LEU* 5.6 10.8 - - + -
397C LEU* 5.6 9.6 - - + -
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Residues in contact with VAL 430 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415A VAL* 3.9 20.4 - - + -
418A PHE* 6.1 0.4 - - + -
419A ALA* 4.4 12.3 - - + -
423A GLU* 5.5 8.5 - - + -
426A ASP 3.1 15.2 + - - +
427A VAL* 3.1 21.5 - - - +
429A ALA* 1.3 76.6 - - - +
431A CYS* 1.3 61.3 + - - +
433A THR* 3.3 5.5 + - - -
434A LEU* 2.9 30.3 + - + +
408C LEU* 5.6 8.1 - - + -
411C LEU* 3.5 29.2 - - + -
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Residues in contact with CYS 431 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415A VAL* 4.2 17.5 - - - -
427A VAL* 3.0 37.4 + - - +
428A LYS 3.9 2.5 - - - +
430A VAL* 1.3 77.9 - - - +
432A LEU* 1.3 63.8 + - - +
434A LEU* 3.4 6.4 + - - +
435A PHE* 3.0 25.8 + - - +
431C CYS* 5.1 1.4 - - - +
434C LEU* 4.5 26.2 - - + -
435C PHE* 4.0 25.5 - - + +
438C ALA* 4.6 7.6 - - + -
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Residues in contact with LEU 432 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428A LYS* 3.0 23.6 + - + +
429A ALA* 3.6 9.9 - - + +
430A VAL 3.3 0.2 - - - -
431A CYS* 1.3 76.6 - - - +
433A THR* 1.3 59.7 + - - +
435A PHE* 3.3 3.9 + - + +
436A LEU* 2.9 60.4 + - + +
451A LEU* 5.3 4.9 - - + +
455A MET* 4.0 32.5 - - + -
435C PHE* 3.7 35.1 - - + -
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Residues in contact with THR 433 (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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429A ALA* 2.8 20.7 + - - +
430A VAL* 3.9 4.7 - - - -
432A LEU* 1.3 75.9 - - - +
434A LEU* 1.3 66.6 + - - +
436A LEU* 3.4 7.1 + - + -
437A LEU* 3.0 50.8 + - + +
396C LEU* 5.7 5.4 - - - +
397C LEU* 6.0 2.1 - - - -
404C GLN* 4.0 25.4 - - + +
408C LEU* 5.9 3.4 - - + -
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Residues in contact with LEU 434 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430A VAL* 2.9 19.8 + - + +
431A CYS* 3.7 8.3 - - - +
433A THR* 1.3 77.5 - - - +
435A PHE* 1.3 56.8 + - - +
437A LEU* 3.8 5.5 - - - +
438A ALA* 2.9 29.3 + - - +
411C LEU* 5.9 5.2 - - + -
431C CYS* 4.5 8.5 - - + -
434C LEU* 6.2 3.1 - - + -
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Residues in contact with PHE 435 (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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431A CYS 3.0 17.6 + - - +
432A LEU* 3.8 5.4 - - + +
434A LEU* 1.3 75.2 - - - +
436A LEU* 1.3 65.3 + - + +
438A ALA* 3.7 3.9 - - + +
439A LEU* 2.9 36.9 + - + +
451A LEU* 5.8 7.9 - - + -
428C LYS* 4.0 11.9 - - + -
431C CYS* 3.8 19.7 - - + +
432C LEU* 3.6 44.6 - - + -
435C PHE* 4.4 20.4 - + + -
451C LEU* 6.4 2.2 - - + -
455C MET* 4.6 22.2 - - + -
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Residues in contact with LEU 436 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432A LEU* 2.9 43.0 + - + +
433A THR* 3.8 7.6 - - + +
435A PHE* 1.3 80.6 - - + +
437A LEU* 1.3 65.9 + - + +
439A LEU* 3.3 6.0 + - - +
440A ARG* 2.9 27.4 + - - +
448A ALA* 3.4 38.2 - - + +
451A LEU* 3.9 18.6 - - + -
452A GLU* 3.7 28.3 - - + +
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Residues in contact with LEU 437 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433A THR* 3.0 44.1 + - + +
434A LEU* 4.0 4.3 - - - +
436A LEU* 1.3 82.1 - - + +
438A ALA* 1.3 61.0 + - - +
440A ARG* 3.4 8.5 + - + +
441A ALA* 2.9 27.2 + - - +
401C ARG* 5.4 5.8 - - + +
404C GLN* 4.7 4.7 - - + +
405C LYS* 4.4 29.4 - - + +
408C LEU* 5.7 4.0 - - + -
33L T 4.0 3.5 + - - -
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Residues in contact with ALA 438 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434A LEU 2.9 18.6 + - - +
435A PHE* 3.7 11.0 - - + +
437A LEU* 1.3 74.3 - - - +
439A LEU* 1.3 65.0 + - - +
441A ALA* 3.0 16.8 + - - +
442A ARG* 3.1 15.2 + - - +
427C VAL* 5.0 14.4 - - + +
428C LYS* 5.0 11.2 - - - +
431C CYS* 4.7 10.5 - - + -
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Residues in contact with LEU 439 (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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435A PHE* 2.9 29.4 + - + +
436A LEU* 3.3 6.3 + - - +
438A ALA* 1.3 76.5 - - - +
440A ARG* 1.3 62.4 + - - +
441A ALA 3.3 0.2 + - - -
442A ARG* 3.3 7.2 + - - -
444A GLU* 3.1 38.5 + - + +
447A GLN* 5.5 2.2 - - + -
448A ALA* 3.8 22.9 - - + +
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Residues in contact with ARG 440 (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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436A LEU 2.9 17.0 + - - +
437A LEU* 3.7 10.3 - - + +
438A ALA 3.3 0.2 - - - -
439A LEU* 1.3 75.6 - - - +
441A ALA* 1.3 61.7 + - - +
443A ASN* 3.3 12.5 + - - -
444A GLU 4.9 0.4 - - - +
445A HIS* 4.1 31.0 - - + +
448A ALA* 4.8 3.7 - - + +
32L C 4.5 14.0 - - - +
33L T 3.6 9.8 + - - +
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Residues in contact with ALA 441 (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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437A LEU 2.9 12.5 + - - +
438A ALA* 3.0 13.6 + - - +
440A ARG* 1.3 78.4 - - - +
442A ARG* 1.3 56.5 + - - +
443A ASN* 3.2 5.4 + - - +
32L C 4.9 0.2 - - - -
33L T 3.0 28.4 + - - +
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Residues in contact with ARG 442 (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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438A ALA 3.1 13.4 + - - +
439A LEU* 3.3 6.4 + - - +
441A ALA* 1.3 73.6 - - - +
443A ASN* 1.3 67.2 + - - +
444A GLU* 3.1 10.6 + - + +
428C LYS* 5.9 8.1 - - + -
18F C 4.6 5.9 + - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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