Contacts of the helix formed by residues 426 - 442 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419C ALA* 4.4 3.8 + - - +
423C GLU* 3.5 25.5 + - + +
424C GLY 3.4 1.8 + - - +
425C GLY* 1.3 72.7 - - - +
427C VAL* 1.3 63.8 + - - +
428C LYS* 3.3 3.1 - - - -
429C ALA* 3.6 15.1 + - + +
430C VAL* 3.4 19.8 + - - +
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Residues in contact with VAL 427 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438A ALA* 5.2 10.5 - - + -
416C LYS* 5.8 5.6 - - + -
419C ALA* 4.3 18.4 - - + -
425C GLY 3.0 11.5 + - - +
426C ASP* 1.3 70.0 - - - +
428C LYS* 1.3 66.0 + - - +
430C VAL* 3.2 2.6 + - - +
431C CYS* 2.9 26.2 + - - +
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Residues in contact with LYS 428 (chain C).
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* 4.0 10.1 - - + -
438A ALA* 5.0 13.6 - - + +
426C ASP* 3.3 2.1 - - + +
427C VAL* 1.3 79.3 - - - +
429C ALA* 1.3 63.3 + - - +
431C CYS* 3.4 0.3 + - - -
432C LEU* 2.9 26.8 + - - +
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Residues in contact with ALA 429 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396A LEU* 4.5 19.5 - - + +
397A LEU* 5.4 7.4 - - + +
423C GLU* 6.4 0.4 - - + -
426C ASP* 3.6 19.4 + - + +
427C VAL 3.4 0.4 - - - -
428C LYS* 1.3 79.3 - - - +
430C VAL* 1.3 57.3 + - - +
432C LEU* 4.0 4.3 - - - +
433C THR* 2.9 32.9 + - - -
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Residues in contact with VAL 430 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396A LEU* 5.9 2.7 - - - -
411A LEU* 5.0 14.6 - - + -
419C ALA* 4.7 13.7 - - + -
423C GLU* 5.8 4.5 - - + -
426C ASP 3.4 11.6 + - - +
427C VAL* 3.2 9.3 + - - +
428C LYS 3.2 0.8 - - - -
429C ALA* 1.3 79.9 - - - +
431C CYS* 1.3 58.5 + - - +
433C THR* 4.0 3.3 - - - -
434C LEU* 2.9 35.0 + - + +
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Residues in contact with CYS 431 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431A CYS 5.1 1.4 - - - +
434A LEU* 4.5 9.9 - - + +
435A PHE* 3.8 36.1 - - + +
438A ALA* 4.7 5.2 - - + -
427C VAL 2.9 16.7 + - - +
430C VAL* 1.3 77.5 - - - +
432C LEU* 1.3 62.9 + - - +
434C LEU* 3.6 11.4 - - + +
435C PHE* 2.9 26.3 + - - +
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Residues in contact with LEU 432 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435A PHE* 3.6 32.3 - - + -
428C LYS 2.9 18.2 + - - +
429C ALA* 4.1 4.3 - - - +
431C CYS* 1.3 76.9 - - - +
433C THR* 1.3 57.7 + - - +
435C PHE* 3.9 1.0 - - - +
436C LEU* 2.9 39.8 + - + +
455C MET* 5.7 10.1 - - + -
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Residues in contact with THR 433 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396A LEU* 4.9 11.7 - - - -
397A LEU* 6.4 0.2 - - - -
404A GLN* 3.8 25.6 - - - -
429C ALA 2.9 18.0 + - - -
430C VAL* 4.1 4.3 - - - -
432C LEU* 1.3 76.5 - - - +
434C LEU* 1.3 57.0 + - - +
436C LEU* 3.9 7.1 - - - +
437C LEU* 2.9 43.3 + - - +
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Residues in contact with LEU 434 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408A LEU* 4.8 15.7 - - + -
411A LEU* 3.7 30.5 - - + +
412A LYS* 4.5 28.7 - - + +
415A VAL* 4.7 9.4 - - + -
431A CYS* 4.5 21.9 - - + -
434A LEU* 6.2 3.4 - - + -
430C VAL* 2.9 20.0 + - + +
431C CYS* 3.6 11.9 - - + +
433C THR* 1.3 76.6 - - - +
435C PHE* 1.3 57.1 - - - +
437C LEU* 3.8 6.6 - - + +
438C ALA* 2.9 30.0 + - - +
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Residues in contact with PHE 435 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428A LYS* 3.8 28.3 - - + -
431A CYS* 4.0 19.5 - - + +
432A LEU* 3.7 43.3 - - + -
435A PHE* 4.4 21.3 - + + -
451A LEU* 6.3 1.6 - - + -
455A MET* 4.4 15.7 - - + -
431C CYS 2.9 17.4 + - - +
432C LEU 4.1 2.5 - - - +
434C LEU* 1.3 77.9 - - - +
436C LEU* 1.3 59.0 + - + +
438C ALA* 3.3 4.3 + - + +
439C LEU* 2.9 63.6 + - + +
451C LEU* 5.6 7.9 - - + -
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Residues in contact with LEU 436 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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432C LEU* 2.9 27.9 + - + +
433C THR* 3.9 5.6 - - - +
435C PHE* 1.3 78.7 - - + +
437C LEU* 1.3 59.6 + - + +
439C LEU* 3.3 7.6 + - + +
440C ARG* 2.9 28.8 + - - +
448C ALA* 3.5 37.1 - - + +
451C LEU* 4.1 18.2 - - + -
452C GLU* 4.3 17.3 - - + +
455C MET* 6.1 3.8 - - + -
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Residues in contact with LEU 437 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401A ARG* 4.1 31.2 - - + +
404A GLN* 4.0 19.5 - - + +
405A LYS* 3.7 34.3 - - + +
408A LEU* 5.2 7.0 - - + -
433C THR* 2.9 30.0 + - - +
434C LEU* 3.9 6.3 - - + +
436C LEU* 1.3 75.4 - - + +
438C ALA* 1.3 60.8 + - - +
440C ARG* 3.8 8.6 - - + +
441C ALA* 2.9 28.4 + - - +
44J C 3.8 9.2 + - - +
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Residues in contact with ALA 438 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427A VAL* 4.4 23.1 - - + -
428A LYS* 5.1 7.6 - - - -
431A CYS* 4.6 6.7 - - + -
434C LEU 2.9 17.8 + - - +
435C PHE* 3.6 11.9 - - + +
437C LEU* 1.3 74.3 - - - +
439C LEU* 1.3 65.0 + - - +
441C ALA* 3.0 17.5 + - - +
442C ARG* 3.1 19.1 + - + +
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Residues in contact with LEU 439 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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428A LYS* 4.9 7.6 - - + +
455A MET* 5.2 5.6 - - + -
435C PHE* 2.9 58.6 + - + +
436C LEU* 3.6 9.9 - - + +
438C ALA* 1.3 76.2 - - - +
440C ARG* 1.3 62.4 + - - +
442C ARG* 3.4 6.5 + - - +
444C GLU* 3.0 59.3 + - + +
447C GLN* 4.0 17.9 - - + +
448C ALA* 3.8 30.1 - - + +
451C LEU* 5.1 3.1 - - + -
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Residues in contact with ARG 440 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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436C LEU 2.9 16.9 + - - +
437C LEU* 3.8 11.0 - - + +
439C LEU* 1.3 76.3 - - - +
441C ALA* 1.3 63.3 + - - +
443C ASN* 2.9 14.3 + - - +
444C GLU 4.8 3.1 - - - +
445C HIS* 5.4 3.4 - - + +
448C ALA* 4.5 8.6 - - + +
43J C 3.0 49.9 - - - +
44J C 5.4 0.7 - - - +
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Residues in contact with ALA 441 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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437C LEU 2.9 11.1 + - - +
438C ALA* 3.0 14.1 + - - +
440C ARG* 1.3 77.6 - - - +
442C ARG* 1.3 58.8 + - + +
443C ASN* 3.2 10.3 + - - +
43J C 3.3 14.8 + - - +
44J C 3.3 34.0 - - - +
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Residues in contact with ARG 442 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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425A GLY 4.4 4.8 + - - -
426A ASP* 3.6 22.6 + - - +
427A VAL* 4.2 8.7 - - - +
428A LYS* 3.5 48.3 - - - +
438C ALA 3.1 17.3 + - - +
439C LEU* 4.0 5.2 - - - +
440C ARG 3.2 0.4 - - - -
441C ALA* 1.3 75.6 - - + +
443C ASN* 1.3 68.2 + - - +
444C GLU* 3.1 31.5 + - + +
17G T 3.9 17.4 - - - +
18G T 5.1 0.4 + - - +
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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