Contacts of the helix formed by residues 444 - 457 (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 GLU 444 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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428A LYS* 4.3 11.4 - - - +
439C LEU* 3.0 40.5 + - + +
442C ARG* 3.7 28.2 + - + +
443C ASN* 1.3 73.6 - - - +
445C HIS* 1.3 64.9 + - - +
446C ARG 3.2 3.9 + - - +
447C GLN* 3.3 9.0 + - + +
448C ALA* 3.1 22.4 + - - +
18G T 3.5 39.2 + - - +
19G C 5.7 1.9 + - - +
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Residues in contact with HIS 445 (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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440C ARG* 5.5 4.7 - - - +
443C ASN* 3.0 9.4 + - - +
444C GLU* 1.3 76.6 - - - +
446C ARG* 1.3 57.3 + - - +
448C ALA* 3.8 6.8 - - - +
449C ASP* 2.9 32.2 + - - +
18G T 5.4 0.4 + - - -
42J G 5.2 16.6 - - - +
43J C 6.6 0.2 - - - -
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Residues in contact with ARG 446 (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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444C GLU 3.2 0.8 - - - -
445C HIS* 1.3 79.1 - - - +
447C GLN* 1.3 57.8 + - - +
449C ASP* 3.8 3.2 - - - +
450C GLU* 2.9 30.2 + - - +
18G T 4.9 0.6 + - - +
19G C 3.2 29.1 + - - +
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Residues in contact with GLN 447 (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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454A ILE* 5.9 0.8 - - - +
455A MET* 4.1 23.8 - - + +
439C LEU* 4.0 20.8 - - + +
444C GLU* 3.3 15.4 + - + +
446C ARG* 1.3 77.9 - - - +
448C ALA* 1.3 57.0 + - - +
450C GLU* 3.4 7.0 + - - +
451C LEU* 3.0 28.8 + - - +
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Residues in contact with ALA 448 (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* 3.5 22.8 - - + +
439C LEU* 3.8 26.8 - - + +
440C ARG* 4.5 7.9 - - + +
444C GLU 3.1 16.6 + - - +
445C HIS* 3.8 7.4 - - - +
447C GLN* 1.3 75.5 - - - +
449C ASP* 1.3 60.4 + - - +
451C LEU 3.3 0.7 + - - -
452C GLU* 2.9 26.2 + - - +
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Residues in contact with ASP 449 (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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445C HIS 2.9 18.8 + - - +
446C ARG* 4.0 3.6 - - - +
448C ALA* 1.3 76.7 - - - +
450C GLU* 1.3 58.0 + - - +
452C GLU* 3.4 7.6 + - - +
453C ALA* 2.9 28.6 + - - +
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Residues in contact with GLU 450 (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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454A ILE* 4.7 21.8 - - + -
494A ARG* 6.3 0.9 - - - +
446C ARG 2.9 18.7 + - - +
447C GLN* 3.6 7.4 - - - +
448C ALA 3.2 0.2 - - - -
449C ASP* 1.3 77.1 - - - +
451C LEU* 1.3 57.4 + - - +
453C ALA* 3.2 6.9 + - - +
454C ILE* 2.8 38.9 + - + +
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Residues in contact with LEU 451 (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* 6.4 2.5 - - + -
451A LEU* 6.4 1.8 - - + -
454A ILE* 5.9 7.0 - - + +
455A MET* 6.0 2.2 - - + -
435C PHE* 5.6 7.2 - - + -
436C LEU* 4.1 14.8 - - + -
439C LEU* 5.1 6.1 - - + -
447C GLN 3.0 17.4 + - - +
448C ALA* 3.8 3.8 - - - +
450C GLU* 1.3 72.2 - - - +
452C GLU* 1.3 66.8 + - - +
454C ILE* 3.2 9.8 + - + +
455C MET* 2.9 29.9 + - + +
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Residues in contact with GLU 452 (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* 4.3 17.7 - - + +
448C ALA 2.9 16.9 + - - +
449C ASP* 3.7 8.7 - - - +
450C GLU 3.3 0.2 - - - -
451C LEU* 1.3 76.4 - - - +
453C ALA* 1.3 56.9 + - - +
455C MET* 3.4 6.9 + - - +
456C GLN* 2.9 36.3 + - + +
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Residues in contact with ALA 453 (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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449C ASP 2.9 17.2 + - - +
450C GLU* 3.5 8.7 - - - +
452C GLU* 1.3 74.8 - - - +
454C ILE* 1.3 55.8 + - + +
456C GLN* 3.3 7.4 - - - -
457C GLY 2.5 29.3 + - - -
458C ARG* 2.7 28.9 + - + -
459C GLY* 4.4 7.6 - - - +
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Residues in contact with ILE 454 (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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447A GLN* 3.9 33.3 + - + +
450A GLU* 4.7 22.7 - - + +
451A LEU* 5.3 5.6 - - + +
454A ILE* 5.6 13.9 - - + -
450C GLU* 2.8 32.6 + - + +
451C LEU* 3.6 10.3 - - + +
453C ALA* 1.3 78.2 - - + +
455C MET* 1.3 72.5 + - + +
457C GLY* 3.3 13.0 + - - -
459C GLY* 3.1 34.5 - - - +
460C SER* 4.9 5.2 - - - -
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Residues in contact with MET 455 (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* 4.6 25.4 - - + -
447A GLN* 3.7 38.1 + - - +
432C LEU* 5.7 7.9 - - + -
436C LEU* 6.1 4.5 - - + -
451C LEU* 2.9 22.3 + - + +
452C GLU* 3.7 7.2 - - - +
453C ALA 3.3 0.2 - - - -
454C ILE* 1.3 84.8 - - + +
456C GLN* 1.3 65.1 + - + +
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Residues in contact with GLN 456 (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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452C GLU* 2.9 22.4 + - + +
453C ALA* 3.3 7.6 - - - +
455C MET* 1.3 80.7 + - - +
457C GLY* 1.3 61.2 + - - +
458C ARG* 3.5 6.6 + - + +
463C GLN* 4.9 6.2 - - - +
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Residues in contact with GLY 457 (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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453C ALA 2.5 14.7 + - - -
454C ILE* 3.3 14.2 + - - -
456C GLN* 1.3 76.7 - - - +
458C ARG* 1.3 55.3 + - - -
459C GLY 3.7 2.2 - - - -
461C GLY* 3.3 16.4 - - - +
463C GLN* 3.0 30.4 + - - +
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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