Contacts of the helix formed by residues 436 - 447 (chain C) in PDB entry 4QYJ
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 436 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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435B ASN* 2.8 34.7 + - - +
437B LEU* 4.7 1.3 - - - -
277C LEU* 4.7 1.4 - - + +
279C ASP* 4.2 13.8 - - - +
434C THR* 3.2 14.5 + - - +
435C ASN* 1.3 78.2 - - - +
437C LEU* 1.3 58.9 - - - +
438C SER* 4.3 1.4 - - - -
439C ALA* 3.7 25.5 + - + +
440C ALA* 3.0 28.6 + - - +
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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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494A ILE* 3.5 35.0 - - + -
496A TYR* 4.7 5.6 - - + -
434B THR 4.2 7.2 - - - +
435B ASN* 2.9 25.3 + - - +
437B LEU* 3.8 37.4 - - + +
440B ALA* 5.4 6.5 - - + -
441B LEU* 5.7 0.7 - - + -
454B VAL* 4.3 6.5 - - + -
455B ASN* 4.1 19.7 - - - +
435C ASN 3.7 1.0 + - - -
436C ASP* 1.3 69.4 - - - +
438C SER* 1.3 68.5 + - - +
440C ALA* 4.7 1.6 - - - -
441C LEU* 3.1 55.0 + - + +
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Residues in contact with SER 438 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496A TYR* 3.7 32.9 + - - -
435B ASN* 3.2 17.3 + - - -
436C ASP* 4.3 2.7 - - - -
437C LEU* 1.3 80.9 - - - +
439C ALA* 1.3 57.8 + - - +
441C LEU* 4.1 1.4 - - - +
442C ARG* 3.0 40.7 + - - +
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Residues in contact with ALA 439 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277C LEU* 4.0 15.3 - - + -
414C ILE* 4.3 17.9 - - + -
436C ASP* 3.7 27.6 + - + +
437C LEU 3.3 0.6 - - - -
438C SER* 1.3 75.0 - - - +
440C ALA* 1.3 68.6 + - - +
441C LEU 3.1 0.3 + - - -
442C ARG* 4.4 6.7 - - - +
443C ILE* 2.8 32.6 + - + +
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Residues in contact with ALA 440 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437B LEU* 5.0 6.3 - - + -
277C LEU* 4.8 0.4 - - - +
432C ILE* 3.4 21.4 - - + +
434C THR* 3.8 22.2 - - + +
436C ASP* 3.0 19.2 + - - +
437C LEU* 3.9 4.0 - - - +
439C ALA* 1.3 78.9 - - - +
441C LEU* 1.3 63.9 + - + +
444C ASN* 3.3 16.6 + - - +
454C VAL* 4.3 20.0 - - + +
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Residues in contact with LEU 441 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A ARG* 5.8 0.4 - - + -
494A ILE* 4.4 14.1 - - + -
496A TYR* 3.6 40.9 + - + -
437B LEU* 5.6 4.5 - - + -
437C LEU* 3.1 48.4 + - + +
440C ALA* 1.3 77.9 - - + +
442C ARG* 1.3 53.9 + - - +
444C ASN* 3.2 12.1 - - + +
445C ASP* 2.9 33.7 + - - +
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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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147A GLU 4.1 16.0 + - - -
149A ARG* 3.9 35.1 - - - +
496A TYR* 3.0 34.3 + - + -
414C ILE* 6.3 3.1 - - - -
438C SER* 3.0 28.9 + - - +
439C ALA* 3.5 5.6 - - - +
441C LEU* 1.3 74.3 - - - +
443C ILE* 1.3 66.6 + - + +
444C ASN 3.1 0.7 - - - -
445C ASP* 3.2 23.2 - - - +
446C GLU* 3.3 14.0 + - + +
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Residues in contact with ILE 443 (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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275C ILE* 4.8 11.4 - - + -
277C LEU* 4.2 22.4 - - + -
414C ILE* 4.2 28.7 - - + -
417C VAL* 5.3 2.0 - - + -
418C VAL* 3.9 21.1 - - + -
432C ILE* 3.9 39.0 - - + -
439C ALA* 2.8 25.5 + - - +
442C ARG* 1.3 72.1 - - + +
444C ASN* 1.3 57.0 + - - +
446C GLU* 2.9 18.4 + - - +
447C LEU* 3.0 22.4 + - + +
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Residues in contact with ASN 444 (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 ILE* 4.2 9.4 - - + +
440C ALA 3.3 13.3 + - - +
441C LEU* 3.2 14.9 - - - +
443C ILE* 1.3 79.3 - - - +
445C ASP* 1.3 65.4 + - - +
446C GLU 3.4 0.2 + - - -
447C LEU* 3.9 16.5 + - - +
452C VAL* 3.5 31.3 - - + +
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Residues in contact with ASP 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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149A ARG* 2.4 39.1 + - - +
496A TYR* 2.7 33.2 + - - -
441C LEU 2.9 16.4 + - - +
442C ARG* 3.2 9.9 - - - +
444C ASN* 1.3 77.9 - - - +
446C GLU* 1.3 67.0 + - + +
447C LEU 4.5 2.4 - - - +
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Residues in contact with GLU 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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149A ARG* 3.3 25.4 + - - +
418C VAL* 4.2 20.6 - - + +
422C ASN* 3.1 20.0 + - - -
442C ARG* 3.3 17.9 + - + +
443C ILE 2.9 9.4 + - - +
445C ASP* 1.3 82.0 - - + +
447C LEU* 1.3 66.4 + - - +
448C GLU* 4.4 3.5 - - - +
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Residues in contact with LEU 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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273C PRO* 5.5 0.2 - - + -
275C ILE* 4.6 9.9 - - + -
418C VAL* 4.3 15.9 - - + -
421C ALA* 3.7 29.8 - - + -
422C ASN* 3.7 6.1 - - - +
430C ALA* 3.9 28.0 - - + -
432C ILE* 4.7 3.1 - - + -
443C ILE* 3.0 31.6 + - + +
444C ASN 3.9 10.7 + - - +
445C ASP 3.6 3.5 - - - +
446C GLU* 1.3 80.1 - - - +
448C GLU* 1.3 60.1 + - - +
449C ALA* 3.3 13.8 + - + +
452C VAL* 4.1 19.7 - - + -
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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