Contacts of the helix formed by residues 536 - 543 (chain B) in PDB entry 1Q6X
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 536 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38B TYR* 4.6 3.5 + - - -
50B GLN* 4.7 3.3 - - - +
53B LYS* 6.0 0.7 - - - +
54B SER* 2.5 37.9 + - - -
57B ILE* 3.7 22.5 - - + +
58B VAL* 5.8 1.4 - - - +
532B GLU 3.2 16.7 + - - +
533B MET 3.7 11.9 - - - +
534B PHE 3.4 0.2 - - - -
535B MET* 1.3 78.0 - - - +
537B GLU* 1.3 77.1 + - - +
538B THR* 3.1 16.2 + - - +
539B TYR* 2.9 17.7 + - + +
540B LEU* 3.2 9.5 + - - +
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Residues in contact with GLU 537 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B GLN* 3.7 12.8 - - + +
535B MET 3.2 5.1 + - - +
536B ASP* 1.3 74.8 + - - +
538B THR* 1.3 57.1 + - - +
540B LEU* 3.2 15.9 + - - +
541B MET* 2.9 50.3 + - + +
544B ARG* 2.9 33.8 + - - -
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Residues in contact with THR 538 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B TYR* 3.5 14.8 - - + +
39B LEU* 6.2 1.3 - - + -
42B MET* 3.7 30.3 - - + +
46B VAL* 4.5 11.5 - - + +
50B GLN* 2.8 27.7 + - - +
51B PHE* 5.7 1.8 - - + -
54B SER* 2.5 33.9 + - - +
536B ASP* 3.1 6.9 + - - -
537B GLU* 1.3 78.6 - - - +
539B TYR* 1.3 56.3 + - - +
541B MET* 3.5 5.5 + - - +
542B SER* 3.0 26.7 + - - -
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Residues in contact with TYR 539 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B TYR* 3.2 27.9 + + - +
516B LEU* 4.3 26.5 + - + +
517B LEU* 4.7 2.1 - - - -
520B ARG* 3.2 39.5 + - - +
533B MET* 3.7 17.7 - - + +
534B PHE* 3.6 50.8 - + - -
536B ASP* 2.9 12.2 + - + +
538B THR* 1.3 77.3 - - - +
540B LEU* 1.3 71.9 + - + +
542B SER* 2.7 27.1 + - - -
543B ASN* 3.3 31.0 + - - -
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Residues in contact with LEU 540 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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534B PHE 4.1 15.7 - - - +
535B MET* 3.8 18.4 - - - +
536B ASP 3.2 7.6 + - - +
537B GLU* 3.2 24.2 + - - +
539B TYR* 1.3 83.4 - - + +
541B MET* 1.3 62.4 + - - +
543B ASN* 3.2 14.7 + - - +
544B ARG* 3.4 39.8 + - - +
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Residues in contact with MET 541 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B MET* 4.6 6.5 - - + -
45B LEU 5.0 3.8 - - - +
46B VAL* 4.0 16.4 - - + -
47B PRO* 5.0 2.5 - - + -
50B GLN* 2.8 45.8 - - - +
444B PRO* 3.5 18.5 - - + +
537B GLU* 2.9 31.6 + - + +
538B THR* 3.7 5.2 - - - +
540B LEU* 1.3 77.2 - - - +
542B SER* 1.3 61.5 + - - +
543B ASN 3.1 1.0 + - - -
544B ARG* 3.1 37.9 + - - +
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Residues in contact with SER 542 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B TYR* 4.2 7.7 - - - -
42B MET* 3.5 35.9 - - - -
444B PRO* 4.0 5.0 - - - +
463B ARG* 3.1 32.9 + - - +
516B LEU* 6.0 0.2 - - - +
538B THR 3.0 12.6 + - - -
539B TYR* 2.7 27.2 + - - -
541B MET* 1.3 75.7 - - - +
543B ASN* 1.3 65.6 + - - +
544B ARG 3.5 0.2 - - - -
545B PHE* 3.4 7.6 - - - -
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Residues in contact with ASN 543 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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463B ARG* 3.5 19.1 + - - -
513B ASP* 4.4 4.2 - - - +
520B ARG* 4.6 5.5 - - - +
539B TYR* 3.3 48.6 + - - -
540B LEU* 3.2 10.8 + - - +
541B MET 3.0 1.2 - - - -
542B SER* 1.3 80.7 + - - +
544B ARG* 1.3 59.2 + - - +
545B PHE* 3.6 26.4 + - + -
566B VAL* 5.6 0.2 - - - +
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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