Contacts of the helix formed by residues 56 - 65 (chain 2) in PDB entry 6Q8W
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 THR 56 (chain 2).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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502 ALA* 3.8 1.3 - - - -
552 THR* 1.3 80.8 + - - +
572 PRO* 1.3 73.7 - - - +
582 THR 3.1 2.1 + - - -
592 GLU* 3.1 24.1 + - - +
602 VAL* 3.3 13.2 + - - +
1973 ASP* 6.1 0.4 - - - -
1983 GLU* 2.7 43.6 + - + +
1993 VAL* 5.1 4.7 - - + -
2153 ASP* 3.7 10.5 - - - +
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Residues in contact with PRO 57 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462 ILE* 3.8 6.3 - - + +
472 GLU* 4.5 18.2 - - + -
502 ALA* 3.6 21.7 - - + -
552 THR 4.1 0.7 - - - +
562 THR* 1.3 86.2 - - - +
582 THR* 1.3 56.1 + - - +
602 VAL* 3.1 5.1 + - + +
612 MET* 2.9 31.9 + - - +
2143 MET* 3.8 29.6 - - + +
2153 ASP* 3.8 16.8 - - - +
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Residues in contact with THR 58 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
562 THR* 3.1 5.9 - - - -
572 PRO* 1.3 77.7 - - - +
592 GLU* 1.3 57.9 + - - +
612 MET* 3.4 3.7 + - + +
622 GLY* 3.0 25.5 + - - -
1983 GLU 4.0 4.7 - - - +
1993 VAL* 3.9 1.1 - - - -
2003 LEU* 3.5 16.4 - - - +
2013 ASP* 3.5 34.3 - - + +
2023 PHE 5.0 0.3 - - - +
2033 ILE* 5.4 1.8 - - + +
2123 GLY 3.9 10.3 - - - +
2133 THR* 2.8 20.4 + - - -
2143 MET* 3.3 7.8 + - - +
2153 ASP* 2.4 28.8 + - - +
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Residues in contact with GLU 59 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1951 LEU* 5.6 3.6 - - - +
1961 ARG* 5.8 2.4 + - - +
242 ARG* 4.0 20.4 + - - +
552 THR* 3.7 20.2 - - + +
562 THR* 3.1 11.5 + - - +
582 THR* 1.3 78.6 - - - +
602 VAL* 1.3 57.8 + - - +
622 GLY* 3.4 1.8 + - - -
632 VAL* 3.0 37.2 + - - +
1883 VAL* 5.8 0.3 - - - +
1923 GLU* 6.0 0.5 - - - +
1983 GLU* 4.1 32.8 - - + +
2003 LEU 4.6 3.3 - - - +
2013 ASP* 2.8 32.9 - - - +
4403 ARG* 4.5 13.8 + - - -
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Residues in contact with VAL 60 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272 ILE* 4.2 17.4 - - + +
312 LEU* 4.9 2.9 - - + -
462 ILE* 3.5 30.3 - - + +
492 ILE* 4.0 20.6 - - + -
502 ALA* 3.7 20.6 - - + +
532 VAL* 4.6 0.4 - - + -
552 THR* 3.6 20.6 - - + -
562 THR 3.4 14.1 - - - +
572 PRO 3.1 6.6 + - - +
592 GLU* 1.3 76.4 - - - +
612 MET* 1.3 57.2 + - - +
632 VAL* 3.3 8.8 + - - +
642 ALA* 2.9 26.9 + - - +
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Residues in contact with MET 61 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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462 ILE* 3.9 12.7 - - + +
572 PRO 2.9 12.1 + - - +
582 THR* 3.9 2.9 - - - +
602 VAL* 1.3 73.1 - - - +
622 GLY* 1.3 59.8 + - - +
642 ALA 4.3 0.4 - - - +
652 SER* 2.3 42.4 + - - +
722 PHE* 5.0 6.3 - - + -
2033 ILE* 3.5 31.6 - - + -
2123 GLY* 5.5 0.4 - - - -
2133 THR* 3.8 21.8 - - - +
2143 MET* 2.9 55.6 - - + +
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Residues in contact with GLY 62 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1961 ARG* 3.3 25.1 + - - -
582 THR 3.0 15.0 + - - -
592 GLU* 3.4 3.8 + - - -
612 MET* 1.3 76.9 - - - +
632 VAL* 1.3 63.7 + - - +
652 SER* 3.7 2.5 - - - -
662 PHE* 3.6 5.5 + - - +
2013 ASP* 5.3 3.4 - - - -
2023 PHE 3.2 26.2 + - - -
2033 ILE* 3.5 8.2 - - - +
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Residues in contact with VAL 63 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1941 GLY 3.2 27.6 - - - +
1951 LEU* 4.1 16.2 - - - +
1961 ARG* 4.3 8.5 - - + +
242 ARG* 5.1 3.1 - - - +
272 ILE* 4.1 22.7 - - + -
282 MET* 5.0 9.0 - - + -
312 LEU* 4.4 4.7 - - + -
592 GLU* 3.0 23.1 + - - +
602 VAL* 3.4 10.5 - - - +
612 MET 3.2 0.2 - - - -
622 GLY* 1.3 76.4 - - - +
642 ALA* 1.3 65.4 + - - +
662 PHE* 3.0 20.5 + - - +
672 TYR* 3.5 22.4 - - + +
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Residues in contact with ALA 64 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312 LEU* 3.8 37.0 - - + -
412 ILE* 4.7 1.6 - - + -
462 ILE* 4.4 6.1 - - + -
602 VAL 2.9 19.7 + - - +
612 MET 3.2 1.8 + - - +
632 VAL* 1.3 73.8 - - - +
652 SER* 1.3 57.9 + - - +
662 PHE 3.1 4.7 + - - -
672 TYR 3.7 3.8 + - - +
702 TYR* 3.4 24.1 - - + +
722 PHE* 3.4 26.5 - - + -
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Residues in contact with SER 65 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612 MET* 2.3 31.1 + - - +
622 GLY 3.6 0.2 + - - -
642 ALA* 1.3 74.2 - - - +
662 PHE* 1.3 60.7 + - - +
672 TYR 3.4 4.6 + - - +
722 PHE* 3.4 23.1 - - - -
2033 ILE* 2.6 48.5 + - - +
2043 GLU* 3.5 17.8 - - - +
2053 ARG 4.5 0.7 + - - -
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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