Contacts of the helix formed by residues 69 - 76 (chain K) in PDB entry 6D6Q
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 69 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68K PRO* 1.3 73.4 - - - +
70K THR* 1.3 82.3 + - - +
71K ASN* 3.4 19.1 + - + +
72K VAL* 3.0 19.6 + - + +
73K LEU* 3.3 7.6 + - - +
94K VAL* 4.2 7.4 - - - -
146K ASN* 4.0 15.1 - - - +
149K ILE* 3.1 33.1 - - - +
173K PHE* 4.6 12.6 - - + -
174K ILE 3.2 15.7 + - - +
175K THR* 4.7 8.3 - - + -
176K ASN 5.6 0.7 - - - +
180K ASN* 5.0 9.9 + - - -
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Residues in contact with THR 70 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69K ASP* 1.3 84.0 + - - +
71K ASN* 1.3 70.1 + - - +
73K LEU* 2.7 17.2 + - - +
74K LEU* 2.9 33.6 + - + -
94K VAL* 3.9 24.2 - - - +
97K GLU* 2.2 43.9 + - + +
98K VAL* 4.6 7.4 - - + +
101K ARG* 3.9 11.9 - - - +
149K ILE* 5.0 1.6 - - - +
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Residues in contact with ASN 71 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69K ASP* 3.4 13.1 + - + +
70K THR* 1.3 81.3 - - - +
72K VAL* 1.3 56.4 + - - +
74K LEU* 3.2 16.5 + - - +
75K HIS* 2.9 43.3 + - + +
101K ARG* 5.6 1.0 + - - -
176K ASN* 3.9 29.4 + - + +
177K ASP* 5.1 5.5 + - - -
180K ASN* 4.8 12.5 - - - +
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Residues in contact with VAL 72 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68K PRO* 3.8 18.4 - - + -
69K ASP* 3.0 19.9 + - + +
70K THR 3.0 0.8 - - - -
71K ASN* 1.3 77.4 - - - +
73K LEU* 1.3 56.4 + - - +
76K GLN* 2.7 44.4 + - + +
79K VAL* 6.4 0.4 - - + -
80K LEU* 4.3 15.0 - - + -
174K ILE* 4.2 5.2 - - + -
175K THR* 3.6 22.7 - - - +
176K ASN* 4.0 7.0 - - + +
194K CYS* 3.3 36.3 - - - -
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Residues in contact with LEU 73 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68K PRO* 3.3 33.9 - - + -
69K ASP 3.5 9.9 - - - +
70K THR 2.7 13.5 + - - +
72K VAL* 1.3 73.0 - - - +
74K LEU* 1.3 59.4 + - - +
75K HIS 3.5 0.3 + - - -
77K ILE* 3.6 16.9 - - + +
80K LEU* 4.1 15.5 - - + -
90K VAL* 5.9 8.5 - - + -
94K VAL* 3.9 19.7 - - + -
98K VAL* 3.7 18.8 - - + -
105K VAL* 3.4 18.3 - - + +
109K ILE* 3.3 41.3 - - + -
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Residues in contact with LEU 74 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70K THR* 2.9 35.5 + - + +
71K ASN* 3.6 18.6 - - - +
73K LEU* 1.3 78.6 - - - +
75K HIS* 1.3 80.1 + - + +
77K ILE* 5.1 2.0 - - - +
98K VAL* 4.4 25.1 - - + -
101K ARG* 4.0 31.0 - - + +
102K SER* 4.6 13.9 - - - -
105K VAL* 4.6 14.6 - - + +
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Residues in contact with HIS 75 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71K ASN* 2.9 33.0 + - + +
74K LEU* 1.3 96.8 + - + +
76K GLN* 1.3 70.4 + - + +
77K ILE* 3.8 2.2 - - - -
176K ASN* 4.5 16.6 - - - +
211K LEU* 4.3 13.7 - - - +
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Residues in contact with GLN 76 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72K VAL* 2.7 27.2 + - + +
75K HIS* 1.3 84.5 - - + +
77K ILE* 1.3 64.2 + - - +
78K ASP* 3.0 3.6 - - - +
79K VAL* 2.8 45.9 + - + +
80K LEU* 3.3 7.9 + - - +
176K ASN* 4.6 14.9 + - - +
194K CYS* 2.8 47.6 - - - +
195K GLU* 5.1 1.4 - - - +
211K LEU* 4.0 21.3 - - + +
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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