Contacts of the helix formed by residues 66 - 74 (chain A) in PDB entry 1Q8G
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 66 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64A VAL* 3.4 6.3 - - - +
65A ASP* 1.3 106.1 - - + +
67A PRO* 1.3 68.5 - - - +
68A TYR 3.4 0.4 - - - -
69A ALA* 3.3 28.3 + - + +
70A THR* 3.6 6.6 + - - -
146A ARG* 4.8 14.9 + - - +
162A GLU* 2.9 17.8 - - - +
164A LYS* 4.2 25.8 + - - +
165A PRO* 4.7 1.1 - - - +
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Residues in contact with PRO 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A LYS* 3.7 9.0 - - + -
55A ILE* 3.7 25.7 - - + +
56A LEU 3.9 7.4 - - - +
59A ASP* 5.7 0.9 - - + -
60A VAL* 3.2 35.7 - - + +
64A VAL* 3.9 6.0 - - + -
65A ASP 4.2 0.2 - - - +
66A ASP* 1.3 79.8 - - - +
68A TYR* 1.3 51.9 + - - +
69A ALA 2.9 4.9 - - - -
70A THR* 2.7 33.6 + - - +
71A PHE* 3.2 9.2 + - - +
85A TYR* 3.3 12.3 - - + +
162A GLU* 3.1 27.6 - - - +
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Residues in contact with TYR 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A ASP 3.4 0.2 - - - -
67A PRO* 1.3 79.1 - - - +
69A ALA* 1.3 59.6 + - - +
71A PHE* 3.5 22.5 - + + +
72A VAL* 3.9 9.4 + - - +
85A TYR* 3.1 35.7 + + - +
102A ILE* 5.4 6.7 - - + +
135A LEU* 5.5 0.2 - - - +
143A VAL* 3.1 22.9 + - + -
144A LYS* 4.5 5.9 - - + +
145A ASP 3.0 40.7 + - - -
146A ARG* 3.4 43.3 - - - +
148A THR* 4.2 4.5 - - - +
149A LEU* 3.8 30.6 + - + +
161A LEU* 4.5 4.3 - - + -
162A GLU* 3.3 13.2 + - - +
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Residues in contact with ALA 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A ASP* 3.3 23.6 + - + +
67A PRO 2.9 0.6 - - - -
68A TYR* 1.3 78.1 - - - +
70A THR* 1.3 64.2 + - - +
71A PHE 3.1 0.4 - - - -
72A VAL* 3.9 3.0 + - - +
73A LYS* 3.0 30.3 + - + +
144A LYS* 5.8 7.4 - - - -
146A ARG* 4.7 5.3 - - - +
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Residues in contact with THR 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A ILE* 3.4 21.2 - - + +
64A VAL* 4.2 12.8 - - + +
66A ASP 3.6 9.5 + - - -
67A PRO* 2.7 22.1 + - - +
69A ALA* 1.3 71.2 - - - +
71A PHE* 1.3 66.7 + - - +
73A LYS* 3.1 15.8 - - + +
74A MET* 2.9 38.4 - - + +
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Residues in contact with PHE 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A ALA* 3.3 25.4 - - + -
37A LEU* 3.0 27.8 - - + -
55A ILE* 3.2 9.3 - - + +
67A PRO 3.2 5.0 + - - +
68A TYR* 3.5 22.4 - + + +
69A ALA 3.1 0.6 - - - -
70A THR* 1.3 80.4 - - - +
72A VAL* 1.3 64.3 + - + +
73A LYS 2.7 10.7 + - - -
74A MET* 2.8 12.3 + - - +
75A LEU* 3.0 47.0 + - + +
83A ALA* 3.2 19.3 - - + -
85A TYR* 4.3 8.7 - + + -
102A ILE* 3.0 41.5 - - + -
104A TRP* 5.2 0.2 - - + -
143A VAL* 3.7 10.8 - - + -
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Residues in contact with VAL 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A TYR* 3.9 9.2 + - + +
69A ALA 3.9 4.1 + - - +
71A PHE* 1.3 80.4 - - + +
73A LYS* 1.3 62.1 + - - +
75A LEU* 3.0 21.2 + - + +
104A TRP* 6.3 0.2 - - + -
140A TYR* 3.1 51.4 + - + +
143A VAL* 3.2 46.0 - - + +
144A LYS* 3.4 27.4 - - + -
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Residues in contact with LYS 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A ALA* 3.0 27.9 + - + +
70A THR* 3.1 14.0 - - + +
71A PHE 2.7 4.8 + - - -
72A VAL* 1.3 76.1 - - - +
74A MET* 1.3 59.8 + - + +
75A LEU 3.5 1.2 + - - -
76A PRO* 4.3 3.3 - - - +
140A TYR* 4.1 9.7 + - - -
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Residues in contact with MET 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A LEU* 3.4 31.5 - - + +
52A GLY 5.1 1.6 - - - +
53A LYS* 4.1 33.1 - - + +
54A GLU 4.1 4.3 - - - +
55A ILE* 3.7 21.3 - - + -
70A THR* 2.9 36.1 - - + +
71A PHE 2.8 7.9 + - - +
73A LYS* 1.3 73.1 - - + +
75A LEU* 1.3 58.6 + - - +
76A PRO* 3.1 12.6 - - - +
81A ARG* 3.5 21.1 + - - +
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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