Contacts of the strand formed by residues 66 - 72 (chain Q) in PDB entry 6D84
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 TYR 66 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7Q LEU* 3.5 0.2 - - - -
8Q PHE* 2.6 75.7 + + + +
10Q ARG* 3.3 27.8 + - - -
39Q ILE* 3.9 20.6 - - + -
40Q LEU* 3.6 19.7 - - + -
44Q HIS* 4.7 7.6 + - - -
59Q TYR* 5.8 1.6 - + + -
60Q LYS 4.1 5.6 - - - +
61Q ARG* 3.5 36.6 + - + -
63Q ALA 3.2 22.0 - - - -
64Q SER* 3.2 13.7 + - - -
65Q LEU* 1.3 75.0 - - - +
67Q PHE* 1.3 68.9 + - - +
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Residues in contact with PHE 67 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224O ALA* 5.9 5.6 - - + -
6Q LEU 3.6 3.1 - - - +
7Q LEU* 3.6 28.0 - - + -
8Q PHE* 4.9 0.2 - - - -
59Q TYR* 3.2 6.6 - - - +
60Q LYS 3.1 33.1 + - - +
62Q TYR* 3.5 27.4 - + + -
65Q LEU* 3.6 37.9 - - + -
66Q TYR* 1.3 84.5 - - - +
68Q CYS* 1.3 62.2 - - - +
69Q CYS* 6.4 0.2 - - - -
84Q VAL* 3.7 26.5 - - + -
87Q TYR* 5.9 4.0 - + - -
88Q VAL* 3.6 24.9 - - + -
91Q LEU* 5.2 11.7 - - + -
103Q ILE* 5.3 4.0 - - + -
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Residues in contact with CYS 68 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4Q PHE* 3.8 13.4 - - - -
5Q ILE* 4.1 0.7 - - - +
6Q LEU* 2.6 53.0 + - + +
7Q LEU* 5.4 0.2 - - - +
8Q PHE* 4.1 7.4 - - + -
35Q ILE* 3.7 26.7 - - - -
39Q ILE* 3.7 11.4 - - + -
57Q LEU* 3.7 23.3 - - - -
58Q VAL 3.8 4.7 - - - -
59Q TYR* 4.2 0.2 - - - +
67Q PHE* 1.3 76.6 - - - +
69Q CYS* 1.3 74.6 + - - +
84Q VAL* 6.1 0.6 - - - +
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Residues in contact with CYS 69 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2Q ILE* 4.3 10.3 - - + -
4Q PHE* 3.5 15.9 - - - +
5Q ILE* 3.6 32.1 - - - -
57Q LEU* 3.3 9.4 - - - +
58Q VAL* 2.8 31.7 + - - +
67Q PHE* 6.4 0.4 - - - -
68Q CYS* 1.3 80.4 - - - +
70Q ALA* 1.3 63.5 + - - +
80Q THR* 4.3 17.7 - - + -
83Q ILE* 6.2 1.6 - - - -
84Q VAL* 4.3 22.0 - - + -
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Residues in contact with ALA 70 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2Q ILE* 3.3 3.7 - - - -
3Q HIS* 3.1 27.7 + - - -
4Q PHE* 3.6 34.1 + - + -
55Q LEU* 3.9 26.9 - - + -
57Q LEU* 4.1 9.2 - - + +
58Q VAL* 4.2 6.1 - - - +
69Q CYS* 1.3 78.9 - - - +
71Q ILE* 1.3 62.3 + - - +
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Residues in contact with ILE 71 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248K ARG* 5.3 10.5 - - - +
251K ARG* 5.6 1.8 - - - +
1Q MET* 3.4 22.0 - - - +
2Q ILE* 3.7 24.8 - - + +
3Q HIS* 4.3 0.9 - - - -
55Q LEU* 3.8 10.6 - - - +
56Q LYS 4.0 13.6 + - - +
58Q VAL* 4.6 1.5 - - + +
69Q CYS 4.4 0.4 - - - -
70Q ALA* 1.3 76.2 - - - +
72Q GLU* 1.3 71.4 + - - +
73Q ASN 3.6 1.4 + - - -
75Q ASP* 3.6 21.5 - - + +
76Q ASN 4.2 4.9 - - - +
77Q GLU* 3.4 38.4 - - - +
79Q LEU* 6.3 1.6 - - + -
80Q THR* 3.6 26.7 - - + +
83Q ILE* 5.8 2.9 - - + -
121Q GLY 5.5 0.7 - - - +
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Residues in contact with GLU 72 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203K GLU* 4.4 4.9 - - - +
1Q MET* 3.0 39.4 + - - +
3Q HIS* 3.8 17.3 - - + +
55Q LEU* 4.8 0.9 - - - -
71Q ILE* 1.3 85.3 - - - +
73Q ASN* 1.3 67.0 + - - +
74Q GLN* 2.8 49.2 + - + +
75Q ASP* 3.4 14.7 + - - +
77Q GLU* 4.1 0.3 - - - +
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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