Contacts of the strand formed by residues 70 - 75 (chain Q) in PDB entry 2WUB
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 70 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18L ARG* 4.7 1.7 + - - -
20L THR* 4.4 1.9 - - - +
65L SER* 4.3 11.9 + - - +
72L THR* 3.8 29.4 + - + +
74L THR* 4.6 8.1 + - - -
23Q CYS 3.5 4.3 - - - -
24Q ARG* 3.5 34.7 + - - +
66Q GLY* 3.4 17.5 - - - -
67Q SER 3.4 9.6 + - - +
68Q GLY 3.8 0.6 - - - -
69Q THR* 1.3 100.7 + - - +
71Q PHE* 1.3 63.0 + - - +
72Q THR* 5.2 3.1 - - + +
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Residues in contact with PHE 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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4Q MET* 5.2 0.9 - - + -
22Q THR* 3.2 1.7 - - - -
23Q CYS* 2.7 46.0 + - + +
25Q ALA* 4.7 2.7 - - + -
29Q VAL* 3.4 20.2 - - + -
30Q SER 3.1 27.1 - - - -
31Q THR* 3.9 8.7 - - - -
33Q VAL* 3.4 42.8 - - + -
35Q TRP* 4.3 14.1 - - + +
51Q ALA* 4.4 6.1 - - + -
65Q SER 3.4 12.1 - - - +
66Q GLY* 3.5 17.7 - - - -
67Q SER* 3.5 11.2 - - - -
68Q GLY 3.7 12.3 - - - -
69Q THR 4.0 2.9 - - - -
70Q ASP* 1.3 81.2 - - - +
72Q THR* 1.3 72.0 + - - +
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Residues in contact with THR 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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67L SER 5.2 5.8 + - - +
70L ASP* 4.5 16.9 + - + +
20Q THR* 4.1 16.6 - - - +
21Q ILE 3.0 12.1 - - - -
22Q THR* 3.9 17.9 - - + -
35Q TRP* 3.9 6.8 + - - -
64Q GLY* 3.5 2.1 - - - -
65Q SER* 3.0 41.7 + - - +
66Q GLY* 6.1 0.4 - - - -
70Q ASP* 5.2 2.0 - - + -
71Q PHE* 1.3 85.3 - - - +
73Q LEU* 1.3 59.9 + - - +
74Q THR* 4.1 6.6 + - - -
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Residues in contact with LEU 73 (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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19Q VAL 4.2 0.3 - - - +
20Q THR* 3.4 3.7 - - - +
21Q ILE* 2.8 39.4 + - + +
35Q TRP* 3.7 44.6 - - + -
47Q LEU* 4.2 6.1 - - + -
48Q ILE* 4.1 20.0 - - + -
62Q PHE* 4.4 12.1 - - + -
63Q SER 3.4 25.1 - - - +
64Q GLY* 4.3 1.3 - - - -
72Q THR* 1.3 72.6 - - - +
74Q THR* 1.3 67.8 + - - +
75Q ILE* 5.0 5.1 - - + +
86Q TYR* 3.8 32.3 - - + -
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Residues in contact with THR 74 (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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18Q ARG* 3.9 25.8 + - + +
19Q VAL 3.5 12.1 - - - +
20Q THR* 3.8 19.5 + - - +
61Q ARG 3.3 3.2 - - - +
62Q PHE* 3.6 1.6 - - - -
63Q SER* 2.7 50.1 + - - +
65Q SER* 5.6 0.3 + - - -
72Q THR* 4.1 6.8 + - - -
73Q LEU* 1.3 76.4 - - - +
75Q ILE* 1.3 76.7 + - - +
76Q SER* 4.0 3.8 - - - +
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Residues in contact with ILE 75 (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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17Q ASP 3.6 1.6 - - - +
18Q ARG* 3.2 2.4 - - - +
19Q VAL* 3.0 38.5 + - + +
21Q ILE* 5.9 3.4 - - + -
61Q ARG* 3.3 21.5 - - + +
62Q PHE* 3.4 32.3 - - + -
73Q LEU* 5.0 6.7 - - + +
74Q THR* 1.3 85.3 - - - +
76Q SER* 1.3 69.5 + - - +
77Q SER 4.0 17.5 - - - +
78Q LEU* 4.1 24.7 - - + -
82Q ASP* 4.2 4.3 - - + +
86Q TYR* 4.0 19.1 - - + +
104Q VAL* 5.8 2.7 - - + -
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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