Contacts of the strand formed by residues 41 - 47 (chain W) in PDB entry 3TDD
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 VAL 41 (chain W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36W HIS* 3.1 3.8 - - - -
38W TYR* 2.8 42.6 + - + +
39W GLY 3.3 0.2 - - - -
40W HIS* 1.3 84.1 - - - +
42W PHE* 1.3 64.8 + - - +
74W ILE* 3.2 33.4 - - + +
75W GLU 3.7 2.0 - - - +
76W PRO* 3.7 27.8 - - + -
79W PHE* 3.8 33.7 - - + -
101W VAL* 4.1 15.5 - - + -
102W ALA 4.0 4.0 - - - +
103W GLY* 4.9 0.7 - - - -
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Residues in contact with PHE 42 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219V VAL* 4.3 0.9 - - + -
221V ILE* 3.7 26.0 - - + -
14W ILE* 4.3 13.2 - - + -
34W ILE* 4.1 10.1 - - + -
35W PHE 3.3 6.7 - - - +
36W HIS* 3.5 26.2 - + + -
40W HIS 3.4 23.6 - - - -
41W VAL* 1.3 76.3 - - - +
43W LEU* 1.3 61.4 + - - +
44W GLY 4.3 0.2 - - - -
100W VAL 3.8 0.2 - - - +
101W VAL* 3.4 8.1 - - - +
102W ALA* 2.8 41.9 + - + +
176W TYR* 3.6 34.3 - + - -
178W ILE* 3.5 27.6 - - + -
184W VAL* 3.7 22.2 - - + -
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Residues in contact with LEU 43 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14W ILE* 4.5 2.0 - - - -
34W ILE* 3.4 2.1 - - - -
35W PHE* 2.7 45.6 + - + +
38W TYR* 3.7 28.9 - - + +
41W VAL 4.2 0.2 + - - -
42W PHE* 1.3 73.9 - - - +
44W GLY* 1.3 64.8 + - - +
45W ILE* 3.7 24.0 - - + -
59W PHE* 3.6 33.4 - - + -
79W PHE* 4.1 9.6 - - + -
83W VAL* 4.7 2.7 - - + -
99W PRO* 4.2 11.7 - - + -
100W VAL 3.3 20.4 - - - +
101W VAL* 3.8 17.0 - - + -
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Residues in contact with GLY 44 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3W VAL* 4.3 11.9 - - - -
14W ILE* 3.8 14.8 - - - +
33W LYS 3.0 11.4 - - - -
34W ILE* 4.1 5.6 - - - -
43W LEU* 1.3 73.0 - - - +
45W ILE* 1.3 67.8 + - - +
46W THR 4.3 0.2 - - - -
98W GLY 4.8 0.2 - - - -
99W PRO* 3.4 0.5 - - - +
100W VAL* 2.8 35.7 + - - -
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Residues in contact with ILE 45 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3W VAL* 4.2 1.4 - - - +
33W LYS* 2.8 27.7 + - - +
35W PHE* 3.9 14.4 - - + -
43W LEU* 3.7 30.5 - - + -
44W GLY* 1.3 80.9 - - - +
46W THR* 1.3 60.7 - - - +
52W VAL* 3.2 49.7 - - + +
55W LEU* 4.0 17.3 - - + -
56W ASN 4.2 3.4 - - - +
59W PHE* 5.1 0.4 - - + -
97W VAL* 3.5 36.8 - - + -
98W GLY 4.1 3.1 - - - +
99W PRO* 4.6 6.1 - - + -
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Residues in contact with THR 46 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1W GLY 4.0 4.7 - - - +
2W ILE* 3.6 8.5 - - - +
3W VAL* 3.5 44.9 - - + +
33W LYS* 4.8 6.3 - - + +
45W ILE* 1.3 75.5 - - - +
47W GLY* 1.3 60.4 + - - +
52W VAL* 4.0 2.9 - - - +
97W VAL* 3.1 9.5 - - - +
98W GLY* 2.9 27.8 + - - -
127W SER* 2.5 32.0 + - - +
128W GLY* 3.4 15.8 + - - -
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Residues in contact with GLY 47 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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-6W PRO 4.4 3.4 - - - -
-5W SER* 4.7 18.8 - - - -
-2W ASN* 3.9 13.1 - - - +
-1W GLY* 4.6 12.4 + - - +
1W GLY 5.3 0.4 + - - -
46W THR* 1.3 80.0 + - - +
48W LEU* 1.3 66.0 + - - -
49W ALA* 3.1 5.0 + - - -
52W VAL* 4.3 2.8 - - - +
96W PHE 3.3 8.5 - - - -
97W VAL* 4.3 1.1 - - - -
98W GLY 4.9 0.2 - - - -
128W GLY* 5.6 0.4 - - - -
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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