Contacts of the strand formed by residues 38 - 43 (chain W) in PDB entry 3MQT
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 38 (chain W).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30W LYS* 3.5 24.9 - - + -
31W VAL 3.0 12.1 - - - +
32W THR* 3.6 16.4 - - + +
36W GLY 4.0 11.2 - - - -
37W VAL* 1.3 78.4 - - - +
39W GLY* 1.3 58.0 + - - +
40W LEU* 3.9 37.4 - - + +
112W LEU* 4.0 5.6 - - - -
115W LYS* 2.7 48.5 + - - +
373W LEU* 5.7 1.6 - - - +
375W ILE* 4.2 12.3 - - - +
386W PHE* 3.9 20.1 - + - -
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Residues in contact with GLY 39 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29W VAL 3.5 0.9 - - - +
30W LYS* 3.4 5.2 - - - +
31W VAL 2.8 32.5 + - - -
38W TYR* 1.3 74.5 - - - +
40W LEU* 1.3 66.1 + - - +
108W ALA* 3.6 21.2 - - - +
111W ASP* 3.5 7.2 - - - -
112W LEU* 3.6 14.9 - - - +
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Residues in contact with LEU 40 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28W ILE* 4.0 21.8 - - + -
29W VAL 3.3 2.9 - - - +
30W LYS* 4.2 6.1 - - + -
38W TYR* 3.9 28.0 - - + -
39W GLY* 1.3 80.6 - - - +
41W GLY* 1.3 60.2 + - - +
108W ALA* 3.5 10.7 - - - -
111W ASP* 2.8 17.8 + - - +
115W LYS* 5.8 0.4 - - - +
315W ILE* 4.4 7.0 - - + -
369W LEU* 3.7 22.3 - - - +
371W ILE* 4.0 33.9 - - + +
373W LEU* 4.0 30.1 - - + -
386W PHE* 4.1 12.6 - - + -
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Residues in contact with GLY 41 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28W ILE* 3.6 6.9 - - - +
29W VAL 2.8 31.1 + - - +
40W LEU* 1.3 73.8 - - - +
42W GLU* 1.3 62.5 + - - +
104W GLY 3.5 17.9 - - - -
107W MET* 3.9 6.5 - - - -
108W ALA* 3.5 8.2 - - - +
315W ILE* 3.7 12.1 - - - +
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Residues in contact with GLU 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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26W THR* 2.6 30.8 + - - +
27W VAL 3.1 15.5 - - - +
29W VAL 4.3 0.9 - - - +
41W GLY* 1.3 74.6 - - - +
43W ALA* 1.3 59.9 + - - +
104W GLY* 3.3 14.1 - - - -
107W MET* 3.7 7.6 - - - +
284W ASN* 3.2 21.8 - - - +
312W LYS* 3.4 6.4 - - + +
313W THR* 3.1 34.9 + - - +
315W ILE* 3.7 20.1 - - + +
316W THR* 2.3 44.6 + - - +
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Residues in contact with ALA 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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12W PHE* 4.4 13.2 - - + -
26W THR* 4.3 1.7 + - - -
27W VAL* 3.1 34.9 + - + +
29W VAL* 4.1 10.4 - - + +
42W GLU* 1.3 74.5 - - - +
44W ASP* 1.3 67.9 + - - +
45W GLY 4.0 0.2 + - - -
50W MET* 4.6 3.6 - - + -
100W PHE 3.5 24.9 - - - +
101W ALA* 4.4 0.4 - - - -
104W GLY* 3.9 6.9 - - - -
284W ASN* 4.1 2.5 - - - -
312W LYS* 4.2 6.2 + - - -
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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