Contacts of the strand formed by residues 24 - 33 (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 GLU 24 (chain W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15W VAL 3.9 0.7 - - - +
16W ASN* 3.8 0.8 + - - -
17W VAL* 3.0 49.4 + - + +
23W SER* 1.3 72.5 - - - +
25W ASN* 1.3 64.8 + - - +
341W TRP* 4.8 4.3 + - - -
343W GLY* 3.5 13.4 - - - -
344W THR* 3.0 29.2 + - - +
345W LEU* 3.2 37.7 + - + +
346W THR* 4.2 2.9 + - - -
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Residues in contact with ASN 25 (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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59J GLU* 3.2 38.3 + - - +
15W VAL 3.2 12.8 - - - +
16W ASN* 3.2 26.9 + - - +
23W SER* 4.2 6.7 + - - +
24W GLU* 1.3 84.1 - - - +
26W THR* 1.3 64.1 + - - +
45W GLY 5.0 0.9 - - - +
47W PRO* 3.7 20.1 - - + +
312W LYS* 3.0 23.4 + - - +
345W LEU* 3.7 8.6 - - - +
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Residues in contact with THR 26 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15W VAL* 3.1 49.0 + - + +
25W ASN* 1.3 77.0 - - - +
27W VAL* 1.3 73.6 + - - +
28W ILE* 4.0 16.8 - - + -
42W GLU* 2.6 35.5 + - - +
43W ALA 4.3 0.3 + - - -
47W PRO* 3.6 7.2 - - - +
312W LYS* 3.7 16.7 + - - +
313W THR* 4.1 10.1 - - - +
345W LEU* 4.2 6.1 - - + -
349W LEU* 4.2 5.6 - - + -
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Residues in contact with VAL 27 (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* 3.8 39.3 - - + -
13W ILE 3.5 8.5 - - - +
14W PRO* 4.8 1.8 - - + -
26W THR* 1.3 79.4 + - - +
28W ILE* 1.3 65.3 + - - +
29W VAL* 3.5 0.6 + - + -
42W GLU* 3.1 6.6 - - - -
43W ALA* 3.1 44.1 + - + +
45W GLY 4.1 6.7 - - - +
47W PRO* 3.4 36.6 - - + +
50W MET* 3.9 15.0 - - + -
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Residues in contact with ILE 28 (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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11W GLU 3.3 2.6 - - - +
12W PHE* 3.5 1.9 - - - -
13W ILE* 2.7 56.9 + - + +
15W VAL* 3.7 25.8 - - + -
26W THR* 4.1 7.4 - - + -
27W VAL* 1.3 73.1 - - - +
29W VAL* 1.3 63.2 + - - +
40W LEU* 4.0 25.8 - - + -
41W GLY 3.6 9.2 - - - +
42W GLU* 4.6 0.9 - - - +
315W ILE* 4.0 20.6 - - + -
349W LEU* 4.3 10.8 - - + -
373W LEU* 4.6 6.3 - - + -
378W VAL* 4.2 28.0 - - + -
386W PHE* 5.1 2.9 - - + -
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Residues in contact with VAL 29 (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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10W VAL* 4.2 2.9 - - + -
11W GLU 3.4 3.8 - - - +
12W PHE* 3.8 41.1 - - + -
27W VAL* 4.2 1.3 - - + +
28W ILE* 1.3 75.5 - - - +
30W LYS* 1.3 61.1 + - - +
31W VAL* 4.2 12.1 - - + -
39W GLY 3.5 1.2 - - - +
40W LEU* 3.3 8.0 - - - +
41W GLY 2.8 36.3 + - - +
43W ALA* 4.1 12.8 - - + +
104W GLY* 3.7 37.0 - - - +
105W ILE* 3.9 15.0 - - + -
108W ALA* 3.8 1.1 - - + +
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Residues in contact with LYS 30 (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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9W SER* 3.7 1.7 + - - +
10W VAL* 3.5 2.1 - - - -
11W GLU* 3.0 49.3 + - + +
13W ILE* 4.2 18.2 - - + -
28W ILE* 4.0 0.4 + - + -
29W VAL* 1.3 74.4 - - - +
31W VAL* 1.3 62.3 + - - +
32W THR* 3.9 12.2 + - - +
38W TYR* 3.5 47.4 - - + -
39W GLY 3.4 2.9 - - - -
40W LEU* 4.2 8.5 - - + -
386W PHE* 3.7 47.0 + - + -
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Residues in contact with VAL 31 (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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7W ILE* 3.5 34.5 - - + -
9W SER 3.3 5.2 - - - +
10W VAL* 4.1 16.8 - - + -
29W VAL* 4.2 10.8 - - + -
30W LYS* 1.3 76.3 - - - +
32W THR* 1.3 59.7 + - - +
38W TYR* 3.0 4.1 - - - -
39W GLY 2.8 35.0 + - - +
70W VAL* 5.6 0.4 - - + -
105W ILE* 4.5 5.8 - - + -
108W ALA* 3.6 26.9 - - + -
109W LEU* 3.9 25.1 - - + -
112W LEU* 3.8 10.0 - - + +
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Residues in contact with THR 32 (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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7W ILE* 3.7 3.3 - - - -
8W VAL* 2.8 34.9 + - + +
9W SER* 3.0 29.1 + - - +
30W LYS* 3.9 17.0 + - - +
31W VAL* 1.3 75.5 - - - +
33W ASP* 1.3 64.2 + - - +
36W GLY* 3.7 18.2 - - - +
37W VAL 3.3 12.1 - - - +
38W TYR* 3.6 10.9 - - + +
112W LEU* 4.7 1.6 - - - -
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Residues in contact with ASP 33 (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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5W ALA* 4.1 7.2 - - - +
6W ASN 3.2 17.5 - - - +
7W ILE* 4.1 0.7 - - - +
8W VAL* 3.6 8.8 - - - +
31W VAL 4.3 0.2 - - - -
32W THR* 1.3 81.3 - - - +
34W GLU* 1.3 60.3 + - - +
35W ASN* 2.8 18.9 + - - -
36W GLY* 3.0 21.5 + - - -
37W VAL* 2.8 32.2 + - - +
112W LEU* 4.3 8.8 - - + +
116W GLN* 2.5 41.9 + - - +
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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