Contacts of the helix formed by residues 41 - 51 (chain A) in PDB entry 2QQ6
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 PRO 41 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39A SER 3.4 7.4 - - - +
40A ALA* 1.4 94.9 - - + +
42A ALA* 1.3 63.6 + - - +
43A ALA* 4.2 4.5 - - + +
44A GLY* 3.2 21.1 + - - +
45A ILE* 3.4 9.4 + - - +
47B HIS* 4.1 5.2 - - + +
48B ILE* 3.9 35.2 - - + +
51B ASN* 3.5 35.7 - - + +
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Residues in contact with ALA 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A ALA* 4.4 9.6 - - + -
19A PRO* 4.5 15.9 - - + +
21A VAL* 3.8 25.0 - - + +
39A SER 4.8 1.1 - - - -
40A ALA 3.8 1.8 + - - -
41A PRO* 1.3 69.3 - - - +
43A ALA* 1.3 67.0 + - - +
44A GLY 3.1 0.2 + - - -
45A ILE* 3.2 8.0 + - - +
46A HIS* 3.0 22.9 + - - +
389A HIS* 4.7 14.8 - - + +
394A VAL* 3.7 11.0 - - + +
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Residues in contact with ALA 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A PRO* 4.8 4.3 - - + -
42A ALA* 1.3 77.6 - - - +
44A GLY* 1.3 63.0 + - - +
46A HIS* 3.1 16.0 - - - +
47A HIS* 3.1 17.9 + - - +
393A GLY* 4.4 13.5 - - - +
394A VAL* 3.6 13.8 - - + +
47B HIS* 2.9 42.6 - - + +
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Residues in contact with GLY 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A PRO* 3.2 21.2 + - - +
42A ALA 3.0 1.2 - - - -
43A ALA* 1.3 78.6 - - - +
45A ILE* 1.3 66.1 + - - +
46A HIS 3.1 0.3 + - - -
47A HIS* 3.2 2.4 + - - +
48A ILE* 3.0 31.7 + - - +
44B GLY* 4.4 13.3 - - - -
47B HIS* 4.0 9.1 - - - +
48B ILE* 5.1 2.7 - - - -
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Residues in contact with ILE 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A PRO 5.8 1.1 - - - +
21A VAL* 4.3 19.5 - - + +
36A CYS* 3.8 28.5 - - + +
37A TYR 3.6 24.0 - - - +
38A PRO* 5.1 1.1 - - + -
39A SER* 3.7 25.1 - - - +
40A ALA* 6.2 0.4 - - + -
41A PRO 3.4 10.6 + - - +
42A ALA* 3.2 6.8 + - - +
44A GLY* 1.3 72.7 - - - +
46A HIS* 1.3 54.0 + - - +
48A ILE* 2.9 14.0 + - + +
49A VAL* 2.7 55.3 + - + +
84A ALA* 5.6 5.8 - - + +
87A THR* 4.7 4.0 - - + -
88A ALA* 3.9 11.4 - - + +
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Residues in contact with HIS 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A THR* 2.6 35.9 + - - +
21A VAL* 4.9 4.4 - - + +
42A ALA 3.0 12.0 + - - +
43A ALA 3.1 10.3 - - - +
45A ILE* 1.3 78.5 - - - +
47A HIS* 1.3 97.1 + + - +
49A VAL* 3.0 5.8 + - - +
50A MSE 2.9 48.5 + - + +
393A GLY 4.9 3.6 - - - -
394A VAL* 3.6 23.1 - - + +
395A PRO* 4.3 22.0 - - + +
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Residues in contact with HIS 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A ALA 3.1 22.8 + - - +
44A GLY 4.0 2.9 - - - +
46A HIS* 1.3 104.6 + + - +
48A ILE* 1.3 56.7 + - - +
50A MSE 4.5 4.9 - - + +
51A ASN* 2.9 28.9 + - - +
393A GLY 5.0 6.7 - - - -
41B PRO* 3.2 12.6 - - + +
43B ALA* 3.2 32.0 - - + +
44B GLY* 4.2 4.5 - - - +
47B HIS* 3.7 22.7 + + - -
393B GLY 3.9 19.1 + - - -
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Residues in contact with ILE 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A GLY* 3.0 22.6 + - - +
45A ILE* 2.9 11.0 + - - +
47A HIS* 1.3 77.3 - - - +
49A VAL* 1.3 65.6 + - - +
51A ASN* 3.3 14.8 + - - +
52A MSE 3.4 13.6 + - - +
75A ASN* 5.6 2.9 - - - +
84A ALA* 3.9 32.5 - - + -
85A VAL* 4.1 24.5 - - + +
88A ALA* 3.4 20.2 - - + -
89A LEU* 6.2 1.8 - - + -
40B ALA* 5.2 2.2 - - + -
41B PRO* 4.1 19.1 - - + -
44B GLY* 5.0 6.7 - - - -
48B ILE* 5.7 3.4 - - + -
84B ALA* 5.2 5.4 - - + -
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Residues in contact with VAL 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A VAL* 4.4 10.4 - - + +
11A THR* 3.9 13.9 - - + -
21A VAL* 5.6 0.2 - - + -
23A VAL* 3.6 39.7 - - + -
36A CYS* 4.5 0.2 - - - -
45A ILE* 2.7 28.5 + - + +
46A HIS* 3.5 6.1 - - - +
48A ILE* 1.3 74.2 - - - +
50A MSE 1.3 61.5 + - - +
52A MSE 2.9 25.1 + - - +
53A GLU 3.8 2.1 + - - -
88A ALA* 3.6 30.3 - - + +
92A ILE* 3.7 16.6 - - + +
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Residues in contact with MSE 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A VAL* 3.0 36.8 - - + +
10A GLU* 4.0 10.1 - - - -
11A THR* 4.3 10.8 - - + +
46A HIS* 2.9 45.3 + - + +
47A HIS* 4.5 5.8 - - + +
49A VAL* 1.3 73.9 - - - +
51A ASN* 1.3 56.5 - - - +
52A MSE 3.0 5.4 + - - -
53A GLU* 3.0 51.1 + - + +
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Residues in contact with ASN 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A HIS 2.9 20.8 + - - +
48A ILE 3.4 8.4 - - - +
49A VAL 3.1 0.6 - - - -
50A MSE 1.3 78.0 - - - +
52A MSE 1.3 67.4 + - - +
53A GLU 3.4 0.8 + - - -
54A GLU* 4.7 10.0 + - - +
55A GLN* 5.5 0.5 - - - +
74A TRP* 5.1 8.3 + - - -
75A ASN* 5.6 1.7 - - - +
40B ALA* 4.7 2.5 - - - -
41B PRO* 3.2 38.9 - - + +
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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