Contacts of the helix formed by residues 39 - 49 (chain A) in PDB entry 2P1A
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 SER 39 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29A LEU 3.9 3.8 - - - -
30A LYS* 3.8 25.4 - - - -
31A ILE 5.6 0.2 - - - -
32A ALA 3.6 4.5 - - - -
38A ARG* 1.3 75.5 - - - +
40A LEU* 1.3 64.2 - - - +
41A PHE* 4.1 2.9 - - - +
42A GLU* 3.2 26.1 + - - +
43A MSE 3.2 27.0 + - - +
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Residues in contact with LEU 40 (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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24A TYR* 5.4 3.4 - - + -
29A LEU* 3.2 31.3 + - + +
32A ALA* 3.1 35.2 + - + +
33A PRO* 3.8 12.3 - - + -
39A SER* 1.3 71.8 - - - +
41A PHE* 1.3 57.5 + - - +
43A MSE 3.3 24.6 - - + +
44A TYR* 2.9 37.3 + - + +
136A ILE* 5.1 3.4 - - + +
139A LEU* 3.9 22.7 - - + +
140A LEU* 3.3 35.7 - - + -
142A GLU* 5.0 3.1 - - - +
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Residues in contact with PHE 41 (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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26A GLU* 3.8 42.4 - - + -
29A LEU* 3.0 26.9 + - + +
30A LYS* 3.7 39.5 - - + -
39A SER* 3.2 3.3 - - - +
40A LEU* 1.3 77.4 - - - +
42A GLU* 1.3 56.0 + - - +
44A TYR* 3.7 0.6 - - - -
45A ALA* 2.8 36.7 + - + +
75A PRO 4.1 10.3 - - - -
76A GLU* 3.6 28.9 - - - -
77A THR* 4.8 2.9 - - - -
78A ILE* 4.9 2.2 - - + -
81A MSE 3.3 30.2 - - + +
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Residues in contact with GLU 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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39A SER* 3.2 23.9 + - - +
41A PHE* 1.3 81.8 - - + +
43A MSE 1.3 59.3 + - + +
45A ALA* 3.5 7.6 - - + +
46A HIS* 3.0 27.7 + - + +
74A THR* 5.3 0.7 - - - +
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Residues in contact with MSE 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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38A ARG* 3.9 26.9 - - + -
39A SER* 3.2 24.3 + - - +
40A LEU* 3.3 35.4 - - + +
41A PHE 3.2 0.6 - - - -
42A GLU* 1.3 77.0 - - + +
44A TYR* 1.3 58.9 + - - +
45A ALA 3.2 0.2 - - - -
46A HIS* 3.3 2.3 + - - -
47A LEU 2.9 15.1 + - - -
132A HIS* 2.6 38.6 + - + +
135A GLN* 5.5 5.2 - - - +
136A ILE* 4.0 21.1 - - + -
139A LEU* 3.4 30.1 - - + -
138B ILE* 4.8 6.5 - - - -
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Residues in contact with TYR 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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17A SER* 4.2 11.2 - - - -
20A MSE 3.2 39.4 - - + +
21A LEU* 3.5 38.3 - - + +
24A TYR* 4.1 6.4 - + - -
29A LEU* 4.0 21.3 - - + -
40A LEU* 2.9 26.5 + - + +
41A PHE* 3.9 3.4 - - - +
43A MSE 1.3 73.0 - - - +
45A ALA* 1.3 65.0 + - - +
47A LEU* 3.3 17.1 + - + +
48A SER* 3.1 23.9 + - - -
81A MSE 3.9 17.1 - - + +
85A MSE 5.9 1.0 - - + +
133A ARG* 6.5 0.7 - - + -
136A ILE* 3.7 35.8 - - + +
140A LEU* 3.7 12.8 - - + +
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Residues in contact with ALA 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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41A PHE* 2.8 21.7 + - + +
42A GLU* 3.5 9.9 - - - +
44A TYR* 1.3 77.2 - - - +
46A HIS* 1.3 59.1 + - - +
48A SER* 2.6 25.3 + - - -
49A LEU* 3.7 5.7 + - - +
74A THR* 3.2 30.3 - - + -
75A PRO* 3.8 9.2 - - - +
81A MSE 3.3 20.1 - - + +
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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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42A GLU 3.0 18.5 + - - +
43A MSE 3.3 5.8 + - - +
45A ALA* 1.3 73.9 - - - +
47A LEU* 1.3 64.1 + - - +
49A LEU* 3.3 13.9 + - - +
50A ILE* 3.6 10.3 + - + +
70A TYR* 3.3 51.9 - + + -
74A THR* 4.8 2.4 - - - +
128A HIS* 4.5 13.7 - + - -
132A HIS* 3.1 31.6 + + + -
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Residues in contact with LEU 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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17A SER* 3.7 24.5 - - - +
43A MSE 2.9 14.5 + - - +
44A TYR* 3.5 23.1 - - + +
46A HIS* 1.3 75.1 - - - +
48A SER* 1.3 62.2 + - - +
49A LEU 3.2 0.7 + - - -
50A ILE* 3.2 42.9 + - + +
51A CYS 4.9 0.5 + - - -
85A MSE 4.8 3.4 - - - -
129A PHE* 3.6 45.0 - - + +
132A HIS* 3.8 15.2 + - + -
133A ARG* 4.0 9.0 - - + +
136A ILE* 3.8 18.6 - - + -
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Residues in contact with SER 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 TYR 3.1 11.8 + - - -
45A ALA* 2.6 23.3 + - - -
47A LEU* 1.3 76.8 - - - +
49A LEU* 1.3 55.7 + - - +
50A ILE 3.9 0.3 + - - -
51A CYS* 4.9 4.2 + - - +
52A HIS* 4.5 1.9 + - - -
75A PRO* 3.5 18.9 - - - +
81A MSE 3.4 33.2 - - - +
84A THR* 3.4 20.6 - - - +
85A MSE 3.5 25.1 + - - +
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Residues in contact with LEU 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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45A ALA 4.0 9.6 - - - +
46A HIS* 3.3 8.8 + - - +
47A LEU 3.2 1.0 - - - -
48A SER* 1.3 75.6 + - - +
50A ILE* 1.3 53.9 + - - +
51A CYS 3.4 1.6 - - - -
52A HIS* 3.4 5.9 + - - +
53A ALA* 2.8 35.9 + - - +
69A PHE* 3.5 30.7 - - + +
70A TYR* 3.8 31.9 - - + -
73A GLN 3.7 17.5 - - - +
74A THR* 3.6 34.8 - - - +
75A PRO* 4.2 3.8 - - + -
84A THR* 3.9 21.3 - - + -
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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