Contacts of the helix formed by residues 35 - 50 (chain E) in PDB entry 2P6T
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 35 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29E SER* 3.9 0.9 - - - -
34E LEU* 1.3 75.0 - - - +
36E PRO* 1.3 71.6 - - - +
37E SER* 5.6 0.2 - - - -
38E PRO* 3.0 23.6 - - - +
39E CYS* 2.8 28.9 + - - +
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Residues in contact with PRO 36 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25E ASN* 3.1 26.4 - - + +
26E VAL* 5.3 9.6 - - + -
29E SER* 3.7 21.7 - - - +
34E LEU 4.6 0.2 - - - +
35E SER* 1.3 86.2 - - - +
37E SER* 1.3 57.3 + - - +
39E CYS 3.2 0.3 + - - -
40E LEU* 2.6 34.6 + - - +
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Residues in contact with SER 37 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36E PRO* 1.3 81.9 - - - +
38E PRO* 1.3 64.8 - - - +
40E LEU* 3.7 6.5 - - - +
41E ARG* 3.2 25.8 + - - +
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Residues in contact with PRO 38 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34E LEU* 4.8 10.3 - - + -
35E SER* 3.0 40.8 - - - +
37E SER* 1.3 94.1 - - - +
39E CYS* 1.3 62.8 + - - +
41E ARG* 3.8 15.8 + - + +
42E ARG* 3.2 31.8 + - - +
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Residues in contact with CYS 39 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13E ILE* 4.5 3.3 - - - +
25E ASN* 3.3 23.6 - - - -
28E LEU* 4.3 13.0 - - - -
29E SER* 3.5 32.3 - - - -
32E VAL* 4.4 6.1 - - - -
34E LEU* 3.8 20.6 - - + +
35E SER 2.8 20.9 + - - +
36E PRO 3.4 2.5 - - - +
38E PRO* 1.3 78.0 - - - +
40E LEU* 1.3 58.0 + - - +
42E ARG* 3.2 5.4 + - - +
43E LEU* 3.0 26.9 + - - +
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Residues in contact with LEU 40 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25E ASN* 3.3 34.5 - - + +
36E PRO 2.6 20.0 + - - +
37E SER* 3.7 7.2 - - - +
38E PRO 3.3 0.2 - - - -
39E CYS* 1.3 74.0 - - - +
41E ARG* 1.3 57.7 + - - +
43E LEU* 4.5 14.6 - - + -
44E LYS* 2.9 34.9 + - + +
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Residues in contact with ARG 41 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37E SER 3.2 13.4 + - - +
38E PRO* 4.2 14.5 + - + +
39E CYS 3.3 0.2 - - - -
40E LEU* 1.3 78.4 - - - +
42E ARG* 1.3 79.5 + - - +
44E LYS* 3.5 7.1 - - + +
45E GLN* 2.6 69.9 + - + +
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Residues in contact with ARG 42 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7E ASP* 2.9 34.0 + - - -
9E THR* 3.6 17.2 + - - +
10E ASP* 3.0 39.9 + - - +
13E ILE* 3.8 8.1 - - + -
34E LEU* 3.3 34.4 - - - +
38E PRO* 3.2 18.5 + - - +
39E CYS 3.2 6.3 + - - +
41E ARG* 1.3 93.8 - - - +
43E LEU* 1.3 56.6 + - - +
45E GLN* 2.9 9.7 + - - +
46E LEU* 2.7 39.6 + - - +
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Residues in contact with LEU 43 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13E ILE* 4.2 9.1 - - + +
17E LEU* 3.2 20.0 - - + -
25E ASN* 4.6 4.5 - - - +
28E LEU* 3.7 24.0 - - + -
39E CYS* 3.0 13.5 + - - +
40E LEU* 3.9 18.6 - - + +
42E ARG* 1.3 78.7 - - - +
44E LYS* 1.3 65.1 + - - +
46E LEU* 3.4 13.3 + - + +
47E GLU* 3.3 24.1 + - + +
52E VAL* 5.1 3.8 - - + -
55E TYR* 3.0 26.2 - - - +
22F ARG* 3.9 21.1 - - - +
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Residues in contact with LYS 44 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40E LEU* 2.9 22.4 + - + +
41E ARG* 3.5 8.3 - - + +
43E LEU* 1.3 75.2 - - - +
45E GLN* 1.3 58.8 - - - +
47E GLU* 2.6 38.6 + - + +
48E ASP* 2.8 38.6 + - - +
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Residues in contact with GLN 45 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5E THR* 4.7 9.7 + - - +
10E ASP* 3.5 25.9 + - - -
41E ARG* 2.6 53.0 + - + +
42E ARG* 3.2 6.9 - - - +
44E LYS* 1.3 73.5 - - - +
46E LEU* 1.3 63.5 + - - +
48E ASP* 3.2 13.8 - - - +
49E ALA* 3.1 22.4 + - + +
51E ILE* 6.4 0.2 - - + -
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Residues in contact with LEU 46 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6E LEU* 4.3 4.5 - - + -
10E ASP* 3.8 32.3 - - - +
13E ILE* 3.9 21.3 - - + -
14E LEU* 4.0 23.1 - - + -
42E ARG 2.7 30.2 + - - +
43E LEU* 3.4 21.3 - - + +
45E GLN* 1.3 75.8 - - + +
47E GLU* 1.3 61.5 + - - +
49E ALA* 3.4 2.8 - - - +
50E GLY 3.2 3.1 + - - -
51E ILE* 3.1 61.8 + - + +
52E VAL* 4.4 9.4 - - + -
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Residues in contact with GLU 47 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43E LEU* 3.3 24.8 + - - +
44E LYS* 2.6 20.7 + - + +
46E LEU* 1.3 69.4 - - - +
48E ASP* 1.3 66.9 + - - +
49E ALA 3.1 1.6 - - - -
50E GLY* 3.0 14.6 + - - -
52E VAL* 4.1 25.1 - - + +
55E TYR* 3.2 41.5 + - + +
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Residues in contact with ASP 48 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44E LYS* 2.8 53.6 + - - +
45E GLN* 3.2 14.6 - - - +
47E GLU* 1.3 73.1 - - - +
49E ALA* 1.3 62.8 + - - +
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Residues in contact with ALA 49 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45E GLN* 3.1 8.5 + - + +
46E LEU 3.4 9.9 - - - +
47E GLU 3.1 0.2 - - - -
48E ASP* 1.3 82.7 - - - +
50E GLY* 1.3 58.4 + - - +
51E ILE* 3.9 20.6 - - + +
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Residues in contact with GLY 50 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47E GLU 3.0 14.3 + - - -
48E ASP 4.6 0.2 - - - -
49E ALA* 1.3 77.6 - - - +
51E ILE* 1.3 64.5 + - - +
52E VAL 3.2 12.0 + - - -
53E ARG* 3.9 3.0 + - - +
60F SER* 3.2 24.4 + - - -
63F SER* 4.7 3.6 - - - -
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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