Contacts of the helix formed by residues 39 - 50 (chain E) in PDB entry 3PHW
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 ASN 39 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37E ASP* 2.9 18.5 + - - +
38E GLY* 1.3 79.7 + - - +
40E CYS* 1.3 65.2 + - - +
41E PHE 3.1 3.1 - - - -
42E TYR* 3.0 22.3 + - + +
43E HIS* 3.0 22.5 + - - +
58E TYR* 3.6 33.4 + - + -
62E LYS* 4.1 13.1 - - - +
96E ASP* 2.9 19.3 + - - +
97E ASN* 3.0 33.9 - - - +
98E GLU 4.2 0.8 + - - +
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Residues in contact with CYS 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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34E GLN* 4.4 2.2 - - + +
35E PRO 3.9 6.5 - - - +
37E ASP* 3.5 3.2 + - - -
38E GLY 3.5 0.2 - - - -
39E ASN* 1.3 77.0 - - - +
41E PHE* 1.3 62.2 + - - +
43E HIS* 3.4 12.8 - - - +
44E SER* 2.8 31.9 + - - -
151E HIS* 3.9 10.5 - - + -
152E PHE* 3.3 34.8 - - - +
75F GLY 3.4 3.1 - - - -
76F NEH 1.8 67.3 - - + -
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Residues in contact with PHE 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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38E GLY 5.1 0.2 + - - -
39E ASN 3.0 1.2 + - - -
40E CYS* 1.3 83.1 - - - +
42E TYR* 1.3 86.1 + + + +
44E SER* 3.3 3.3 + - - -
45E ILE* 3.2 34.8 + - + +
100E GLY* 3.8 25.1 - - - +
101E SER 3.8 22.2 - - - -
104E GLU* 3.8 19.5 - - + -
105E ALA* 3.8 24.0 - - + -
108E LEU* 4.0 11.2 - - + -
118E ILE* 4.7 1.1 - - + -
144E LEU* 3.7 25.1 - - + -
152E PHE* 3.8 38.6 - + + -
75F GLY 4.4 0.6 + - - +
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Residues in contact with TYR 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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39E ASN* 3.0 14.8 + - + +
41E PHE* 1.3 97.3 - + + +
43E HIS* 1.3 59.4 + - - +
45E ILE* 3.4 2.7 + - - +
46E ALA* 2.8 31.2 + - - +
58E TYR* 3.8 22.9 - - + +
61E ILE* 3.8 25.3 - - + +
62E LYS* 3.4 39.0 - - + -
65E THR* 3.5 20.0 - - - -
93E MET* 3.6 19.1 + - - +
98E GLU* 3.8 21.8 + - - +
99E TRP 4.5 1.2 + - - -
100E GLY* 3.6 15.5 + - - -
104E GLU* 3.6 20.7 - - + +
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Residues in contact with HIS 43 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34E GLN* 3.5 16.5 - - - +
35E PRO* 3.8 23.6 - - + +
37E ASP* 3.3 36.5 + - - -
39E ASN* 3.0 21.7 + - - +
40E CYS* 3.4 11.7 - - - +
42E TYR* 1.3 76.9 - - - +
44E SER* 1.3 56.2 + - - +
46E ALA* 3.2 6.1 + - - +
47E GLU* 2.8 24.6 + - - +
53E LYS* 3.6 14.0 - - - +
54E THR 4.8 0.2 + - - -
55E ASP* 3.3 26.4 - - + -
58E TYR* 3.2 37.3 + + - +
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Residues in contact with SER 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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34E GLN* 3.4 16.0 - - - +
40E CYS 2.8 21.3 + - - -
41E PHE 3.7 5.2 - - - -
43E HIS* 1.3 73.1 - - - +
45E ILE* 1.3 66.2 + - - +
47E GLU* 3.4 11.1 + - - +
48E LEU* 3.4 20.3 + - - +
144E LEU* 3.7 20.6 - - - -
152E PHE* 3.4 10.7 + - - +
153E ASP* 3.3 26.7 - - - -
154E ALA* 3.8 2.9 - - - +
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Residues in contact with ILE 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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41E PHE* 3.2 33.5 + - + +
42E TYR 3.7 6.5 - - - +
44E SER* 1.3 77.5 - - - +
46E ALA* 1.3 57.9 + - - +
48E LEU* 3.1 2.8 + - - +
49E THR* 2.7 42.2 + - + +
61E ILE* 3.8 32.3 - - + -
108E LEU* 4.7 3.4 - - + -
112E MET* 4.6 9.9 - - - -
114E ILE* 5.4 1.1 - - + -
116E ILE* 3.9 23.6 - - + -
142E VAL* 3.9 21.8 - - + -
144E LEU* 4.0 17.9 - - + -
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Residues in contact with ALA 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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42E TYR 2.8 18.2 + - - +
43E HIS* 3.4 7.0 - - - +
44E SER 3.2 0.2 - - - -
45E ILE* 1.3 74.8 - - - +
47E GLU* 1.3 66.3 + - - +
48E LEU 3.0 1.4 + - - -
49E THR* 3.9 6.1 - - - -
50E MET* 3.1 48.0 + - - +
53E LYS* 3.9 8.0 - - + +
57E SER* 4.0 15.7 - - - -
58E TYR 4.2 6.5 - - - +
61E ILE* 4.0 8.3 - - + +
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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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32E VAL* 3.5 26.9 - - + +
34E GLN* 3.4 13.7 + - - +
43E HIS 2.8 14.1 + - - +
44E SER 3.5 10.1 - - - +
45E ILE 3.3 0.2 - - - -
46E ALA* 1.3 75.2 - - - +
48E LEU* 1.3 59.3 + - + +
50E MET 4.7 5.4 - - - +
53E LYS* 3.1 38.5 + - - +
154E ALA* 3.9 9.4 - - + -
156E ARG* 2.9 38.9 + - - +
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Residues in contact with LEU 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 SER 3.5 15.0 - - - +
45E ILE 3.1 4.1 + - - +
46E ALA 3.0 0.8 - - - -
47E GLU* 1.3 81.3 - - + +
49E THR* 1.3 63.2 + - - +
50E MET 3.8 0.2 - - - -
142E VAL* 3.6 34.5 - - + +
143E ASN 3.2 31.4 - - - +
144E LEU* 4.1 1.8 - - + -
154E ALA* 3.9 15.3 - - + -
155E LEU 3.5 19.5 - - - +
156E ARG* 3.7 29.8 - - + +
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Residues in contact with THR 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 ILE* 2.7 27.5 + - + +
48E LEU* 1.3 84.1 - - - +
50E MET* 1.3 72.0 + - - +
51E PRO* 3.9 6.1 - - - +
61E ILE* 3.8 10.6 - - - +
112E MET* 3.9 25.1 - - + +
114E ILE* 4.3 8.1 - - + -
142E VAL* 3.8 24.2 - - + -
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Residues in contact with MET 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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46E ALA* 3.1 19.5 + - - +
47E GLU 4.7 3.8 - - - +
48E LEU 3.8 0.2 - - - -
49E THR* 1.3 91.8 - - - +
51E PRO* 1.3 72.8 - - + +
52E ASN 3.5 1.7 + - - -
53E LYS* 3.7 18.1 + - + +
57E SER* 3.5 39.5 - - - +
60E TYR* 3.7 42.8 - - + -
61E ILE* 4.0 5.6 - - + -
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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