Contacts of the helix formed by residues 36 - 50 (chain D) in PDB entry 1E50
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 36 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35D ARG* 1.3 107.6 - - + +
37D HIS* 1.3 65.9 - - - +
38D GLU* 3.2 10.8 - - + +
39D GLU* 3.0 19.9 + - + +
40D ARG 2.9 17.8 + - - -
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Residues in contact with HIS 37 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35D ARG 3.3 3.6 + - - -
36D PRO* 1.3 71.6 - - - +
38D GLU* 1.3 73.6 + - - +
40D ARG* 3.2 14.9 + - - +
41D GLN* 2.9 50.0 + - - +
117D GLN 2.8 28.4 + - - -
118D ARG* 3.9 12.8 - - - -
119D LEU* 3.7 23.5 - - + +
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Residues in contact with GLU 38 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36D PRO* 3.2 9.2 - - + +
37D HIS* 1.3 98.2 + - - +
39D GLU* 1.3 63.0 + - - +
41D GLN* 3.1 20.8 + - - +
42D ALA* 3.2 18.5 + - - +
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Residues in contact with GLU 39 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32D PHE* 4.5 0.7 - - - -
35D ARG* 3.2 46.7 + - - +
36D PRO* 3.0 21.2 + - + +
38D GLU* 1.3 77.5 - - - +
40D ARG* 1.3 59.5 + - - +
42D ALA* 3.0 9.7 + - + +
43D ARG* 2.8 73.2 + - - +
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Residues in contact with ARG 40 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28D LYS* 6.0 0.4 - - - +
29D TYR* 3.1 38.7 + - + -
30D THR 3.6 6.9 + - - -
31D GLY 2.7 27.8 + - - -
32D PHE* 3.2 19.8 + - + +
33D ARG* 3.7 23.9 + - - +
35D ARG* 3.2 32.3 - - + +
36D PRO 2.9 8.0 + - - +
37D HIS* 3.5 17.8 + - - +
39D GLU* 1.3 75.5 - - - +
41D GLN* 1.3 57.0 + - - +
43D ARG* 3.6 9.4 - - - +
44D PHE* 2.9 32.1 + - - +
119D LEU* 3.7 34.7 - - + +
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Residues in contact with GLN 41 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D HIS* 2.9 39.4 + - - +
38D GLU* 3.1 34.5 - - - +
39D GLU 3.1 0.2 - - - -
40D ARG* 1.3 77.5 - - - +
42D ALA* 1.3 63.9 + - - +
44D PHE* 3.6 3.5 + - - +
45D GLN* 3.3 21.7 + - - +
116D LEU 3.4 18.4 + - - +
117D GLN* 3.2 42.8 + - - +
119D LEU* 3.8 16.2 - - + +
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Residues in contact with ALA 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38D GLU 3.2 8.3 + - - +
39D GLU* 3.0 14.1 + - + +
41D GLN* 1.3 77.1 - - - +
43D ARG* 1.3 67.4 + - + +
45D GLN* 3.0 7.8 + - - +
46D ASN* 2.9 31.4 + - - +
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Residues in contact with ARG 43 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29D TYR* 3.8 3.1 - - - +
32D PHE* 3.6 58.0 - - + -
35D ARG* 5.6 1.6 - - - +
39D GLU* 2.8 54.3 + - - +
40D ARG* 3.6 7.2 - - - +
42D ALA* 1.3 74.5 - - - +
44D PHE* 1.3 58.2 + - - +
46D ASN* 3.1 13.2 + - - +
47D ALA* 2.8 32.6 + - - +
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Residues in contact with PHE 44 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29D TYR* 3.3 39.7 + + + -
40D ARG 2.9 18.5 + - - +
41D GLN 3.7 5.6 - - - +
43D ARG* 1.3 76.8 - - - +
45D GLN* 1.3 59.5 + - - +
47D ALA* 3.9 2.8 - - + +
48D CYS* 3.0 52.9 + - - +
53D SER* 3.5 18.4 - - - -
55D ILE* 4.5 2.0 - - + -
95D VAL* 3.9 7.9 - - + -
97D LEU* 4.3 2.7 - - + -
114D ILE* 3.6 44.0 - - + -
116D LEU* 3.8 26.2 - - + -
119D LEU* 3.8 20.2 - - + -
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Residues in contact with GLN 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41D GLN 3.3 10.1 + - - +
42D ALA* 3.0 9.8 + - - +
44D PHE* 1.3 76.9 - - - +
46D ASN* 1.3 67.7 + - - +
48D CYS* 3.6 4.9 - - + +
49D ARG* 2.9 56.2 + - + +
88D LEU* 4.1 18.2 - - + +
116D LEU* 4.2 35.6 - - + +
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Residues in contact with ASN 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42D ALA* 2.9 21.6 + - - +
43D ARG* 3.4 14.7 - - - +
45D GLN* 1.3 77.8 - - - +
47D ALA* 1.3 61.6 + - - +
49D ARG* 2.9 25.9 + - - +
50D ASP* 2.8 36.1 + - - +
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Residues in contact with ALA 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29D TYR* 5.3 5.4 - - + +
32D PHE* 6.1 3.6 - - + -
43D ARG 2.8 20.2 + - - +
44D PHE* 4.0 4.7 - - - +
46D ASN* 1.3 72.5 - - - +
48D CYS* 1.3 56.2 + - - +
50D ASP* 3.3 6.5 + - - -
51D GLY 3.2 4.7 + - - -
52D ARG* 2.7 62.0 + - + +
53D SER* 4.8 5.6 - - - +
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Residues in contact with CYS 48 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44D PHE* 3.0 59.4 + - - +
45D GLN* 3.6 7.9 - - + +
47D ALA* 1.3 73.6 - - - +
49D ARG* 1.3 56.7 + - + +
50D ASP 3.0 4.3 - - - -
51D GLY* 2.7 26.2 + - - -
52D ARG 3.2 6.9 + - - +
53D SER* 4.6 0.4 - - - -
68D PHE* 4.2 7.4 - - - -
86D VAL* 3.8 24.6 - - + +
88D LEU* 6.2 1.6 - - + -
95D VAL* 4.5 5.2 - - + -
97D LEU* 4.1 21.3 - - - -
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Residues in contact with ARG 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45D GLN* 2.9 40.2 + - - +
46D ASN* 2.9 31.8 + - - +
48D CYS* 1.3 78.6 - - + +
50D ASP* 1.3 67.9 + - - +
51D GLY 3.2 0.4 - - - -
80D THR* 4.4 10.0 + - - +
81D PRO* 3.1 20.6 - - - +
86D VAL* 4.6 7.0 - - + -
88D LEU* 3.9 24.2 - - + -
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Residues in contact with ASP 50 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46D ASN* 2.8 27.1 + - - +
47D ALA* 3.4 7.9 - - - +
48D CYS 3.0 1.4 - - - -
49D ARG* 1.3 87.8 + - - +
51D GLY* 1.3 58.2 + - - +
52D ARG* 3.7 6.4 + - + +
69D PHE* 3.9 9.2 - - - -
80D THR* 5.5 3.5 + - - +
81D PRO* 4.0 6.3 - - - -
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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