Contacts of the helix formed by residues 35 - 45 (chain B) in PDB entry 1EGE
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 ILE 35 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30B PHE* 3.1 44.0 + - + +
31B ALA* 3.4 17.3 - - - +
34B GLU* 1.3 75.0 - - - +
36B ILE* 1.3 59.3 + - - +
38B VAL* 3.2 6.9 - - - +
39B ALA* 2.8 32.3 + - + +
52B LEU* 4.0 19.5 - - + -
87B LEU* 4.2 20.4 - - + +
90B GLY 3.8 24.5 - - - +
91B CYS* 3.9 4.5 - - + +
94B VAL* 3.9 28.9 - - + -
98B ILE* 5.7 2.0 - - + -
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Residues in contact with ILE 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B ALA 2.9 12.9 + - - +
32B ARG* 3.3 22.7 - - + +
35B ILE* 1.3 78.3 - - - +
37B PRO* 1.4 79.8 - - + +
39B ALA* 3.4 16.8 + - + +
40B ALA* 4.5 1.2 + - - +
89B TYR* 3.9 17.5 - - + +
90B GLY* 3.8 17.0 - - - +
269B ARG* 3.1 50.1 + - - +
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Residues in contact with PRO 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B ARG 4.3 0.7 - - - +
33B GLU 3.3 28.3 - - - +
34B GLU* 3.4 9.9 - - - +
35B ILE 3.5 1.8 - - - -
36B ILE* 1.4 102.6 - - + +
38B VAL* 1.3 69.7 + - + +
40B ALA* 4.4 6.8 + - - +
41B GLU* 5.0 2.3 + - - +
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Residues in contact with VAL 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B GLU 3.4 16.2 - - - +
35B ILE 3.2 13.5 - - - +
37B PRO* 1.3 80.4 - - + +
39B ALA* 1.3 66.5 + - - +
40B ALA 3.4 0.2 - - - -
41B GLU* 2.7 29.0 + - + +
42B TYR* 3.1 35.6 + - + +
52B LEU* 4.0 17.0 - - + -
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Residues in contact with ALA 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B ILE* 2.8 18.5 + - + +
36B ILE* 3.4 15.6 + - + +
38B VAL* 1.3 71.2 - - - +
40B ALA* 1.3 56.6 + - - +
42B TYR* 2.8 29.9 + - - +
43B ASP* 2.9 13.0 + - - +
52B LEU* 6.2 0.2 - - - -
90B GLY 4.1 19.5 - - - +
91B CYS* 4.1 18.3 - - + -
94B VAL* 6.0 2.5 - - - -
269B ARG* 5.8 1.1 - - - +
364B LYS* 4.6 8.7 - - + -
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Residues in contact with ALA 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B ILE 4.5 0.8 + - - +
37B PRO 4.4 6.3 + - - +
38B VAL 3.1 0.8 + - - -
39B ALA* 1.3 78.3 - - - +
41B GLU* 1.3 62.5 + - - +
43B ASP* 3.2 9.7 + - - +
44B LYS* 3.0 40.1 + - - +
364B LYS* 4.9 7.8 - - + +
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Residues in contact with GLU 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B PRO 5.0 1.5 + - - +
38B VAL* 2.7 26.1 + - + +
40B ALA* 1.3 74.1 - - - +
42B TYR* 1.3 64.7 + - + +
44B LYS* 3.5 14.1 + - - +
45B THR* 3.0 46.6 + - + +
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Residues in contact with TYR 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B VAL* 3.1 53.7 + - + +
39B ALA* 2.8 10.3 + - - +
41B GLU* 1.3 85.0 - - + +
43B ASP* 1.3 51.3 + - - +
45B THR* 3.0 4.0 + - - -
46B GLY* 2.7 35.3 + - - -
47B GLU* 3.6 43.5 + - - +
48B TYR 4.2 2.5 - - - -
49B PRO* 3.5 33.4 - - + -
51B PRO* 3.6 27.9 - - + +
52B LEU* 4.9 5.1 - - + +
94B VAL* 5.4 2.7 - - + -
219B CYS* 4.4 14.6 - - + +
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Residues in contact with ASP 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B ALA 2.9 6.0 + - - +
40B ALA* 3.2 9.6 + - - +
42B TYR* 1.3 78.8 - - - +
44B LYS* 1.3 66.4 + - - +
46B GLY* 3.4 8.1 + - - -
217B GLN* 5.2 0.3 + - - -
218B ARG* 3.3 36.2 + - - +
219B CYS* 5.2 3.3 - - - +
364B LYS* 3.5 37.7 - - + +
367B ARG* 3.0 43.2 + - - -
368B ASP* 4.8 2.9 - - - +
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Residues in contact with LYS 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B ALA* 3.0 29.5 + - - +
41B GLU* 3.7 15.3 - - - +
43B ASP* 1.3 83.4 - - - +
45B THR* 1.3 64.7 + - + +
218B ARG* 4.0 11.3 + - - +
358B THR* 4.3 25.1 - - + -
359B GLU* 4.3 13.9 + - - +
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Residues in contact with THR 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B GLU* 3.0 34.6 + - - +
42B TYR* 3.0 8.5 + - - -
44B LYS* 1.3 81.3 - - + +
46B GLY* 1.3 61.2 + - - +
47B GLU* 3.1 28.5 + - + +
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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