Contacts of the helix formed by residues 35 - 40 (chain B) in PDB entry 1EE8
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 35 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A ASN* 5.4 5.7 + - - -
33B TYR 3.9 2.0 + - - -
34B ARG* 1.3 102.5 + - - +
36B THR* 1.3 64.2 + - - +
37B ALA* 3.1 4.7 - - - +
38B LEU* 3.2 24.0 + - + +
106B GLY* 3.4 22.7 + - - +
107B VAL* 6.1 0.4 - - - +
114B GLU* 6.2 2.2 - - - +
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Residues in contact with THR 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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25B VAL* 3.6 34.1 + - + +
27B HIS* 3.0 23.2 + - - -
33B TYR* 3.9 33.6 + - + -
34B ARG 4.0 4.7 - - - +
35B ASN* 1.3 73.0 - - - +
37B ALA* 1.3 64.9 + - - +
38B LEU 2.9 4.9 - - - -
39B ALA* 2.9 22.0 + - - +
40B GLU* 3.6 9.0 + - - +
64B LEU* 4.7 5.8 - - + -
104B LEU* 4.1 12.6 - - + -
106B GLY* 4.6 4.9 - - - -
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Residues in contact with ALA 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A LEU* 3.3 28.9 - - + +
42A ARG* 4.3 1.9 + - - -
62A VAL* 5.6 0.5 - - - +
108A ARG* 4.8 11.4 + - + -
35B ASN* 3.1 2.6 - - - -
36B THR* 1.3 81.1 + - - +
38B LEU* 1.3 62.2 + - - +
40B GLU* 3.3 36.3 + - - +
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Residues in contact with LEU 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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37A ALA* 3.0 46.9 - - + +
38A LEU* 3.4 13.0 - - + +
42A ARG* 3.7 2.4 + - - -
35B ASN* 3.2 18.5 + - + +
36B THR 2.9 0.2 - - - -
37B ALA* 1.3 80.6 - - - +
39B ALA* 1.3 50.7 + - - +
40B GLU 3.6 0.2 + - - -
42B ARG* 2.7 43.7 + - - +
62B VAL* 3.8 16.3 - - + +
106B GLY 3.7 26.7 - - - +
107B VAL* 3.8 17.5 - - - +
108B ARG* 4.2 3.6 - - + +
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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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22B LEU* 3.7 24.2 - - + +
25B VAL* 4.5 1.3 - - + -
35B ASN 4.4 0.2 + - - -
36B THR* 2.9 11.6 + - - +
38B LEU* 1.3 79.4 - - - +
40B GLU* 1.3 62.7 - - - +
41B GLY 3.7 0.5 + - - -
42B ARG* 3.5 19.9 + - - +
58B LEU* 3.3 26.5 - - + +
62B VAL* 4.3 4.9 - - + -
64B LEU* 4.2 20.6 - - + -
106B GLY* 5.1 2.5 - - - -
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Residues in contact with GLU 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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42A ARG* 2.7 32.2 + - - -
60A GLY 4.2 1.2 - - - +
108A ARG* 2.8 52.2 + - - +
22B LEU* 3.8 4.9 - - - -
23B ARG 3.7 2.2 - - - +
24B GLN* 3.1 15.1 + - - +
25B VAL* 2.7 44.8 + - + +
36B THR* 3.8 10.8 - - - +
37B ALA* 3.3 21.2 + - - +
39B ALA* 1.3 79.6 - - - +
41B GLY* 1.3 58.2 + - - +
42B ARG* 3.8 0.3 - - - +
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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