Contacts of the helix formed by residues 36 - 45 (chain B) in PDB entry 2E52
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 ARG 36 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35B ASN* 1.3 74.6 - - - +
37B ASN* 1.3 61.7 + - - +
39B VAL* 3.1 9.4 + - - +
40B ILE* 3.0 38.1 + - + +
77B LEU* 3.9 46.8 + - + +
176B LEU* 2.8 41.2 + - - +
179B ASP* 3.4 34.6 + - - +
180B LEU 4.8 1.6 + - - +
181B GLU* 5.3 6.5 + - - -
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Residues in contact with ASN 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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35B ASN* 3.3 8.3 + - - +
36B ARG* 1.3 81.7 - - - +
38B GLU* 1.3 56.9 + - + +
40B ILE* 3.5 18.2 + - - +
41B GLU* 3.0 26.3 + - - +
177B GLN* 4.7 11.8 + - - +
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Residues in contact with GLU 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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2B LYS 5.0 2.6 - - - +
4B ALA* 3.5 16.9 + - + +
7B LYS* 2.7 32.5 + - - +
34B LEU* 3.8 23.8 - - + +
35B ASN* 3.0 50.3 + - - +
36B ARG 3.1 0.2 - - - -
37B ASN* 1.3 75.4 - - + +
39B VAL* 1.3 65.1 + - - +
41B GLU* 3.3 11.6 + - - +
42B LEU* 3.1 22.7 + - - +
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Residues in contact with VAL 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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31B ILE* 4.3 6.3 - - + +
34B LEU* 3.9 22.7 - - + +
35B ASN 3.0 19.7 + - - +
36B ARG* 3.1 7.2 + - - +
38B GLU* 1.3 74.2 - - - +
40B ILE* 1.3 58.3 + - - +
42B LEU* 3.1 8.6 + - - +
43B VAL* 2.8 39.6 + - + +
70B VAL* 4.8 5.2 - - + +
73B LYS* 3.9 35.4 - - + -
74B ALA 4.7 4.9 - - - +
77B LEU* 3.8 23.8 - - + -
176B LEU* 4.6 4.7 - - + -
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Residues in contact with ILE 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 ARG* 3.0 34.0 + - + +
37B ASN* 3.7 17.5 - - - +
39B VAL* 1.3 77.0 - - + +
41B GLU* 1.3 62.7 + - - +
43B VAL* 3.3 8.9 + - - +
44B ARG* 3.0 55.2 + - - +
173B ALA* 4.4 12.8 - - + +
176B LEU* 3.7 27.8 - - + +
177B GLN* 3.8 31.6 - - - +
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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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3B SER* 3.4 19.0 + - - -
4B ALA* 2.8 27.4 + - - +
5B LEU* 3.0 30.7 + - - +
37B ASN 3.0 15.2 + - - +
38B GLU* 3.5 12.0 - - - +
39B VAL 3.3 0.2 - - - -
40B ILE* 1.3 76.0 - - - +
42B LEU* 1.3 57.4 + - - +
44B ARG* 3.2 13.0 + - + +
45B SER* 2.8 38.2 + - - +
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Residues in contact with LEU 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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4B ALA* 3.9 6.7 - - + +
5B LEU* 3.8 34.5 - - + +
8B LEU* 4.1 17.9 - - + -
30B PHE* 4.4 7.2 - - + -
31B ILE* 4.1 12.1 - - + -
34B LEU* 3.5 28.9 - - + -
38B GLU 3.1 10.4 + - - +
39B VAL* 3.1 10.1 + - - +
41B GLU* 1.3 74.4 - - - +
43B VAL* 1.3 59.2 + - - +
45B SER* 4.3 3.1 - - - -
46B ILE* 2.8 42.3 + - + +
70B VAL* 3.6 28.9 - - + -
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Residues in contact with VAL 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 VAL* 2.8 22.9 + - + +
40B ILE* 3.3 9.6 + - - +
42B LEU* 1.3 72.4 - - - +
44B ARG* 1.3 62.0 + - - +
46B ILE* 3.9 5.8 + - - -
70B VAL* 3.6 23.5 - - + +
74B ALA* 4.3 10.3 - - + -
169B TRP* 3.2 55.9 - - + +
172B LEU* 4.1 7.6 - - + -
173B ALA* 3.7 17.9 - - + +
176B LEU* 3.9 19.5 - - + -
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Residues in contact with ARG 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 ILE* 3.0 31.8 + - - +
41B GLU* 3.4 13.3 - - + +
43B VAL* 1.3 77.3 - - - +
45B SER* 1.3 58.8 + - - +
47B GLY 4.9 1.4 + - - -
48B ILE* 4.8 10.9 - - - +
169B TRP* 5.2 5.3 - - - +
170B GLU* 5.4 4.9 - - - +
173B ALA* 3.9 19.2 + - + -
174B ILE* 6.2 0.4 - - - +
177B GLN* 2.9 38.6 + - - +
233B LEU* 4.7 9.1 + - - +
236B LYS* 4.7 4.2 - - - +
237B GLU* 3.7 34.1 + - + +
240B PHE* 3.6 45.7 - - + -
241B ILE* 5.5 5.0 - - - +
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Residues in contact with SER 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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5B LEU* 4.2 24.0 - - - +
41B GLU* 2.8 33.7 + - - +
42B LEU* 3.1 6.9 + - - -
44B ARG* 1.3 78.6 - - - +
46B ILE* 1.3 63.5 + - - +
47B GLY 3.3 3.1 - - - -
48B ILE* 3.2 11.5 + - - +
63B PHE* 4.2 2.1 - - - -
244B ARG* 3.0 33.3 + - - +
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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