Contacts of the helix formed by residues 35 - 45 (chain Q) in PDB entry 1OCR
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 ALA 35 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34Q SER* 1.3 75.9 - - - +
36Q SER* 1.3 65.2 + - - +
38Q LYS* 3.1 11.0 + - - +
39Q ALA* 3.0 19.6 + - - +
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Residues in contact with SER 36 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34Q SER* 3.3 11.4 + - - -
35Q ALA* 1.3 78.0 - - - +
37Q GLN* 1.3 57.7 + - - +
39Q ALA* 3.2 9.3 + - - +
40Q LEU* 2.9 26.0 + - - +
58Q GLU* 5.5 4.7 - - - -
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Residues in contact with GLN 37 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30Q VAL* 4.8 3.4 - - - +
32Q ASN 3.8 6.1 - - - +
33Q LEU* 3.5 20.3 - - + +
34Q SER* 3.0 36.1 + - - +
36Q SER* 1.3 72.9 - - - +
38Q LYS* 1.3 61.5 + - - +
39Q ALA 3.1 1.6 - - - -
40Q LEU* 3.1 8.0 + - - +
41Q LYS* 2.8 36.3 + - - +
58Q GLU* 4.0 21.0 + - - +
62Q LEU* 3.8 29.7 - - + +
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Residues in contact with LYS 38 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33Q LEU* 3.4 36.9 + - + +
34Q SER 2.8 17.3 + - - +
35Q ALA* 3.3 11.7 - - - +
37Q GLN* 1.3 76.8 - - - +
39Q ALA* 1.3 62.2 + - - +
41Q LYS* 3.5 10.1 + - - +
42Q GLU* 3.1 24.9 + - - +
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Residues in contact with ALA 39 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35Q ALA 3.0 11.2 + - - +
36Q SER* 3.4 12.3 - - - +
37Q GLN 3.1 0.2 - - - -
38Q LYS* 1.3 75.4 - - - +
40Q LEU* 1.3 53.6 + - - +
42Q GLU* 2.8 26.0 + - - +
43Q LYS* 2.8 20.0 + - - +
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Residues in contact with LEU 40 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36Q SER 2.9 12.7 + - - +
37Q GLN* 3.3 10.5 - - - +
39Q ALA* 1.3 74.0 - - - +
41Q LYS* 1.3 64.5 + - - +
43Q LYS* 3.0 8.4 + - + +
44Q GLU* 3.0 20.8 + - - +
51Q LEU* 3.8 23.8 - - + -
55Q GLU* 3.7 28.0 - - + +
58Q GLU* 3.5 47.6 - - + +
59Q LEU* 3.5 24.9 - - + +
62Q LEU* 4.7 4.7 - - + -
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Residues in contact with LYS 41 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33Q LEU* 3.7 30.1 - - + -
37Q GLN 2.8 20.4 + - - +
38Q LYS* 3.5 8.1 - - - +
40Q LEU* 1.3 77.9 - - - +
42Q GLU* 1.3 61.5 + - - +
44Q GLU* 2.7 49.0 + - - +
45Q LYS* 3.6 22.9 + - - +
59Q LEU* 4.3 7.3 + - + +
62Q LEU* 3.8 24.1 - - + +
63Q LYS* 6.0 4.6 - - - +
59R ASN 4.9 0.8 + - - -
60R ASP* 5.8 2.2 + - - +
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Residues in contact with GLU 42 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38Q LYS 3.1 14.8 + - - +
39Q ALA* 2.8 12.5 + - - +
41Q LYS* 1.3 73.2 - - - +
43Q LYS* 1.3 66.4 + - - +
44Q GLU 3.0 1.6 - - - -
45Q LYS* 2.9 48.7 + - - +
46Q ALA* 4.0 1.7 + - - +
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Residues in contact with LYS 43 (chain Q).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39Q ALA 2.8 11.0 + - - +
40Q LEU* 3.4 13.2 - - + +
42Q GLU* 1.3 76.1 - - - +
44Q GLU* 1.3 56.4 + - - +
46Q ALA* 2.9 34.7 + - + +
47Q SER 4.6 3.5 - - - +
50Q SER* 3.8 24.4 + - - -
51Q LEU* 4.1 13.1 - - + +
55Q GLU* 3.0 43.2 + - - +
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Residues in contact with GLU 44 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40Q LEU 3.0 10.7 + - - +
41Q LYS* 2.7 47.7 + - - +
42Q GLU 3.0 0.2 - - - -
43Q LYS* 1.3 73.7 - - - +
45Q LYS* 1.3 57.7 + - - +
46Q ALA 3.1 6.6 + - - +
48Q TRP* 3.0 28.6 + - - +
51Q LEU* 4.5 4.9 - - - +
59Q LEU* 3.4 25.5 - - + +
56R ARG* 2.9 20.8 + - - -
59R ASN* 3.2 24.4 - - + +
60R ASP* 3.9 2.1 - - - +
61R PHE* 3.0 27.6 + - - +
62R ALA* 4.2 2.8 + - - +
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Residues in contact with LYS 45 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41Q LYS* 3.6 20.0 + - - +
42Q GLU* 2.9 44.7 + - + +
44Q GLU* 1.3 77.4 + - + +
46Q ALA* 1.3 64.8 + - - +
56R ARG* 3.7 6.1 + - - -
59R ASN* 3.9 36.3 + - + +
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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