Contacts of the helix formed by residues 34 - 42 (chain F) in PDB entry 3X0X
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 THR 34 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30F LYS 5.0 1.3 + - - -
31F TRP* 3.3 4.9 + - - -
33F ALA* 1.3 79.6 - - + +
35F ALA* 1.3 57.5 + - - +
36F VAL 3.3 2.9 - - - -
37F GLU* 2.9 18.1 + - + -
38F ARG* 2.5 67.0 + - - +
48F GLU* 3.5 8.6 + - - -
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Residues in contact with ALA 35 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31F TRP 3.0 11.5 + - - +
32F ARG* 3.0 20.4 + - - +
33F ALA 3.5 0.2 - - - -
34F THR* 1.3 77.1 - - - +
36F VAL* 1.3 60.6 + - + +
38F ARG* 3.4 17.1 + - - +
39F ASP* 3.1 24.9 + - - +
86F ALA 5.2 3.6 - - - +
87F ASP* 5.2 1.6 - - - +
380F ARG* 3.6 33.4 + - - +
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Residues in contact with VAL 36 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33F ALA 5.0 6.1 - - - +
34F THR 3.1 0.4 + - - -
35F ALA* 1.3 77.5 - - + +
37F GLU* 1.3 78.9 + - + +
39F ASP* 4.0 8.1 - - - +
40F ARG* 3.0 40.6 + - + +
374F PRO 3.3 26.0 - - - +
375F ARG* 3.8 17.7 - - - +
376F TYR 4.4 10.3 - - - +
377F GLY* 4.0 13.9 - - - +
380F ARG* 4.9 5.4 - - - +
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Residues in contact with GLU 37 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33F ALA 4.4 5.8 - - - +
34F THR* 2.9 26.6 + - + +
36F VAL* 1.3 97.5 - - + +
38F ARG* 1.3 66.0 + - - +
39F ASP 3.3 0.2 + - - -
40F ARG* 2.8 32.7 + - - +
41F ALA* 3.1 25.6 + - - +
375F ARG* 5.4 2.3 - - - +
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Residues in contact with ARG 38 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31F TRP* 2.9 53.7 + - - +
34F THR* 2.5 51.1 + - - +
35F ALA* 3.4 16.1 - - - +
37F GLU* 1.3 74.2 - - - +
39F ASP* 1.3 62.2 + - + +
41F ALA* 3.3 2.9 + - - +
42F GLY 3.3 18.5 + - - -
45F ALA* 4.8 0.2 - - - -
48F GLU* 3.0 38.9 + - - +
86F ALA 4.3 5.5 + - - -
87F ASP* 2.7 40.0 + - - +
90F LEU* 4.2 3.1 - - - +
212F GLN* 3.3 31.4 + - - +
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Residues in contact with ASP 39 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35F ALA 3.1 13.8 + - - +
36F VAL* 4.2 7.1 - - - +
37F GLU 3.3 0.4 - - - -
38F ARG* 1.3 76.2 - - - +
40F ARG* 1.3 64.0 + - - +
42F GLY* 3.9 5.1 + - - +
87F ASP* 6.2 0.4 - - - +
211F ARG* 2.4 47.6 + - - +
212F GLN* 5.2 4.0 - - - -
377F GLY* 4.8 6.8 - - - +
380F ARG* 3.6 27.6 - - + +
383F ARG* 3.0 35.8 + - - -
384F ASN* 5.3 3.7 + - - +
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Residues in contact with ARG 40 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36F VAL* 3.0 36.0 + - + +
37F GLU* 2.8 31.4 + - - +
39F ASP* 1.3 81.7 + - - +
41F ALA* 1.3 64.4 + - - +
211F ARG* 4.2 9.4 + - - +
374F PRO* 3.9 22.3 + - - +
375F ARG* 5.2 1.8 - - - +
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Residues in contact with ALA 41 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37F GLU 3.1 18.1 + - - +
38F ARG* 3.7 4.7 - - - +
40F ARG* 1.3 78.8 - - - +
42F GLY* 1.3 68.9 + - - +
43F GLY 4.0 0.5 + - - -
211F ARG* 5.8 0.2 - - - -
212F GLN* 4.9 1.1 - - - +
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Residues in contact with GLY 42 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38F ARG 3.3 8.1 + - - -
39F ASP 3.9 2.2 + - - -
40F ARG 3.7 1.2 - - - -
41F ALA* 1.3 86.3 - - - +
43F GLY* 1.3 64.1 + - - -
44F SER 4.1 1.6 - - - +
211F ARG* 4.3 19.5 - - - -
212F GLN* 2.9 28.1 + - - -
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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