Contacts of the helix formed by residues 39 - 48 (chain D) in PDB entry 3M0V
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 ASP 39 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D GLY 4.4 0.2 + - - -
38D VAL* 1.3 73.9 - - - +
40D ILE* 1.3 65.6 + - - +
41D GLU* 2.9 28.5 + - - +
42D ALA* 2.9 32.5 + - + +
43D VAL* 3.4 8.1 + - - +
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Residues in contact with ILE 40 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26D TYR* 3.5 49.8 - - + +
29D LEU* 4.1 9.9 - - + -
30D GLY* 3.7 37.8 + - - +
33D LEU* 4.0 22.4 - - + +
38D VAL 3.5 6.1 + - - -
39D ASP* 1.3 74.3 + - - +
41D GLU* 1.3 70.9 + - + +
43D VAL* 3.2 5.7 + - - +
44D THR* 3.0 26.2 + - - -
388D ILE* 4.0 19.3 - - + -
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Residues in contact with GLU 41 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26D TYR* 2.7 31.1 + - - -
39D ASP* 2.9 18.0 + - - +
40D ILE* 1.3 87.1 - - + +
42D ALA* 1.3 55.2 + - - +
44D THR* 3.5 2.1 + - - -
45D ALA* 3.0 28.1 + - - +
395D ARG* 2.8 36.7 + - - -
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Residues in contact with ALA 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39D ASP* 2.9 24.7 + - + +
41D GLU* 1.3 76.2 - - - +
43D VAL* 1.3 66.5 + - + +
45D ALA* 3.4 7.7 + - - +
46D LYS* 3.3 29.5 + - - +
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Residues in contact with VAL 43 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38D VAL* 3.9 20.9 - - + -
39D ASP 3.8 11.9 - - - +
40D ILE* 3.6 8.5 - - - +
42D ALA* 1.3 75.9 - - + +
44D THR* 1.3 67.5 + - - +
46D LYS* 3.1 5.2 + - - +
47D VAL* 2.9 37.4 + - + +
351D ALA* 4.4 14.1 - - + +
354D LEU* 4.4 21.8 - - + +
355D LEU* 3.9 14.4 - - + -
388D ILE* 3.8 23.1 - - + -
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Residues in contact with THR 44 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26D TYR* 2.8 28.0 + - - +
40D ILE* 3.0 11.7 + - - +
41D GLU 3.8 4.5 - - - -
42D ALA 3.4 0.2 - - - -
43D VAL* 1.3 76.3 - - - +
45D ALA* 1.3 62.7 + - - +
47D VAL* 3.2 1.7 + - - +
48D GLU* 3.0 31.9 + - - +
388D ILE* 3.5 22.5 - - - +
391D GLU* 4.6 2.5 - - + -
392D ALA* 4.2 28.5 - - + +
395D ARG* 3.9 23.6 - - - +
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Residues in contact with ALA 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41D GLU 3.0 17.6 + - - +
42D ALA* 3.5 9.2 - - - +
43D VAL 3.2 0.2 - - - -
44D THR* 1.3 77.7 - - - +
46D LYS* 1.3 60.7 + - + +
48D GLU* 3.1 29.3 - - - +
49D LYS* 3.4 22.0 - - - +
395D ARG* 5.8 0.4 - - - +
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Residues in contact with LYS 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42D ALA* 3.3 13.6 + - - +
43D VAL* 3.1 8.7 + - - +
45D ALA* 1.3 76.0 - - + +
47D VAL* 1.3 66.5 + - - +
49D LYS* 3.0 20.5 + - + +
50D PHE 3.2 8.8 + - - -
313D GLU* 4.3 19.7 + - - +
350D TYR* 3.8 20.1 + - - +
354D LEU* 3.7 35.1 - - + +
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Residues in contact with VAL 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43D VAL* 2.9 24.2 + - + +
44D THR* 3.6 7.2 - - - +
46D LYS* 1.3 77.0 - - - +
48D GLU* 1.3 60.0 + - - +
49D LYS 3.1 1.4 + - - -
50D PHE* 3.1 6.1 + - - +
347D ARG* 3.0 46.9 + - + -
350D TYR* 4.3 12.3 - - + -
351D ALA* 3.8 30.3 - - + -
354D LEU* 4.7 1.6 - - + -
388D ILE* 4.0 11.4 - - + -
389D LEU* 3.9 18.4 - - + -
392D ALA* 4.1 14.6 - - + -
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Residues in contact with GLU 48 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44D THR* 3.0 21.6 + - - +
45D ALA* 3.1 22.9 - - - +
47D VAL* 1.3 76.1 - - - +
49D LYS* 1.3 64.1 + - + +
50D PHE 3.5 0.2 - - - -
51D PHE* 3.5 11.8 - - - -
93D ARG 4.8 0.5 - - - +
347D ARG* 3.3 21.8 + - - +
392D ALA* 4.1 13.4 - - + +
395D ARG* 4.3 22.0 - - - +
396D THR* 3.8 32.9 - - + +
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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