Contacts of the helix formed by residues 38 - 54 (chain B) in PDB entry 3MYV
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 38 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37B ARG* 1.3 84.7 - - + +
39B VAL* 1.3 65.0 + - - +
40B THR* 3.4 12.3 + - - -
41B ASP* 3.0 41.5 + - - +
42B VAL* 3.1 15.4 + - - +
124B ILE* 3.5 5.4 - - - -
125B GLU* 4.6 11.7 - - + +
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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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38B THR* 1.3 72.4 - - - +
40B THR* 1.3 56.6 + - - +
42B VAL* 3.2 6.3 + - - +
43B ASP* 2.9 26.9 + - - +
124B ILE* 3.6 14.5 - - + +
125B GLU 4.2 11.1 + - - +
126B SER 5.7 0.4 - - - +
128B ASP* 3.9 31.2 - - + +
131B LYS* 3.7 40.8 - - + +
132B LEU* 4.1 17.5 - - + +
135B LEU* 3.8 8.0 - - + +
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Residues in contact with THR 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B THR* 3.2 10.1 + - - -
39B VAL* 1.3 76.0 - - - +
41B ASP* 1.3 62.0 + - - +
43B ASP* 3.2 10.7 + - + +
44B ASN* 3.0 42.9 + - - +
131B LYS* 5.5 5.6 + - - +
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Residues in contact with ASP 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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36B PHE* 4.1 18.0 + - + +
37B ARG* 3.2 19.9 + - - +
38B THR* 3.0 42.2 + - - +
40B THR* 1.3 78.5 - - - +
42B VAL* 1.3 58.6 + - - +
44B ASN* 3.4 12.3 + - - +
45B ALA* 3.0 28.6 + - - +
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Residues in contact with VAL 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B PHE* 4.4 9.4 - - + -
38B THR 3.1 9.0 + - - +
39B VAL 3.2 7.6 + - - +
41B ASP* 1.3 72.6 - - - +
43B ASP* 1.3 61.2 + - - +
45B ALA* 3.2 6.5 + - - +
46B VAL* 2.8 35.0 + - + +
115B ILE* 3.9 22.2 - - + -
119B ILE* 4.1 12.6 - - + -
124B ILE* 3.4 42.8 - - + -
132B LEU* 4.1 6.7 - - + -
135B LEU* 4.0 24.5 - - + -
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Residues in contact with ASP 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B VAL 2.9 13.3 + - - +
40B THR* 3.2 14.8 + - - +
42B VAL* 1.3 76.0 - - - +
44B ASN* 1.3 62.3 + - - +
46B VAL* 3.2 2.1 + - - +
47B ASN* 2.9 28.6 + - - +
131B LYS* 3.8 23.9 + - - +
135B LEU* 3.7 17.7 - - + +
209B ASN* 5.1 1.4 + - - -
212B ARG* 2.9 32.6 + - - -
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Residues in contact with ASN 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 THR* 3.0 39.1 + - - +
41B ASP* 3.8 11.2 + - - +
43B ASP* 1.3 80.7 - - - +
45B ALA* 1.3 57.9 + - - +
47B ASN* 3.3 9.8 - - - +
48B GLY* 3.0 23.9 + - - -
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Residues in contact with ALA 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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36B PHE* 3.6 31.0 - - + -
41B ASP 3.0 18.7 + - - +
42B VAL 3.5 5.2 - - - +
44B ASN* 1.3 74.1 - - - +
46B VAL* 1.3 64.9 + - - +
48B GLY* 3.2 11.0 + - - -
49B LEU* 3.3 14.6 + - - +
115B ILE* 3.6 14.6 - - + +
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Residues in contact with VAL 46 (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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42B VAL* 2.8 32.2 + - + +
43B ASP 3.2 4.5 + - - +
45B ALA* 1.3 72.2 - - - +
47B ASN* 1.3 63.3 + - - +
49B LEU* 3.0 31.8 + - + +
50B TYR* 3.3 15.1 - - + -
115B ILE* 4.2 5.4 - - + -
135B LEU* 4.2 14.4 - - + +
138B GLU* 3.6 24.7 - - + +
139B THR* 3.2 26.9 - - - +
142B VAL* 5.5 0.2 - - + -
212B ARG* 3.2 24.2 - - - +
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Residues in contact with ASN 47 (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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43B ASP 2.9 13.4 + - - +
44B ASN* 3.3 14.8 - - - +
46B VAL* 1.3 76.2 - - - +
48B GLY* 1.3 56.6 + - - +
50B TYR* 3.0 26.5 + - - +
51B ASP* 3.1 25.8 + - - -
212B ARG* 3.1 30.9 + - - +
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Residues in contact with GLY 48 (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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44B ASN 3.0 13.3 + - - -
45B ALA* 3.2 6.1 + - - -
47B ASN* 1.3 72.0 - - - +
49B LEU* 1.3 65.4 + - - +
51B ASP* 3.2 16.4 + - - +
52B LEU* 3.0 32.2 + - - +
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Residues in contact with LEU 49 (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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45B ALA 3.3 8.3 + - - +
46B VAL* 3.0 20.2 + - + +
48B GLY* 1.3 74.4 - - - +
50B TYR* 1.3 60.8 + - + +
52B LEU* 3.3 11.4 + - + +
53B MSE 2.9 28.0 + - - +
108B ILE* 4.0 14.8 - - + +
111B GLU* 3.8 17.3 - - + -
112B ALA* 3.7 42.6 - - + +
115B ILE* 4.0 17.5 - - + -
139B THR* 4.1 11.0 - - + +
142B VAL* 4.2 27.8 - - + -
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Residues in contact with TYR 50 (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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46B VAL* 3.3 29.4 - - + -
47B ASN* 3.0 9.2 + - - +
49B LEU* 1.3 77.0 - - + +
51B ASP* 1.3 65.6 + - - +
53B MSE 3.1 26.3 + - + +
54B SER* 2.9 24.8 + - - -
138B GLU* 2.8 40.0 + - - +
142B VAL* 3.8 16.5 - - + +
211B GLY 3.6 16.6 - - - +
212B ARG* 3.6 24.0 - - + -
213B MSE 3.1 24.0 + - + +
276B PHE* 3.6 28.7 - + - -
278B ILE* 5.4 3.8 - - + +
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Residues in contact with ASP 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B ASN* 3.1 24.0 + - - +
48B GLY* 3.2 21.0 + - - +
50B TYR* 1.3 76.0 - - - +
52B LEU* 1.3 63.7 + - + +
54B SER* 2.8 24.3 + - - -
55B GLY* 3.8 2.9 + - - -
104B ARG* 4.8 0.5 + - - -
284B ASP* 4.5 15.4 - - - +
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Residues in contact with LEU 52 (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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48B GLY 3.0 22.2 + - - +
49B LEU* 3.4 12.3 - - + +
50B TYR 3.2 0.2 - - - -
51B ASP* 1.3 77.5 - - + +
53B MSE 1.3 60.6 + - - +
55B GLY 3.3 4.5 + - - -
104B ARG* 2.8 49.1 + - - +
107B TYR* 3.7 40.2 - - + -
108B ILE* 3.7 17.3 - - + -
111B GLU* 4.2 14.6 - - + +
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Residues in contact with MSE 53 (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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49B LEU 2.9 13.1 + - - +
50B TYR* 3.1 46.8 + - + +
52B LEU* 1.3 77.9 - - - +
54B SER* 1.3 56.0 + - - +
55B GLY 3.2 1.3 + - - +
58B TYR* 3.8 13.9 - - + +
59B TYR* 2.9 62.2 + - + +
108B ILE* 3.7 11.2 - - + +
142B VAL* 4.3 22.0 - - + -
145B LEU* 4.1 12.3 - - - -
146B CYS* 6.0 1.8 - - - -
213B MSE 5.3 0.2 - - + -
276B PHE* 3.8 24.5 - - - -
278B ILE* 4.4 4.0 - - + -
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Residues in contact with SER 54 (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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50B TYR 2.9 13.4 + - - -
51B ASP* 2.8 18.0 + - - -
53B MSE 1.3 72.8 - - - +
55B GLY* 1.3 68.4 + - - +
60B GLY* 3.2 15.1 - - - +
278B ILE* 3.5 30.8 - - - +
279B ALA 5.3 3.1 - - - -
280B ASN* 4.4 7.4 + - - -
284B ASP* 4.9 7.4 + - - -
286B PRO* 3.4 15.1 - - - +
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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