Contacts of the helix formed by residues 38 - 54 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36A PHE 3.8 0.2 - - - -
37A ARG* 1.3 88.0 + - + +
39A VAL* 1.3 63.8 + - - +
40A THR* 3.3 12.2 + - - -
41A ASP* 3.0 37.7 + - - +
42A VAL* 3.1 15.6 + - - +
124A ILE* 3.5 9.3 - - - +
125A GLU* 4.0 24.9 - - - +
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Residues in contact with VAL 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A THR* 1.3 69.6 - - - +
40A THR* 1.3 60.1 + - - +
42A VAL* 3.1 8.2 + - - +
43A ASP* 2.9 26.0 + - - +
124A ILE* 3.4 19.6 - - + +
125A GLU* 4.5 6.7 + - - +
128A ASP* 3.8 39.9 - - + +
131A LYS* 4.0 33.7 - - + +
132A LEU* 3.9 17.5 - - + +
135A LEU* 3.8 11.4 - - + +
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Residues in contact with THR 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A THR* 3.2 9.9 + - - -
39A VAL* 1.3 74.8 - - - +
41A ASP* 1.3 68.9 + - - +
43A ASP* 3.1 8.0 + - + +
44A ASN* 3.0 37.8 + - - +
131A LYS* 5.4 5.2 + - - +
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Residues in contact with ASP 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A PHE* 4.1 14.8 + - + +
37A ARG* 2.9 33.7 + - - +
38A THR* 3.0 29.4 + - - +
40A THR* 1.3 76.7 - - - +
42A VAL* 1.3 57.7 + - - +
44A ASN* 3.4 12.0 + - - +
45A ALA* 3.0 27.7 + - - +
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Residues in contact with VAL 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A PHE* 4.2 13.7 - - + -
38A THR 3.1 13.3 + - - +
39A VAL* 3.1 9.4 + - - +
41A ASP* 1.3 73.0 - - - +
43A ASP* 1.3 66.2 + - - +
45A ALA* 3.1 7.3 + - - +
46A VAL* 2.9 23.2 + - + +
115A ILE* 4.2 13.0 - - + -
119A ILE* 4.1 19.7 - - + -
124A ILE* 3.6 28.7 - - + -
132A LEU* 4.0 10.8 - - + -
135A LEU* 4.0 25.8 - - + -
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Residues in contact with ASP 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A VAL 2.9 12.5 + - - +
40A THR* 3.5 11.0 - - + +
42A VAL* 1.3 75.1 - - - +
44A ASN* 1.3 60.9 + - - +
46A VAL* 3.3 2.1 + - - +
47A ASN* 2.9 28.3 + - - +
131A LYS* 3.5 28.2 + - - +
135A LEU* 3.5 18.1 - - + +
209A ASN* 5.2 0.7 + - - -
212A ARG* 2.9 35.4 + - - -
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Residues in contact with ASN 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A THR* 3.0 34.7 + - - +
41A ASP* 3.6 13.3 + - - +
43A ASP* 1.3 77.8 - - - +
45A ALA* 1.3 64.7 + - - +
47A ASN* 3.4 10.5 + - - +
48A GLY* 3.1 18.0 + - - -
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Residues in contact with ALA 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A PHE* 3.6 33.4 - - + -
41A ASP 3.0 9.9 + - - +
42A VAL 3.1 7.4 + - - +
44A ASN* 1.3 74.4 - - - +
46A VAL* 1.3 63.2 + - - +
48A GLY* 3.1 12.5 + - - +
49A LEU* 3.3 14.4 + - - +
115A ILE* 3.6 17.1 - - + +
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Residues in contact with VAL 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A VAL* 2.9 29.7 + - + +
43A ASP 3.3 4.2 + - - +
45A ALA* 1.3 74.3 - - - +
47A ASN* 1.3 63.3 + - - +
49A LEU* 3.0 31.6 + - + +
50A TYR* 3.3 12.3 - - + -
115A ILE* 4.1 8.3 - - + -
135A LEU* 4.2 11.7 - - + +
138A GLU* 3.7 24.7 - - + +
139A THR* 3.2 26.7 - - - +
142A VAL* 5.4 0.4 - - + -
212A ARG* 3.3 22.7 - - - +
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Residues in contact with ASN 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A ASP 2.9 14.1 + - - +
44A ASN* 3.4 15.3 - - - +
46A VAL* 1.3 76.7 - - - +
48A GLY* 1.3 56.6 + - - +
50A TYR* 3.0 25.0 + - - +
51A ASP* 3.1 26.5 + - - -
212A ARG* 3.3 30.0 + - - +
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Residues in contact with GLY 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A ASN 3.1 13.4 + - - -
45A ALA* 3.1 6.6 + - - -
47A ASN* 1.3 72.0 - - - +
49A LEU* 1.3 64.9 + - - +
51A ASP* 3.6 15.5 - - - +
52A LEU* 3.0 31.9 + - - +
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Residues in contact with LEU 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A ALA 3.3 9.0 + - - +
46A VAL* 3.0 20.9 + - + +
48A GLY* 1.3 76.4 - - - +
50A TYR* 1.3 60.2 + - + +
52A LEU* 3.3 10.6 + - + +
53A MSE 3.0 29.4 + - - +
108A ILE* 3.9 16.3 - - + +
111A GLU* 3.7 17.9 - - + -
112A ALA* 3.7 34.5 - - + +
115A ILE* 3.9 19.5 - - + -
139A THR* 4.3 8.1 - - + +
142A VAL* 4.0 34.8 - - + -
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Residues in contact with TYR 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A VAL* 3.3 22.9 - - + -
47A ASN* 3.0 9.4 + - - +
49A LEU* 1.3 76.1 - - + +
51A ASP* 1.3 66.1 + - - +
53A MSE 3.1 18.1 + - + +
54A SER* 2.9 24.9 + - - -
138A GLU* 2.6 39.6 + - - +
142A VAL* 3.8 16.4 - - + +
211A GLY 3.5 17.0 - - - +
212A ARG* 3.5 37.0 - - + -
213A MSE 3.1 19.4 + - + +
276A PHE* 3.6 25.4 - + - -
278A ILE* 5.3 4.4 - - + +
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Residues in contact with ASP 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A ASN* 3.1 30.1 + - - +
48A GLY* 3.4 17.6 + - - +
50A TYR* 1.3 76.2 - - - +
52A LEU* 1.3 62.1 + - + +
54A SER* 2.7 24.2 + - - -
55A GLY* 4.0 2.4 + - - -
104A ARG* 5.1 0.3 + - - -
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Residues in contact with LEU 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A GLY 3.0 23.2 + - - +
49A LEU* 3.5 9.9 - - + +
50A TYR 3.2 0.2 - - - -
51A ASP* 1.3 76.4 - - + +
53A MSE 1.3 61.8 - - - +
55A GLY 3.3 4.0 + - - -
104A ARG* 2.9 46.9 + - - +
107A TYR* 3.7 41.1 - - + -
108A ILE* 3.6 19.5 - - + -
111A GLU* 4.2 13.5 - - + -
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Residues in contact with MSE 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A LEU 3.0 17.0 + - - +
50A TYR* 3.1 31.8 + - + +
52A LEU* 1.3 78.1 - - - +
54A SER* 1.3 57.6 + - - +
55A GLY 3.2 1.5 + - - +
58A TYR* 3.8 15.5 - - + +
59A TYR* 2.9 55.7 + - + +
108A ILE* 3.7 11.9 - - + +
142A VAL* 4.0 26.7 - - + -
145A LEU* 4.0 21.8 - - + -
146A CYS* 5.5 2.5 - - - -
213A MSE 5.2 0.2 - - + -
276A PHE* 3.9 22.7 - - + -
278A ILE* 4.4 4.3 - - + -
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Residues in contact with SER 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A TYR 2.9 12.2 + - - -
51A ASP* 2.7 22.2 + - - -
53A MSE 1.3 74.2 - - - +
55A GLY* 1.3 66.0 + - - +
60A GLY* 3.3 14.5 - - - +
278A ILE* 3.4 32.3 - - - +
279A ALA 4.9 6.3 - - - -
285A THR 4.9 6.8 + - - -
286A PRO* 3.5 17.4 - - - +
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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