Contacts of the helix formed by residues 37 - 47 (chain A) in PDB entry 1MBU
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 ASN 37 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5A GLU* 3.5 25.0 + - - +
6A LEU* 3.6 15.0 - - - +
9A SER* 3.4 26.0 + - - +
33A ALA 3.6 1.0 + - - -
34A LEU* 2.9 24.4 + - + +
36A SER* 1.3 77.8 - - - +
38A PRO* 1.3 70.9 - - - +
39A SER* 3.4 7.9 + - - -
40A ALA 3.1 24.9 + - - -
41A ARG* 2.8 22.5 + - - +
105A GLY* 3.3 21.8 - - - +
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Residues in contact with PRO 38 (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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5A GLU* 3.3 37.7 - - + +
36A SER 3.3 9.8 - - - +
37A ASN* 1.3 85.8 - - + +
39A SER* 1.3 63.9 + - - +
41A ARG* 3.6 28.8 - - - +
42A GLU* 2.8 33.3 + - + +
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Residues in contact with SER 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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3A ASN* 5.6 2.7 - - - -
5A GLU* 4.9 3.2 + - - -
37A ASN* 3.4 11.1 + - - -
38A PRO* 1.3 80.7 - - - +
40A ALA* 1.3 63.1 + - - +
42A GLU* 3.6 5.8 + - - +
43A ALA* 3.4 18.4 + - - +
104A THR* 3.2 14.6 + - - -
105A GLY 3.9 5.6 - - - -
106A ALA* 2.9 31.8 + - - +
137A PHE* 4.8 2.3 - - - -
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Residues in contact with ALA 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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34A LEU* 3.7 28.3 - - + +
37A ASN* 3.1 7.8 + - - +
39A SER* 1.3 78.5 + - - +
41A ARG* 1.3 66.4 + - - +
43A ALA* 3.2 4.2 + - - +
44A LEU* 3.0 29.9 + - + +
105A GLY 3.7 22.4 - - - +
106A ALA* 4.0 7.9 - - - +
109A LEU* 3.9 13.8 - - + +
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Residues in contact with ARG 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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34A LEU 3.8 1.9 + - - -
35A LEU 3.4 24.2 - - - +
36A SER* 4.2 19.2 + - - +
37A ASN 2.8 21.9 + - - +
38A PRO* 3.6 27.8 - - - +
40A ALA* 1.3 73.4 - - - +
42A GLU* 1.3 72.7 + - - +
44A LEU* 3.0 9.5 + - - +
45A GLU* 2.8 48.6 + - - +
51A LEU* 3.9 12.8 - - + -
143A YBT 3.2 32.6 + - - -
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Residues in contact with GLU 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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38A PRO* 2.8 28.3 + - + +
39A SER* 3.8 6.1 - - - +
41A ARG* 1.3 84.6 + - - +
43A ALA* 1.3 58.6 + - - +
45A GLU* 3.0 8.9 + - - +
46A ALA* 2.9 29.6 + - - +
137A PHE* 3.8 18.5 - - + -
143A YBT 2.6 56.6 + - - -
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Residues in contact with ALA 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 SER 3.4 9.2 + - - +
40A ALA* 3.2 9.5 + - - +
41A ARG 3.2 0.6 - - - -
42A GLU* 1.3 77.6 - - - +
44A LEU* 1.3 65.1 + - - +
46A ALA* 3.3 3.3 + - - +
47A CYS* 3.2 27.9 + - - -
106A ALA* 4.8 4.0 - - + -
109A LEU* 4.1 15.9 - - + -
134A VAL* 4.3 16.6 - - + -
137A PHE* 3.5 30.5 - - + -
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Residues in contact with LEU 44 (chain A).
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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31A LEU* 4.9 6.3 - - + -
34A LEU* 5.1 2.0 - - + +
35A LEU* 3.6 32.3 - - + -
40A ALA* 3.0 23.0 + - + +
41A ARG* 3.0 8.0 + - - +
43A ALA* 1.3 72.8 - - - +
45A GLU* 1.3 66.6 + - - +
47A CYS* 3.0 12.9 + - - -
49A VAL* 3.2 36.6 + - + +
51A LEU* 3.8 21.1 - - + -
54A LEU* 4.6 2.9 - - + -
109A LEU* 4.0 18.4 - - + -
124A LEU* 3.9 26.0 - - + -
129A VAL* 4.7 9.9 - - + -
134A VAL* 5.7 0.2 - - + -
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Residues in contact with GLU 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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41A ARG* 2.8 29.1 + - - +
42A GLU* 3.0 13.6 - - - +
44A LEU* 1.3 70.9 - - - +
46A ALA* 1.3 61.8 + - - +
47A CYS 2.9 1.8 - - - -
48A SER* 2.7 23.5 + - - +
49A VAL 4.7 5.4 - - - +
51A LEU* 4.1 17.4 - - + +
143A YBT 2.4 61.1 + - - +
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Residues in contact with ALA 46 (chain A).
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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42A GLU 2.9 10.2 + - - +
43A ALA 3.6 4.5 - - - +
44A LEU 3.2 0.2 - - - -
45A GLU* 1.3 76.4 - - - +
47A CYS* 1.3 61.5 + - - +
48A SER* 3.2 5.0 + - - -
137A PHE* 3.3 42.8 - - + -
142A THR* 4.5 15.8 - - - +
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Residues in contact with CYS 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 ALA 3.2 17.0 + - - +
44A LEU* 3.0 9.0 + - - +
45A GLU 2.9 1.4 - - - -
46A ALA* 1.3 80.5 - - - +
48A SER* 1.3 70.4 + - - +
49A VAL* 3.3 6.1 + - + +
127A HIS 5.0 2.4 - - - +
128A GLU 5.4 2.5 - - - +
129A VAL* 4.0 30.8 - - + +
133A ASP* 3.9 37.7 - - - +
134A VAL* 4.9 3.6 - - - -
137A PHE* 5.6 2.5 - - - -
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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