Contacts of the helix formed by residues 39 - 52 (chain D) 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 PRO 39 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D TYR 3.2 8.0 - - - +
38D THR* 1.3 91.9 - - + +
40D MET* 1.3 65.8 + - - +
41D GLU* 3.2 9.2 - - + +
42D PHE* 3.1 16.6 + - + +
43D VAL* 3.4 9.9 + - - +
97D HIS* 3.4 35.4 - - + +
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Residues in contact with MET 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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12A MET* 3.9 35.4 - - - +
15A ALA* 4.2 5.2 - - + -
16A ARG* 3.8 37.6 - - + +
19A GLU* 3.6 28.7 - - - +
38D THR 3.5 1.8 + - - -
39D PRO* 1.3 70.7 - - - +
41D GLU* 1.3 64.7 + - - +
43D VAL* 3.2 11.9 + - - +
44D ILE* 3.2 26.0 + - + +
62D MET* 3.5 38.8 - - + -
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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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8A LEU* 4.3 20.3 - - + +
12A MET* 3.8 35.8 - - + +
16A ARG* 5.2 2.3 - - - +
39D PRO* 3.2 6.9 - - + +
40D MET* 1.3 78.6 - - - +
42D PHE* 1.3 58.4 + - - +
44D ILE* 3.4 5.9 + - - +
45D ASP* 2.9 28.0 + - + +
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Residues in contact with PHE 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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38D THR* 3.8 14.4 - - + -
39D PRO* 3.1 15.6 + - + +
41D GLU* 1.3 77.3 - - - +
43D VAL* 1.3 60.7 + - - +
45D ASP* 3.1 11.4 + - - +
46D VAL* 2.9 40.1 + - + +
91D TYR* 3.5 42.0 - + - -
92D ALA* 3.7 26.7 - - + -
95D ASN* 3.6 20.2 - - + -
97D HIS* 3.3 35.9 - + + +
99D LEU* 4.0 9.4 - - + -
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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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32D LEU* 4.6 13.0 - - + -
38D THR* 3.8 19.5 - - + +
39D PRO 3.7 14.1 - - - +
40D MET* 3.2 9.3 + - - +
42D PHE* 1.3 75.9 - - - +
44D ILE* 1.3 59.0 + - - +
46D VAL* 3.3 3.3 + - - +
47D LEU* 3.0 41.6 + - + +
62D MET* 3.8 25.4 - - + -
65D VAL* 5.0 13.0 - - + -
99D LEU* 4.3 18.8 - - + -
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Residues in contact with ILE 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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8A LEU* 3.8 21.1 - - + -
12A MET* 3.9 28.7 - - + -
40D MET* 3.2 23.3 + - + +
41D GLU 3.7 5.8 - - - +
43D VAL* 1.3 77.4 - - - +
45D ASP* 1.3 62.7 + - - +
47D LEU* 3.2 3.6 + - - +
48D GLN* 3.0 35.3 + - - +
55D VAL* 4.8 2.7 - - + -
58D ALA* 4.0 16.6 - - + -
59D THR* 3.8 30.3 - - + +
62D MET* 4.0 19.5 - - + -
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Residues in contact with ASP 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* 2.9 15.4 + - + +
42D PHE* 3.3 18.2 - - - +
44D ILE* 1.3 77.2 - - - +
46D VAL* 1.3 58.5 + - - +
48D GLN* 3.2 6.8 + - - +
49D LYS* 2.8 38.2 + - - +
91D TYR* 2.5 37.6 + - - -
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Residues in contact with VAL 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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32D LEU* 4.3 15.0 - - + -
42D PHE* 2.9 40.3 + - + +
43D VAL 3.6 6.5 - - - +
45D ASP* 1.3 77.2 - - - +
47D LEU* 1.3 58.1 + - - +
49D LYS* 4.6 0.4 - - - -
50D PHE* 2.9 38.4 + - + +
51D PHE* 3.8 3.8 - - + -
88D VAL* 3.7 35.4 - - + +
91D TYR* 3.9 18.2 - - + -
99D LEU* 3.7 14.8 - - + -
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Residues in contact with LEU 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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32D LEU* 3.7 24.0 - - + -
43D VAL* 3.0 39.5 + - + +
44D ILE 3.2 4.2 + - - +
46D VAL* 1.3 75.5 - - - +
48D GLN* 1.3 61.5 + - - +
51D PHE* 3.2 26.0 + - + +
52D SER 3.3 6.1 + - - -
53D TYR* 3.3 29.8 + - + -
58D ALA* 3.3 34.1 - - + +
61D LEU* 4.0 13.0 - - + -
62D MET* 3.9 10.5 - - + +
65D VAL* 5.6 0.7 - - + -
73D CYS* 3.7 16.8 - - - -
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Residues in contact with GLN 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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4A GLN* 2.8 29.5 + - - +
8A LEU* 5.1 1.6 - - - +
73B GLU* 5.2 6.8 - - - +
44D ILE* 3.0 29.7 + - + +
45D ASP* 3.7 6.2 - - - +
47D LEU* 1.3 77.1 - - - +
49D LYS* 1.3 64.1 + - + +
52D SER* 3.2 19.9 + - - -
53D TYR 3.1 26.6 + - - +
54D ASP* 3.3 2.4 - - - +
55D VAL* 3.2 34.6 - - - +
58D ALA* 3.9 11.7 - - + -
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Residues in contact with LYS 49 (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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73B GLU* 5.5 3.3 - - - +
76B ARG* 3.4 24.1 + - - +
45D ASP* 2.8 24.9 + - - +
48D GLN* 1.3 81.3 - - + +
50D PHE* 1.3 82.5 + - + +
52D SER* 4.8 1.7 + - - -
91D TYR* 3.7 42.2 - - + +
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Residues in contact with PHE 50 (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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23B GLU* 5.7 0.4 - - - -
76B ARG* 3.7 23.6 - - - +
46D VAL* 2.9 23.6 + - + +
49D LYS* 1.3 103.8 - - + +
51D PHE* 1.3 68.6 + - + +
52D SER* 3.7 1.1 - - - -
84D LYS* 2.7 34.0 + - + +
87D MET* 3.8 38.6 - - + -
88D VAL* 3.8 27.8 - - + -
91D TYR* 3.6 46.7 - + + -
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Residues in contact with PHE 51 (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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30D VAL* 3.8 28.3 - - + -
32D LEU* 4.9 2.9 - - + -
46D VAL* 3.8 18.2 - - + -
47D LEU* 3.2 20.5 + - + +
50D PHE* 1.3 85.3 - - + +
52D SER* 1.3 75.8 + - - +
53D TYR* 3.3 23.7 + - + -
73D CYS* 3.5 40.2 - - + +
76D PHE* 4.3 16.2 - + - -
84D LYS* 4.1 17.0 - - + +
88D VAL* 3.7 30.3 - - + -
101D CYS* 4.5 1.6 - - - -
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Residues in contact with SER 52 (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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23B GLU* 5.7 0.9 + - - -
70B PRO* 3.9 26.0 - - - +
73B GLU* 4.9 6.9 + - - -
47D LEU 3.3 0.2 + - - -
48D GLN 3.2 17.8 + - - -
49D LYS 4.6 1.8 + - - -
50D PHE 3.7 1.1 - - - -
51D PHE* 1.3 80.9 - - - +
53D TYR* 1.3 65.4 + - - +
54D ASP 3.8 0.3 + - - -
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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