Contacts of the helix formed by residues 14 - 23 (chain F) in PDB entry 5BMU
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 14 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6F LEU* 4.4 6.1 - - + -
8F VAL* 2.8 36.6 - - + -
12F ASP 4.0 0.6 - - - -
13F PRO* 1.3 76.0 - - + +
15F LEU* 1.3 60.6 + - - +
16F GLY 3.3 1.6 - - - -
17F ALA* 3.4 24.7 - - + +
18F LEU* 2.9 30.4 + - + +
38F ASN* 3.4 25.0 - - - +
51F VAL* 4.6 11.7 - - + -
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Residues in contact with LEU 15 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13F PRO* 3.0 20.9 + - + +
14F PRO* 1.3 70.0 - - - +
16F GLY* 1.3 68.3 + - - +
18F LEU* 3.2 6.2 + - + +
19F LEU* 2.9 32.3 + - + +
125F TRP* 5.0 8.3 - - + -
126F ALA* 3.6 30.9 - - + +
129F LYS* 4.1 24.7 - - + -
130F GLY* 4.5 7.4 - - - +
163F VAL 6.0 0.2 - - - +
164F GLY* 5.3 14.1 - - - +
167F TRP* 4.7 17.7 - - + +
168F ASP* 5.4 8.3 - - - +
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Residues in contact with GLY 16 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14F PRO* 3.3 0.4 - - - +
15F LEU* 1.3 79.5 - - - +
17F ALA* 1.3 61.6 + - - +
19F LEU* 3.2 7.6 - - - +
20F ALA* 3.0 20.8 + - - +
51F VAL* 6.1 1.5 - - - +
55F LEU* 3.6 11.3 - - - +
122F LEU* 3.9 16.1 - - - +
123F SER* 5.0 2.2 - - - -
126F ALA* 3.1 22.8 - - - +
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Residues in contact with ALA 17 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6F LEU* 4.6 8.1 - - + -
14F PRO* 3.4 29.3 - - + +
15F LEU 3.1 0.6 - - - -
16F GLY* 1.3 76.8 - - - +
18F LEU* 1.3 63.5 + - - +
20F ALA* 2.9 13.0 + - - +
21F VAL* 2.9 19.7 + - + +
51F VAL* 4.7 10.6 - - + +
54F ILE* 4.7 16.4 - - + -
55F LEU* 3.6 17.3 - - + +
58F LEU* 4.8 0.6 - - - +
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Residues in contact with LEU 18 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6F LEU* 3.7 22.0 - - + -
8F VAL* 4.4 9.9 - - + -
13F PRO* 4.1 6.7 - - + -
14F PRO* 2.9 37.5 + - + +
15F LEU* 3.7 7.0 - - + +
17F ALA* 1.3 76.4 - - - +
19F LEU* 1.3 62.2 + - - +
21F VAL* 3.6 10.7 - - + +
22F GLU* 3.4 29.2 + - + +
163F VAL* 3.7 15.0 - - + +
167F TRP* 3.5 51.4 - - + +
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Residues in contact with LEU 19 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15F LEU* 2.9 22.7 + - + +
16F GLY* 3.2 18.2 - - - +
18F LEU* 1.3 79.2 - - - +
20F ALA* 1.3 59.2 + - - +
22F GLU* 4.0 0.9 - - - +
23F HIS* 2.9 34.7 + - - +
122F LEU* 4.0 22.2 - - + +
125F TRP* 3.7 29.6 - - + -
126F ALA* 4.8 0.2 - - + -
159F ALA* 5.0 1.0 - - - +
160F PHE* 3.6 45.3 - - + +
163F VAL* 3.8 25.3 - - + +
164F GLY* 5.4 1.3 - - - +
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Residues in contact with ALA 20 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16F GLY 3.0 8.2 + - - +
17F ALA* 2.9 9.3 + - - +
19F LEU* 1.3 81.5 - - - +
21F VAL* 1.3 63.0 + - - +
23F HIS* 3.5 12.3 + - - +
24F VAL* 3.5 15.2 - - - +
55F LEU* 3.8 17.5 - - + -
58F LEU* 4.7 14.6 - - + +
67F LEU* 4.3 4.8 - - + +
119F LEU* 4.3 7.9 - - + -
122F LEU* 3.5 20.0 - - + -
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Residues in contact with VAL 21 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6F LEU* 3.7 32.3 - - + -
17F ALA* 2.9 19.3 + - + +
18F LEU* 3.6 12.1 - - + +
19F LEU 3.2 0.2 - - - -
20F ALA* 1.3 76.7 - - - +
22F GLU* 1.3 67.8 + - + +
23F HIS 3.1 0.2 - - - -
24F VAL* 2.9 19.7 + - - +
30F ILE* 3.1 53.3 - - + +
31F SER 5.3 0.9 - - - +
40F LEU* 5.7 0.4 - - + -
58F LEU* 3.8 24.7 - - + -
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Residues in contact with GLU 22 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18F LEU* 3.4 19.4 + - + +
19F LEU 4.6 0.9 - - - +
21F VAL* 1.3 80.7 - - + +
23F HIS* 1.3 59.6 + - - +
24F VAL 3.0 5.3 + - - -
25F LYS* 3.2 53.7 + - + +
30F ILE* 5.7 0.2 - - + -
159F ALA* 5.4 8.1 - - + +
162F SER* 4.7 4.7 + - - -
163F VAL* 3.5 34.4 + - + +
166F LYS* 5.0 11.3 + - - +
167F TRP* 4.5 8.1 + - - -
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Residues in contact with HIS 23 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19F LEU* 2.9 26.2 + - - +
20F ALA* 3.5 9.6 - - - +
21F VAL 3.1 0.4 - - - -
22F GLU* 1.3 77.6 - - - +
24F VAL* 1.3 64.0 + - + +
25F LYS 3.8 0.2 - - - -
27F ASP* 5.2 0.5 - - - +
65F ALA* 4.9 4.3 - - - +
67F LEU* 5.2 9.6 - - + +
117F LEU* 3.1 34.9 - - + +
122F LEU* 4.3 8.6 - - + +
157F GLN* 5.4 3.4 + - - -
159F ALA* 3.8 26.6 - - + +
160F PHE* 3.6 23.9 - + - -
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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