Contacts of the helix formed by residues 20 - 29 (chain C) in PDB entry 3LBF
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 ASP 20 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C ILE* 3.7 1.4 - - - +
19C GLN* 1.3 74.5 - - - +
21C GLU* 1.3 62.2 + - - +
22C GLN* 3.1 23.6 + - - +
23C VAL* 3.2 35.9 + - + +
24C LEU* 3.3 16.1 + - - +
69C GLU* 3.5 25.4 + - + +
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Residues in contact with GLU 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C ARG* 2.7 46.4 + - - -
19C GLN 3.0 11.7 + - - +
20C ASP* 1.3 73.1 + - - +
22C GLN* 1.3 56.9 + - - +
24C LEU* 3.3 12.0 + - - +
25C ASN* 3.0 54.7 + - - +
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Residues in contact with GLN 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C ASP* 3.1 13.1 + - - +
21C GLU* 1.3 76.3 - - - +
23C VAL* 1.3 65.0 + - + +
25C ASN* 3.4 12.0 + - - +
26C ALA* 3.1 17.0 + - - +
96C LEU* 3.6 19.4 - - + +
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Residues in contact with VAL 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C ILE* 5.2 2.7 - - + -
20C ASP* 3.2 33.5 + - + +
22C GLN* 1.3 79.5 - - + +
24C LEU* 1.3 56.6 + - - +
26C ALA* 3.2 4.2 + - - +
27C LEU* 2.9 29.0 + - + +
65C ALA* 3.9 36.8 - - + +
68C THR* 3.9 29.2 - - + +
69C GLU* 4.2 11.4 - - + +
73C LEU* 6.0 0.7 - - + -
92C ILE* 4.8 4.8 - - + +
96C LEU* 4.2 13.2 - - + -
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Residues in contact with LEU 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C LEU* 3.4 23.1 - - + +
13C LEU* 3.9 31.2 - - + -
14C ARG* 3.5 42.2 - - + +
18C ILE* 3.7 29.2 - - + +
19C GLN 5.4 0.4 - - - -
20C ASP 3.3 12.4 + - - +
21C GLU* 3.6 23.8 - - - +
22C GLN 3.3 0.4 - - - -
23C VAL* 1.3 76.7 - - - +
25C ASN* 1.3 58.7 + - - +
27C LEU* 3.8 4.0 - - + +
28C ALA* 2.9 30.3 + - - +
65C ALA* 4.8 2.7 - - + -
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Residues in contact with ASN 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C GLU* 3.0 46.0 + - - +
22C GLN* 3.6 10.6 - - - +
24C LEU* 1.3 78.7 - - - +
26C ALA* 1.3 56.7 + - - +
28C ALA* 3.3 8.4 + - - +
29C ALA* 3.0 27.4 + - - +
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Residues in contact with ALA 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C GLN 3.1 13.6 + - - +
23C VAL 3.6 7.2 - - - +
25C ASN* 1.3 74.9 - - - +
27C LEU* 1.3 64.2 + - - +
29C ALA* 3.0 21.5 + - - +
30C VAL* 3.4 16.0 + - - +
92C ILE* 3.9 11.4 - - + +
95C HIS* 3.8 25.0 - - + -
96C LEU* 3.8 20.0 - - + -
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Residues in contact with LEU 27 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C LEU* 4.1 21.5 - - + -
10C LEU* 4.0 17.0 - - + -
13C LEU* 3.9 15.0 - - + -
23C VAL* 2.9 17.3 + - + +
24C LEU* 3.8 6.7 - - + +
26C ALA* 1.3 75.8 - - - +
28C ALA* 1.3 63.4 + - - +
30C VAL* 3.2 22.2 + - - +
45C TRP* 4.4 6.5 - - + -
61C PRO 3.8 23.6 - - - +
64C VAL* 4.5 1.8 - - + -
65C ALA* 4.2 14.1 - - + +
88C TYR* 3.5 25.0 + - - +
92C ILE* 4.1 22.8 - - + +
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Residues in contact with ALA 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2C VAL 6.1 2.0 - - - +
6C VAL* 3.7 33.7 - - + +
10C LEU* 4.2 9.0 - - + -
24C LEU 2.9 18.9 + - - +
25C ASN* 3.6 8.5 - - - +
26C ALA 3.3 0.2 - - - -
27C LEU* 1.3 76.9 - - - +
29C ALA* 1.3 59.6 + - - +
30C VAL 3.3 3.9 + - - +
45C TRP* 4.6 4.7 - - - -
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Residues in contact with ALA 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C ASN 3.0 12.2 + - - +
26C ALA* 3.0 15.0 + - - +
28C ALA* 1.3 75.8 - - - +
30C VAL* 1.3 58.4 + - - +
31C PRO* 3.8 7.8 - - - +
95C HIS* 3.9 28.0 + - + +
120C LEU* 5.7 0.5 - - - +
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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