Contacts of the helix formed by residues 20 - 30 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18D ILE* 3.7 2.3 - - + +
19D GLN* 1.3 75.8 - - - +
21D GLU* 1.3 57.0 + - - +
22D GLN* 3.1 27.7 + - - +
23D VAL* 3.1 33.7 + - + +
24D LEU* 3.0 27.7 + - - +
69D GLU* 3.0 26.7 + - + +
72D GLU* 5.4 2.8 - - - -
73D LEU 5.3 9.2 + - - +
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Residues in contact with GLU 21 (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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14D ARG* 3.1 38.2 + - - +
18D ILE 5.0 1.7 - - - +
19D GLN* 3.2 13.1 + - - +
20D ASP* 1.3 71.7 + - - +
22D GLN* 1.3 68.2 + - - +
24D LEU* 3.4 22.0 - - - +
25D ASN* 2.8 41.3 + - - +
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Residues in contact with GLN 22 (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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20D ASP* 3.2 13.7 - - - +
21D GLU* 1.3 84.4 + - - +
23D VAL* 1.3 65.6 + - + +
25D ASN* 3.4 15.6 + - - +
26D ALA 3.0 17.7 + - - -
73D LEU 6.1 0.7 - - - +
96D LEU* 3.2 23.8 - - + +
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Residues in contact with VAL 23 (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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18D ILE* 5.0 3.8 - - + -
20D ASP* 3.1 34.4 + - + +
22D GLN* 1.3 76.6 - - - +
24D LEU* 1.3 64.9 + - - +
26D ALA* 3.1 3.8 + - - +
27D LEU* 3.0 23.3 + - + +
65D ALA* 3.8 37.0 - - + +
68D THR* 4.0 28.0 - - + +
69D GLU* 4.1 10.8 - - - +
73D LEU* 6.3 1.8 - - + -
92D ILE* 4.5 5.8 - - + +
96D LEU* 4.1 13.5 - - + -
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Residues in contact with LEU 24 (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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10D LEU* 3.9 30.0 - - + +
13D LEU* 3.6 35.4 - - + -
14D ARG* 3.9 10.1 - - + +
18D ILE* 3.8 30.3 - - + +
20D ASP 3.0 19.0 + - - +
21D GLU* 3.4 40.4 - - - +
22D GLN 3.3 0.2 - - - -
23D VAL* 1.3 77.4 - - - +
25D ASN* 1.3 61.7 + - - +
27D LEU* 3.3 10.8 + - + +
28D ALA* 3.2 20.1 + - - +
65D ALA* 5.5 2.0 - - + -
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Residues in contact with ASN 25 (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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21D GLU* 2.8 32.9 + - - +
22D GLN* 3.4 15.9 + - - +
23D VAL 3.2 0.2 - - - -
24D LEU* 1.3 76.0 - - - +
26D ALA* 1.3 59.6 + - - +
28D ALA* 3.1 10.0 + - - +
29D ALA* 3.0 26.7 + - - +
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Residues in contact with ALA 26 (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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22D GLN 3.0 13.2 + - - +
23D VAL 3.1 8.7 + - - +
25D ASN* 1.3 75.8 - - - +
27D LEU* 1.3 61.7 + - - +
29D ALA* 3.1 18.0 + - - +
30D VAL* 3.3 20.3 - - - +
92D ILE* 3.7 31.9 - - + +
95D HIS* 3.8 13.6 - - + -
96D LEU* 3.8 11.7 - - + -
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Residues in contact with LEU 27 (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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10D LEU* 5.3 5.8 - - + -
13D LEU* 5.9 6.1 - - + -
23D VAL* 3.0 14.6 + - + +
24D LEU* 3.4 14.8 - - + +
26D ALA* 1.3 77.2 - - - +
28D ALA* 1.3 55.9 + - - +
30D VAL* 3.1 23.9 - - - +
44D ALA 5.3 4.9 + - - -
64D VAL* 6.6 0.2 - - + -
65D ALA* 6.2 3.8 - - + -
88D TYR* 4.8 9.1 + - - +
92D ILE* 3.6 18.5 - - + +
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Residues in contact with ALA 28 (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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6D VAL* 5.1 19.0 - - + +
10D LEU* 4.6 13.8 - - + +
24D LEU 3.2 11.1 + - - +
25D ASN* 3.1 12.9 + - - +
27D LEU* 1.3 72.7 - - - +
29D ALA* 1.3 62.0 + - - +
30D VAL* 3.1 9.7 + - - -
31D PRO* 5.5 0.2 - - - +
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Residues in contact with ALA 29 (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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25D ASN 3.0 12.0 + - - +
26D ALA* 3.3 12.6 - - - +
28D ALA* 1.3 75.3 - - - +
30D VAL* 1.3 59.2 + - - +
31D PRO* 3.6 8.9 - - - +
95D HIS* 3.2 40.8 + - + +
120D LEU* 5.4 2.3 - - - +
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Residues in contact with VAL 30 (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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26D ALA 3.3 15.3 + - - +
27D LEU 3.1 12.8 + - - +
28D ALA 3.1 4.7 - - - +
29D ALA* 1.3 80.9 - - - +
31D PRO* 1.4 59.4 - - + +
32D ARG* 3.2 8.5 + - - +
35D PHE* 3.5 29.6 - - + -
44D ALA* 4.9 4.7 + - - +
88D TYR* 3.6 22.5 + - + -
91D ALA* 3.8 21.5 - - + -
92D ILE* 3.6 20.6 - - + -
95D HIS* 3.8 20.4 - - + +
120D LEU* 5.5 1.6 - - + -
122D LEU* 5.6 0.2 - - + -
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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