Contacts of the helix formed by residues 14 - 26 (chain D) in PDB entry 2BS3
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 GLY 14 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12D GLY 3.5 3.2 - - - -
13D GLY* 1.3 80.4 - - - +
15D LEU* 1.3 66.2 + - - -
16D ALA 3.3 2.7 - - - -
17D GLY 3.5 2.0 + - - +
18D LEU* 3.0 22.5 + - - +
42D SER* 3.6 8.1 - - - -
161D LEU* 3.8 6.3 - - - -
215D ALA 4.8 0.4 + - - -
1656D FAD 3.4 32.7 + - - -
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Residues in contact with LEU 15 (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 GLY* 1.3 71.2 - - - -
16D ALA* 1.3 56.6 + - - +
18D LEU* 4.2 2.3 - - - +
19D ARG* 3.0 32.4 + - - +
44D SER* 3.4 29.6 + - - +
157D GLY* 5.0 2.2 - - - +
160D MET* 3.8 31.6 - - + +
161D LEU* 3.7 34.6 - - + +
164D VAL* 4.2 11.0 - - + +
410D VAL* 4.2 20.9 - - + +
413D ALA* 3.7 17.5 - - + -
414D VAL* 4.0 20.1 - - + -
1656D FAD 3.0 5.3 + - - +
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Residues in contact with ALA 16 (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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15D LEU* 1.3 76.3 - - - +
17D GLY* 1.3 63.8 + - - +
20D ALA* 3.0 24.6 + - - +
213D LEU* 5.6 0.2 - - - -
215D ALA* 4.0 4.0 - - + -
391D ALA* 3.7 18.6 - - + +
392D GLY* 3.7 26.0 - - - -
413D ALA* 3.2 22.6 + - - +
417D GLY* 3.8 5.4 - - - -
1656D FAD 3.0 14.9 + - - +
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Residues in contact with GLY 17 (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 VAL* 3.5 20.5 - - - +
12D GLY 3.4 20.8 + - - -
14D GLY 3.5 5.1 + - - +
16D ALA* 1.3 78.2 - - - +
18D LEU* 1.3 58.5 + - - +
20D ALA* 3.3 3.6 + - - +
21D ALA* 3.0 28.9 + - - +
33D VAL* 5.2 0.2 - - - -
213D LEU* 5.0 0.2 - - - -
215D ALA* 3.6 13.1 - - - +
1656D FAD 4.4 0.4 + - - -
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Residues in contact with LEU 18 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D GLY 4.3 0.4 + - - -
13D GLY* 3.4 31.4 - - - +
14D GLY 3.0 18.0 + - - +
15D LEU* 4.2 0.4 - - - +
17D GLY* 1.3 75.7 - - - +
19D ARG* 1.3 61.9 + - - +
21D ALA* 3.2 1.9 + - - -
22D VAL* 3.1 19.1 + - - +
33D VAL* 4.2 14.8 - - + -
39D VAL* 4.0 14.8 - - + -
161D LEU* 3.8 15.3 - - + +
164D VAL* 3.5 16.2 - - + -
165D ALA* 3.7 31.2 - - + +
168D CYS* 3.3 28.6 - - + -
175D ILE* 4.2 8.1 - - + -
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Residues in contact with ARG 19 (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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15D LEU 3.0 20.1 + - - +
18D LEU* 1.3 77.3 - - - +
20D ALA* 1.3 60.9 + - - +
22D VAL* 3.3 18.0 + - - +
23D ALA* 3.3 19.3 + - - +
26D GLN* 5.3 6.9 + - - +
99D GLU* 2.7 37.8 + - - -
103D TRP* 3.5 29.0 - - - -
164D VAL* 3.5 12.3 - - + +
414D VAL* 3.6 35.8 - - + +
417D GLY* 3.8 14.6 - - - +
418D MET* 3.5 13.4 - - - +
645D LYS* 5.7 0.2 - - - +
646D TYR* 3.6 19.6 + - - -
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Residues in contact with ALA 20 (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 VAL* 5.0 6.1 - - + -
16D ALA 3.0 19.5 + - - +
17D GLY* 3.6 5.8 - - - +
19D ARG* 1.3 75.1 - - - +
21D ALA* 1.3 63.6 + - - +
23D ALA* 3.1 5.0 + - - +
24D THR* 3.1 26.2 + - - +
213D LEU* 4.0 28.0 - - + -
391D ALA* 5.8 0.9 - - + -
417D GLY* 3.4 17.9 + - - +
420D VAL* 6.1 0.2 - - + -
421D GLY* 4.3 7.7 - - - -
424D PHE* 5.1 2.0 - - + -
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Residues in contact with ALA 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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10D VAL* 4.3 6.2 - - + +
17D GLY 3.0 13.5 + - - +
18D LEU 3.2 10.3 + - - +
20D ALA* 1.3 75.1 - - - +
22D VAL* 1.3 60.3 + - - +
24D THR* 3.1 8.3 + - - -
25D GLN* 2.9 34.1 + - - +
31D THR* 3.9 9.8 - - - +
33D VAL* 3.6 27.4 - - + -
168D CYS* 4.1 8.7 - - - -
173D VAL* 4.0 4.2 - - + +
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Residues in contact with VAL 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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18D LEU 3.1 14.4 + - - +
19D ARG* 3.5 20.6 - - - +
21D ALA* 1.3 75.4 - - - +
23D ALA* 1.3 58.2 + - - +
25D GLN* 4.7 0.4 - - - -
26D GLN* 2.9 47.3 + - - +
103D TRP* 4.1 18.8 - - + -
164D VAL* 4.3 9.4 - - + +
167D GLU* 4.1 21.5 - - + +
168D CYS* 3.8 17.0 - - - +
171D LEU* 3.8 22.4 - - + +
173D VAL* 5.1 0.7 - - - -
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Residues in contact with ALA 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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19D ARG* 3.3 15.7 + - - +
20D ALA 3.1 10.9 + - - +
22D VAL* 1.3 80.7 - - - +
24D THR* 1.3 61.0 + - - +
26D GLN* 3.3 15.3 - - - +
27D LYS* 2.9 28.9 + - - +
417D GLY 4.4 1.3 - - - +
418D MET* 4.8 2.0 - - - +
421D GLY* 3.8 30.5 - - - +
422D GLU* 4.3 10.1 - - - +
425D ALA* 4.6 0.9 - - - -
646D TYR* 6.0 0.4 - - - +
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Residues in contact with THR 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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8D SER* 3.6 22.2 - - - +
10D VAL* 5.2 0.5 - - - +
20D ALA 3.1 9.5 + - - +
21D ALA* 3.1 9.0 + - - -
23D ALA* 1.3 74.6 - - - +
25D GLN* 1.3 68.9 + - - +
27D LYS* 3.2 20.7 + - - +
29D LEU* 3.3 17.2 + - - +
31D THR* 3.0 21.8 - - - +
421D GLY 4.3 2.0 - - - +
424D PHE* 3.5 33.1 - - + -
425D ALA* 3.9 19.3 - - + +
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Residues in contact with GLN 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 ALA 2.9 19.5 + - - +
22D VAL 4.1 1.6 - - - +
24D THR* 1.3 77.6 + - - +
26D GLN* 1.3 62.3 + - - +
27D LYS 3.1 1.2 + - - -
28D GLY* 3.1 15.0 + - - -
29D LEU 3.6 7.5 + - - -
30D SER* 4.8 4.6 - - - +
31D THR* 2.9 38.0 + - + +
171D LEU* 3.5 35.4 + - + +
172D GLY 4.2 6.0 + - - +
173D VAL* 3.6 25.4 - - + -
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Residues in contact with GLN 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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19D ARG* 5.3 6.2 + - - +
22D VAL* 2.9 40.3 + - - +
23D ALA* 3.3 18.2 - - - +
25D GLN* 1.3 75.8 - - - +
27D LYS* 1.3 66.1 + - - +
28D GLY 3.4 1.9 + - - -
103D TRP* 5.8 1.2 - - - -
171D LEU* 4.3 19.9 - - + +
645D LYS* 3.0 32.1 - - - +
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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