Contacts of the helix formed by residues 27 - 43 (chain K) in PDB entry 3A0B
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 VAL 27 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1028C CLA 3.6 26.4 - - + +
1056C DGD 4.2 28.7 - - + -
24K VAL* 2.9 43.7 - - + +
26K PRO* 1.3 76.4 - - - +
28K ILE* 1.3 58.2 + - - +
29K PRO 3.6 0.9 - - - -
30K VAL* 4.3 6.6 + - + +
31K LEU* 2.8 24.4 + - + +
25Y ILE* 5.4 6.5 - - + -
28Y ILE* 5.3 2.9 - - + -
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Residues in contact with ILE 28 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59C LEU* 5.5 1.3 - - + -
62C PHE* 2.4 37.5 - - + -
24K VAL 4.5 0.2 + - - -
25K LEU* 3.2 7.8 + - + +
26K PRO 2.4 14.8 + - - -
27K VAL* 1.3 64.0 - - - +
29K PRO* 1.3 87.8 - - + +
30K VAL 3.2 1.8 - - - -
31K LEU* 2.6 48.8 + - + +
32K PHE* 3.1 9.3 + - + +
1051K BCR 2.3 78.1 - - + -
28Y ILE* 5.2 9.4 - - + -
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Residues in contact with PRO 29 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C LEU* 4.4 6.3 - - + -
62C PHE* 3.6 1.8 - - + -
63C TRP* 4.3 3.8 - - + -
1028C CLA 3.8 14.1 - - + -
1034C CLA 3.1 86.7 - - + +
26K PRO 2.4 26.9 - - - +
28K ILE* 1.3 94.7 - - + +
30K VAL* 1.3 65.9 + - - +
32K PHE 3.1 4.7 + - - +
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Residues in contact with VAL 30 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1028C CLA 4.0 13.8 - - + +
1034C CLA 3.8 18.8 - - + +
1056C DGD 3.0 44.6 - - + -
27K VAL* 4.3 10.5 + - + +
28K ILE 3.2 0.2 - - - -
29K PRO* 1.3 80.1 - - - +
31K LEU* 1.3 71.3 + - + +
32K PHE 3.3 0.2 + - - -
33K PHE* 3.8 8.2 + - - +
34K ALA* 3.2 22.4 + - + +
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Residues in contact with LEU 31 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27K VAL* 2.8 15.7 - - + +
28K ILE* 2.6 51.1 + - + +
30K VAL* 1.3 82.6 - - + +
32K PHE* 1.3 49.2 + - - +
34K ALA* 2.9 10.0 + - - +
35K LEU* 2.6 36.9 + - - +
1051K BCR 3.8 43.7 - - + +
25Y ILE* 6.1 4.3 - - + -
28Y ILE* 4.7 17.3 - - + -
29Y GLY* 5.5 4.9 - - - -
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Residues in contact with PHE 32 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C LEU* 4.0 13.2 - - + -
1034C CLA 3.4 19.3 - - + -
1035C CLA 3.4 22.8 - - + +
28K ILE* 3.1 12.0 + - + +
29K PRO 3.1 4.8 + - - +
31K LEU* 1.3 73.1 - - - +
33K PHE* 1.3 62.6 + - - +
34K ALA 3.0 1.1 - - - -
35K LEU* 3.1 15.0 + - + +
36K ALA* 3.2 10.9 + - - +
1051K BCR 3.1 46.9 - - + -
1052K BCR 2.5 101.0 - - + +
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Residues in contact with PHE 33 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1032C CLA 4.4 33.0 - - + -
1034C CLA 3.5 97.3 - - + +
1035C CLA 4.4 7.0 - - + +
30K VAL* 3.8 8.3 + - - +
32K PHE* 1.3 76.0 - - - +
34K ALA* 1.3 71.7 + - + +
35K LEU 3.2 0.5 + - - -
36K ALA* 3.4 17.0 + - - +
37K PHE* 3.9 25.9 + + - -
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Residues in contact with ALA 34 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22J ILE* 6.3 3.4 - - + -
30K VAL* 3.2 18.9 + - + +
31K LEU* 2.9 17.4 + - - +
33K PHE* 1.3 96.6 - - + +
35K LEU* 1.3 58.2 + - - +
37K PHE* 3.5 15.7 - - - +
38K VAL* 3.6 0.3 - - - +
1051K BCR 3.4 28.6 - - + +
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Residues in contact with LEU 35 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1035C CLA 4.7 14.8 - - + -
31K LEU 2.6 14.1 + - - +
32K PHE* 3.4 10.5 - - + +
33K PHE 3.0 0.2 - - - -
34K ALA* 1.3 71.6 - - - +
36K ALA* 1.3 53.5 + - - +
37K PHE 2.4 18.1 + - - -
38K VAL* 2.6 44.9 + - + +
39K VAL* 3.5 13.2 + - + +
1051K BCR 3.7 37.7 - - + -
1052K BCR 4.0 29.8 - - + -
32Y GLY* 3.7 26.9 - - - +
33Y PRO 4.4 0.2 - - - -
35Y ILE* 6.2 0.9 - - + -
36Y ILE* 5.9 0.2 - - + -
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Residues in contact with ALA 36 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1035C CLA 3.5 42.0 - - + +
32K PHE 3.2 6.4 + - - +
33K PHE* 3.4 8.7 + - - +
35K LEU* 1.3 76.2 - - - +
37K PHE* 1.3 59.1 + - - +
39K VAL* 4.5 9.1 - - - +
40K GLN* 3.4 26.0 + - - +
1052K BCR 3.9 25.3 - - + +
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Residues in contact with PHE 37 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C TRP* 4.0 28.3 - + - -
1032C CLA 4.2 42.8 - - + -
1035C CLA 3.3 33.2 - - + -
33K PHE* 4.1 19.7 - + + -
34K ALA* 3.5 12.1 - - - +
35K LEU 2.4 12.3 + - - -
36K ALA* 1.3 71.8 - - - +
38K VAL* 1.3 68.4 + - - +
39K VAL 3.2 1.5 + - - -
40K GLN* 3.3 12.4 + - - +
41K ALA* 3.4 8.3 + - - +
45K PHE* 4.8 4.5 - + - -
1051K BCR 3.4 45.3 - - + +
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Residues in contact with VAL 38 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11J TRP* 4.6 10.6 - - - +
15J THR* 3.6 30.7 - - + +
34K ALA 3.6 0.4 - - - +
35K LEU* 2.6 52.0 + - + +
37K PHE* 1.3 76.8 - - - +
39K VAL* 1.3 64.3 + - + +
41K ALA* 3.3 10.9 + - - +
42K ALA* 3.5 8.3 + - - +
1051K BCR 3.5 32.8 - - + +
33Y PRO* 4.0 22.0 - - + +
36Y ILE* 4.3 5.8 - - + -
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Residues in contact with VAL 39 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1035C CLA 3.9 38.4 - - + +
35K LEU* 4.3 17.3 - - + +
36K ALA* 4.5 9.6 - - - +
37K PHE 3.2 0.4 - - - -
38K VAL* 1.3 76.9 - - + +
40K GLN* 1.3 64.2 + - + +
42K ALA* 2.6 33.0 + - + +
43K VAL* 3.1 17.7 + - + +
1052K BCR 5.9 2.5 - - + -
36Y ILE* 2.6 36.5 - - + +
46Y LEU* 4.6 3.1 - - + +
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Residues in contact with GLN 40 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C GLU* 4.2 1.2 - - - +
35C TRP* 4.1 2.4 - - - +
1035C CLA 3.3 65.5 + - + +
36K ALA 3.4 20.3 + - - +
37K PHE* 3.3 5.4 + - - +
39K VAL* 1.3 85.7 - - - +
41K ALA* 1.3 56.7 + - - +
43K VAL* 3.3 13.1 + - - +
44K GLY 3.1 5.2 + - - -
45K PHE* 3.0 62.1 + - + +
46Y LEU* 6.0 0.2 + - - -
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Residues in contact with ALA 41 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11J TRP* 4.0 22.5 - - + +
14J ALA* 5.7 1.8 - - + -
37K PHE 3.4 2.4 + - - +
38K VAL 3.3 10.0 + - - +
39K VAL 2.9 2.6 + - - -
40K GLN* 1.3 71.9 - - - +
42K ALA* 1.3 58.2 - - - +
43K VAL 2.9 5.2 - - - -
44K GLY* 2.8 19.6 + - - +
45K PHE* 3.7 21.7 - - + -
1051K BCR 4.1 22.2 - - + -
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Residues in contact with ALA 42 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11J TRP* 3.7 43.5 - - + +
38K VAL 3.5 5.3 + - - +
39K VAL* 2.6 22.0 + - - +
41K ALA* 1.3 74.2 - - - +
43K VAL* 1.3 61.4 + - + +
36Y ILE* 4.4 10.3 - - + -
40Y ALA* 5.6 0.7 - - + -
46Y LEU* 4.9 13.0 - - + +
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Residues in contact with VAL 43 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C GLU* 6.0 2.0 - - + -
39K VAL* 3.1 20.8 + - + +
40K GLN* 3.3 18.8 + - - +
41K ALA 2.9 0.6 - - - -
42K ALA* 1.3 83.6 - - + +
44K GLY* 1.3 55.2 + - - +
45K PHE 2.8 21.3 + - - +
46Y LEU* 4.1 39.7 - - + +
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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
------------------------------------------------------------
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