Contacts of the helix formed by residues 26 - 41 (chain L) in PDB entry 4B86
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 LYS 26 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27L ALA* 1.3 66.6 + - - +
28L PHE* 3.1 16.7 - - - +
29L THR* 2.9 28.6 + - - +
30L GLU* 3.6 6.4 + - - +
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Residues in contact with ALA 27 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16L LEU* 5.4 4.0 - - + +
19L ASN 5.7 1.8 - - - +
20L TYR* 5.0 15.7 - - + -
21L ASP 5.6 1.6 - - - +
26L LYS* 1.3 79.2 - - - +
28L PHE* 1.3 57.6 + - - +
30L GLU* 3.2 13.4 + - - +
31L ILE* 2.9 43.0 + - + +
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Residues in contact with PHE 28 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20L TYR* 3.2 42.5 - + + +
26L LYS 3.8 11.2 - - - +
27L ALA* 1.3 78.1 - - - +
29L THR* 1.3 65.1 + - + +
31L ILE* 3.5 14.2 - - + +
32L ASN* 2.9 55.6 + - - +
114L THR* 5.5 9.4 - - + -
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Residues in contact with THR 29 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C ARG* 5.5 2.6 + - - -
26L LYS* 2.9 24.5 + - - +
28L PHE* 1.3 84.7 - - + +
30L GLU* 1.3 59.6 + - - +
32L ASN* 3.0 13.1 + - + +
33L ARG* 2.9 28.1 + - - +
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Residues in contact with GLU 30 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16L LEU* 3.4 33.4 - - + +
26L LYS 3.6 6.9 + - - +
27L ALA* 3.2 13.8 + - - +
29L THR* 1.3 79.7 + - - +
31L ILE* 1.3 55.7 + - - +
33L ARG* 3.2 4.9 + - - +
34L LEU* 2.9 31.3 + - + +
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Residues in contact with ILE 31 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13L ALA* 5.4 1.1 - - - +
16L LEU* 3.7 45.5 - - + +
17L VAL* 3.9 24.7 - - + -
20L TYR* 4.2 24.0 - - + -
27L ALA* 2.9 30.2 + - + +
28L PHE* 3.5 13.7 - - + +
30L GLU* 1.3 75.3 - - - +
32L ASN* 1.3 60.3 + - - +
34L LEU* 4.8 0.9 - - - -
35L LEU* 3.0 50.5 + - + +
110L ILE* 5.3 4.7 - - + -
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Residues in contact with ASN 32 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C ARG* 4.4 10.7 + - - +
28L PHE* 2.9 56.3 + - - +
29L THR* 3.0 16.9 + - - +
31L ILE* 1.3 78.3 - - - +
33L ARG* 1.3 55.5 + - - +
35L LEU* 5.1 3.6 - - - +
36L PRO* 3.3 20.1 - - - +
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Residues in contact with ARG 33 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C GLU* 5.5 11.1 + - - +
33C ARG* 3.0 67.4 - - + +
37C TYR* 6.2 0.2 - - + -
29L THR 2.9 12.8 + - - +
30L GLU* 3.2 4.0 + - - +
31L ILE 3.1 0.2 - - - -
32L ASN* 1.3 78.0 - - - +
34L LEU* 1.3 64.7 + - - +
35L LEU 3.1 2.0 - - - -
36L PRO* 3.1 37.9 - - - +
37L TYR* 3.1 52.4 + - + +
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Residues in contact with LEU 34 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C TYR* 3.6 23.3 - - - +
9L LEU* 4.1 14.7 - - + +
12L SER* 3.5 19.7 - - - -
13L ALA* 3.5 37.2 - - + +
16L LEU* 3.8 18.2 - - + -
30L GLU* 2.9 18.1 + - + +
31L ILE* 4.3 1.8 - - - +
33L ARG* 1.3 77.3 - - - +
35L LEU* 1.3 61.8 + - - +
36L PRO 3.5 0.2 - - - -
37L TYR* 3.5 10.4 + - + +
38L PHE* 3.3 18.9 + - - +
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Residues in contact with LEU 35 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13L ALA* 3.9 24.4 - - + +
17L VAL* 5.0 0.9 - - + -
31L ILE* 3.0 29.2 + - + +
32L ASN* 5.0 2.9 - - - +
34L LEU* 1.3 75.4 - - - +
36L PRO* 1.3 71.2 - - + +
38L PHE* 3.2 14.8 + - + +
39L ARG* 3.1 20.6 + - - +
103L TYR* 4.7 9.4 + - + +
106L LEU* 4.3 9.4 - - + -
107L CYS* 5.0 10.5 - - - -
110L ILE* 3.7 34.5 - - + -
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Residues in contact with PRO 36 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C ARG* 5.7 1.3 - - - +
32L ASN 3.3 21.3 - - - +
33L ARG* 3.1 35.0 - - - +
35L LEU* 1.3 94.7 - - + +
37L TYR* 1.3 56.8 + - - +
39L ARG* 3.4 7.4 + - + +
40L GLN* 3.2 27.0 + - - +
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Residues in contact with TYR 37 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C ARG 4.4 2.2 - - - -
34C LEU* 3.8 32.8 + - + +
37C TYR* 3.8 37.3 - + - +
9L LEU* 3.8 21.7 - - + +
33L ARG* 3.1 58.4 + - + -
34L LEU* 3.5 10.7 + - - +
35L LEU 3.2 0.6 - - - -
36L PRO* 1.3 76.4 - - - +
38L PHE* 1.3 64.5 + - - +
40L GLN* 3.6 26.1 + - - +
41L SER* 3.4 15.8 + - - -
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Residues in contact with PHE 38 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6L ALA 3.6 9.2 - - - -
9L LEU* 3.6 31.1 - - + +
10L TYR* 3.5 46.4 - + + -
13L ALA* 4.2 13.7 - - + -
34L LEU 3.3 10.5 + - - +
35L LEU* 3.2 16.5 + - + +
37L TYR* 1.3 78.3 - - - +
39L ARG* 1.3 59.6 + - - +
41L SER* 2.7 23.7 + - - -
42L LEU* 3.4 32.0 + - + +
99L LEU* 4.5 3.4 - - + -
103L TYR* 3.4 41.3 - + + -
106L LEU* 4.4 8.3 - - + -
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Residues in contact with ARG 39 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35L LEU 3.1 12.1 + - - +
36L PRO* 3.9 7.2 - - + +
37L TYR 3.4 0.2 - - - -
38L PHE* 1.3 73.8 - - - +
40L GLN* 1.3 56.8 + - - +
42L LEU* 3.0 7.4 + - - +
43L SER* 2.7 47.5 + - - +
48L GLY 2.7 27.2 + - - -
49L HIS* 3.9 5.1 - - - +
50L LEU* 3.2 41.3 - - + +
103L TYR* 3.0 46.8 + - + +
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Residues in contact with GLN 40 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36L PRO 3.2 16.8 + - - +
37L TYR* 3.7 28.0 - - - +
39L ARG* 1.3 78.8 - - - +
41L SER* 1.3 56.8 + - - +
43L SER* 3.1 32.0 + - - +
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Residues in contact with SER 41 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5L ASN* 4.9 4.7 - - - -
6L ALA* 3.8 22.2 - - - +
9L LEU* 3.5 29.2 - - - +
37L TYR 3.4 3.6 + - - -
38L PHE* 2.7 23.1 + - - -
39L ARG 3.2 0.2 - - - -
40L GLN* 1.3 77.4 - - - +
42L LEU* 1.3 62.4 + - - +
43L SER 3.5 1.9 - - - +
63L GLN 5.6 0.2 - - - +
65L TYR* 4.2 22.0 - - - -
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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