Contacts of the helix formed by residues 39 - 55 (chain A) in PDB entry 4WB7
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 39 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A GLU 3.4 1.2 + - - -
38A PRO* 1.3 71.5 - - - +
40A ALA* 1.3 63.4 + - - +
41A GLU* 3.1 6.7 - - - +
42A GLU* 3.0 23.4 + - - +
43A LYS* 3.1 20.9 + - - +
350A LYS* 6.0 2.9 - - - -
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Residues in contact with ALA 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A TYR* 3.7 24.6 - - + +
35A ASN* 3.4 43.5 - - - +
37A GLU* 3.4 15.0 + - + +
38A PRO 3.2 5.1 + - - -
39A GLY* 1.3 76.9 - - - +
41A GLU* 1.3 58.5 + - - +
43A LYS* 3.1 4.4 + - - +
44A PHE* 2.9 29.8 + - - +
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Residues in contact with GLU 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A TYR 5.2 0.9 - - - -
32A PRO* 6.3 5.6 - - + -
37A GLU 4.8 1.0 + - - -
39A GLY* 4.8 2.9 - - - +
40A ALA* 1.3 79.7 - - - +
42A GLU* 1.3 61.5 + - - +
44A PHE* 3.4 8.5 + - - +
45A LYS* 3.3 20.8 + - - +
350A LYS* 5.6 5.1 + - - -
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Residues in contact with GLU 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A GLY* 3.0 17.4 + - - +
41A GLU* 1.3 81.3 - - - +
43A LYS* 1.3 67.0 + - - +
45A LYS* 3.5 8.3 + - + +
46A GLU* 3.1 46.8 + - - +
348A ASN 4.4 13.6 - - - +
350A LYS* 4.1 37.1 - - + +
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Residues in contact with LYS 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A TYR* 3.4 43.9 + - + +
39A GLY 3.1 16.0 + - - +
40A ALA* 3.1 8.8 + - - +
42A GLU* 1.3 81.6 - - - +
44A PHE* 1.3 64.4 + - - +
45A LYS 3.1 2.0 - - - -
46A GLU* 3.1 7.2 + - + +
47A ILE* 2.9 33.3 + - + +
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Residues in contact with PHE 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A TYR* 4.9 9.8 + + - -
27A ALA* 3.3 46.0 - - + -
30A TYR* 3.6 23.3 - - + +
31A HIS* 3.6 21.3 - + + -
32A PRO* 3.8 23.3 - - + -
40A ALA 2.9 16.5 + - - +
41A GLU* 3.6 9.6 - - - +
42A GLU 3.4 0.2 - - - -
43A LYS* 1.3 76.1 - - - +
45A LYS* 1.3 62.5 + - - +
47A ILE* 3.8 5.5 + - - +
48A ALA* 3.4 20.4 + - - +
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Residues in contact with LYS 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A GLU 3.3 9.6 + - - +
42A GLU* 3.7 11.0 - - + +
43A LYS 3.1 0.4 - - - -
44A PHE* 1.3 79.7 - - - +
46A GLU* 1.3 66.3 + - - +
48A ALA* 3.2 7.7 + - + +
49A GLU* 3.0 30.4 + - + +
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Residues in contact with GLU 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A LYS* 3.4 29.1 + - - +
4A TYR* 5.4 1.4 - - - -
7A THR* 3.8 13.7 - - + +
42A GLU* 3.1 39.8 + - - +
43A LYS* 3.1 12.2 + - + +
45A LYS* 1.3 83.6 - - - +
47A ILE* 1.3 58.4 + - + +
49A GLU* 3.4 16.9 + - - +
50A ALA* 3.0 29.5 + - - +
348A ASN* 5.6 4.8 - - - +
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Residues in contact with ILE 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A THR* 3.9 22.7 - - + +
8A LEU* 3.6 13.2 - - + +
23A TYR* 3.4 26.7 - - + +
26A GLN* 3.6 31.4 - - + +
27A ALA* 4.4 3.4 - - - +
30A TYR* 3.4 37.0 - - + -
43A LYS* 2.9 22.2 + - + +
44A PHE* 3.9 6.3 - - - +
46A GLU* 1.3 75.4 - - + +
48A ALA* 1.3 56.9 - - - +
50A ALA* 3.4 1.6 + - - +
51A TYR* 3.0 28.1 + - - +
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Residues in contact with ALA 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A TYR* 3.8 20.8 - - + +
44A PHE* 3.4 12.5 + - + +
45A LYS* 3.2 11.8 + - + +
47A ILE* 1.3 76.8 - - - +
49A GLU* 1.3 59.2 + - - +
51A TYR* 3.3 3.5 + - - +
52A ASP* 2.9 37.9 + - - +
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Residues in contact with GLU 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A LYS* 3.3 33.0 + - - +
4A TYR* 2.9 30.7 + - + +
45A LYS* 3.0 17.9 + - + +
46A GLU* 3.4 19.6 + - - +
48A ALA* 1.3 75.7 - - - +
50A ALA* 1.3 64.8 + - - +
52A ASP* 3.4 8.4 + - - +
53A VAL* 3.3 24.9 + - + +
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Residues in contact with ALA 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A TYR* 3.5 46.2 - - + +
7A THR* 3.9 12.8 - - + -
8A LEU* 4.0 8.3 - - + -
46A GLU 3.0 17.6 + - - +
47A ILE 3.8 4.0 - - - +
48A ALA 3.2 0.2 - - - -
49A GLU* 1.3 76.5 - - - +
51A TYR* 1.3 63.4 + - - +
53A VAL* 3.3 2.6 + - - +
54A LEU* 3.0 28.1 + - - +
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Residues in contact with TYR 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A LEU* 4.1 8.8 - - + +
19A ILE* 4.0 9.6 - - + -
20A LYS* 4.2 30.8 - - + +
23A TYR* 3.6 46.2 - + + -
47A ILE 3.0 17.7 + - - +
48A ALA* 3.6 4.3 - - - +
50A ALA* 1.3 77.3 - - - +
52A ASP* 1.3 71.7 + - - +
54A LEU* 5.0 0.4 - - - -
55A SER* 2.8 65.1 + - - +
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Residues in contact with ASP 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A ALA* 2.9 22.7 + - - +
49A GLU* 3.8 8.1 - - - +
50A ALA 3.3 0.2 - - - -
51A TYR* 1.3 91.6 - - - +
53A VAL* 1.3 64.4 + - + +
55A SER* 4.0 5.7 + - - -
56A ASP* 3.9 8.3 - - - +
59A LYS* 3.3 23.5 + - - +
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Residues in contact with VAL 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A TYR* 3.7 42.8 - - + +
49A GLU* 3.3 15.3 + - + +
50A ALA 3.8 6.1 - - - +
51A TYR 3.2 0.4 - - - -
52A ASP* 1.3 78.9 - - + +
54A LEU* 1.3 69.5 + - + +
55A SER 3.3 0.7 + - - -
56A ASP 3.2 19.2 + - - +
59A LYS* 3.7 36.1 - - + +
60A ARG 3.4 5.0 + - - -
63A PHE* 3.9 11.9 - - + -
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Residues in contact with LEU 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A TYR* 3.9 29.2 - - + +
5A TYR* 3.6 54.5 - - + +
8A LEU* 4.2 14.4 - - + -
10A LEU* 4.4 6.7 - - + -
16A ASP* 5.1 2.1 - - - +
19A ILE* 3.6 24.6 - - + +
50A ALA 3.0 16.3 + - - +
53A VAL* 1.3 80.5 - - + +
55A SER* 1.3 59.8 + - - +
56A ASP 3.2 2.1 + - - +
57A PRO* 5.5 0.2 - - - +
60A ARG* 3.6 30.7 + - + +
63A PHE* 4.1 15.3 - - + -
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Residues in contact with SER 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A ASP* 5.5 8.8 - - - +
19A ILE* 4.2 8.7 - - - +
51A TYR* 2.8 61.8 + - - -
52A ASP* 4.0 5.7 + - - -
54A LEU* 1.3 77.9 - - - +
56A ASP* 1.3 57.6 + - - +
57A PRO* 3.7 8.1 - - - +
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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