Contacts of the helix formed by residues 37 - 49 (chain D) in PDB entry 5B31
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 TYR 37 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25C PHE* 3.9 22.4 - + + -
26C PRO* 4.4 15.9 - - + -
29C ARG* 4.8 8.0 - - - -
30C VAL* 4.3 15.4 - - + +
33C LEU* 3.5 26.3 - - + +
55C LEU* 4.7 1.5 - - + +
36D SER* 1.3 76.5 + - - +
38D SER* 1.3 64.7 + - - +
39D ILE 3.4 2.2 - - - -
40D TYR* 2.9 31.7 + + - -
41D VAL* 3.0 24.8 + - + +
63D ASN* 2.9 19.8 + - - +
66D VAL* 3.7 30.8 - - + +
67D ASN* 3.5 27.6 + - - -
70D PHE* 4.4 10.9 - - - +
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Residues in contact with SER 38 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36D SER* 2.9 21.9 + - - -
37D TYR* 1.3 76.0 - - - +
39D ILE* 1.3 61.3 + - - +
42D TYR* 2.9 25.1 + - - +
59D MET* 3.1 38.9 - - - +
63D ASN* 3.0 14.1 + - - +
269J T 6.0 0.4 - - - -
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Residues in contact with ILE 39 (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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37D TYR 3.4 0.6 - - - -
38D SER* 1.3 80.7 - - - +
40D TYR* 1.3 81.2 - - + +
42D TYR* 3.8 6.7 - - - +
43D LYS* 3.0 40.7 + - - +
268J G 3.6 49.8 - - + +
269J T 4.1 29.7 + - + +
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Residues in contact with TYR 40 (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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24C GLN* 3.3 22.2 - - - +
25C PHE* 3.7 25.1 - - + -
26C PRO* 3.4 40.8 - - + +
29C ARG* 3.6 30.0 + - - -
36D SER 3.8 3.1 - - - -
37D TYR* 2.9 21.8 + + - +
39D ILE* 1.3 92.9 - - + +
41D VAL* 1.3 67.6 + - - +
43D LYS* 3.3 15.6 + - - +
44D VAL* 3.0 27.9 + - - +
268J G 2.9 39.9 + - - -
269J T 5.3 0.4 - - - -
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Residues in contact with VAL 41 (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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25C PHE* 4.0 15.2 - - + -
59C THR* 4.3 13.2 - - + -
63C LEU* 3.7 20.2 - - + +
37D TYR* 3.0 26.0 + - + +
38D SER 3.8 1.1 - - - +
40D TYR* 1.3 74.3 - - - +
42D TYR* 1.3 58.4 + - - +
44D VAL* 3.2 2.9 + - - +
45D LEU* 2.9 28.3 + - + +
54D ILE* 4.7 2.7 - - + -
59D MET* 3.6 31.6 - - + -
62D MET* 4.0 26.5 - - + +
63D ASN* 5.3 0.7 - - - +
66D VAL* 4.6 5.8 - - + -
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Residues in contact with TYR 42 (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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38D SER 2.9 19.2 + - - +
39D ILE* 3.8 8.1 - - - +
41D VAL* 1.3 78.4 - - - +
43D LYS* 1.3 62.3 + - + +
45D LEU* 3.3 11.7 + - + +
46D LYS* 3.1 68.3 + - + +
53D GLY* 4.5 2.4 - - - -
54D ILE* 3.9 22.9 - - + -
59D MET* 4.2 6.1 - - + -
20I T 3.5 53.2 + - + -
21I T 4.3 15.3 + - - -
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Residues in contact with LYS 43 (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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24C GLN* 3.6 38.5 + - + +
39D ILE* 3.0 29.0 + - - +
40D TYR* 3.5 21.5 - - - +
42D TYR* 1.3 76.3 - - - +
44D VAL* 1.3 63.7 + - - +
46D LYS* 2.9 20.1 + - - +
47D GLN* 3.1 16.6 + - + +
268J G 4.5 15.0 + - - -
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Residues in contact with VAL 44 (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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24C GLN* 4.1 11.9 - - + -
25C PHE* 3.7 19.7 - - + -
56C GLU* 3.8 18.2 - - + +
59C THR* 4.2 8.1 - - + -
60C ALA* 3.5 44.4 - - + +
63C LEU* 4.3 2.5 - - + -
40D TYR 3.0 16.8 + - - +
41D VAL 3.7 3.8 - - - +
43D LYS* 1.3 75.8 - - - +
45D LEU* 1.3 63.0 + - - +
47D GLN* 3.4 14.9 + - - +
48D VAL* 3.2 22.8 + - + +
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Residues in contact with LEU 45 (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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63C LEU* 3.9 22.8 - - + +
78C ILE* 3.7 25.1 - - + -
41D VAL* 2.9 14.2 + - + +
42D TYR* 3.5 16.4 - - + +
43D LYS 3.1 0.2 - - - -
44D VAL* 1.3 76.8 - - - +
46D LYS* 1.3 53.8 + - - +
48D VAL* 3.1 4.5 + - + +
49D HIS* 2.6 51.1 + - + -
52D THR* 3.4 25.1 - - + +
53D GLY* 3.8 7.0 - - - +
54D ILE* 3.8 37.2 - - + -
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Residues in contact with LYS 46 (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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42D TYR* 3.1 50.9 + - + +
43D LYS* 2.9 8.7 + - - +
45D LEU* 1.3 76.4 - - - +
47D GLN* 1.3 65.5 + - + +
49D HIS 4.0 2.2 - - - -
50D PRO* 3.1 54.8 + - + +
51D ASP 4.5 0.4 - - - -
52D THR 2.9 31.9 + - - +
21I T 5.9 1.7 + - - +
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Residues in contact with GLN 47 (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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24C GLN* 3.9 38.4 - - - +
56C GLU* 4.8 3.5 - - - +
43D LYS* 3.1 11.9 + - + +
44D VAL* 3.6 18.1 - - - +
46D LYS* 1.3 79.1 - - - +
48D VAL* 1.3 64.7 + - + +
50D PRO* 4.7 4.3 - - - +
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Residues in contact with VAL 48 (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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60C ALA* 4.2 27.4 - - + +
63C LEU* 4.0 7.0 - - + -
64C GLU* 3.5 34.6 - - + +
44D VAL* 3.2 13.9 + - + +
45D LEU* 3.1 16.5 + - + +
47D GLN* 1.3 82.8 - - + +
49D HIS* 1.3 90.0 + - + +
50D PRO* 4.0 5.0 - - - +
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Residues in contact with HIS 49 (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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63C LEU 3.3 20.2 - - - -
64C GLU* 2.9 32.2 + - - -
67C GLY* 3.5 12.0 - - - -
68C ASN* 2.9 25.1 + - - -
71C ARG* 4.2 7.0 - - - -
45D LEU* 2.6 24.5 + - + +
46D LYS* 4.0 1.0 - - - -
48D VAL* 1.3 93.6 + - + +
50D PRO* 1.3 56.7 - - - +
51D ASP* 2.8 22.6 + - - -
52D THR* 2.8 39.5 + - - +
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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