Contacts of the helix formed by residues 52 - 61 (chain D) in PDB entry 3B4V
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 52 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28D THR* 5.7 0.2 - - - +
50D HIS 3.3 2.6 + - - -
51D PRO* 1.3 66.7 - - - +
53D ASN* 1.3 59.3 + - - -
54D LYS 3.1 8.8 + - - -
55D ILE* 3.3 23.4 + - - +
56D ASN* 4.2 1.2 - - - +
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Residues in contact with ASN 53 (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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61A THR* 3.8 26.5 + - + +
65A HIS* 4.4 19.4 - - - +
68A MET* 5.0 11.9 - - + +
23B ILE* 4.1 21.9 + - - +
25B TRP* 3.0 28.2 + - - -
51D PRO 3.6 0.9 + - - +
52D GLY* 1.3 70.0 - - - -
54D LYS* 1.3 60.9 + - - +
55D ILE 3.3 0.9 - - - -
56D ASN* 3.2 15.3 - - - +
57D LEU 3.1 21.3 + - - -
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Residues in contact with LYS 54 (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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24B GLY 3.3 23.5 + - - +
25B TRP* 4.0 16.2 - - + +
27B ASP* 3.1 35.4 + - - -
28B TRP* 3.4 51.6 - - + +
240C EDO 5.0 2.0 + - - -
50D HIS* 3.6 18.6 - - + -
51D PRO* 3.4 21.7 + - + +
52D GLY 3.1 0.8 - - - -
53D ASN* 1.3 79.8 + - - +
55D ILE* 1.3 60.7 + - - +
57D LEU* 3.2 6.6 + - + +
58D LEU 3.0 22.2 + - - -
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Residues in contact with ILE 55 (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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11D VAL* 3.7 20.2 - - + -
13D TRP* 3.5 33.9 - - + +
25D VAL* 4.7 3.8 - - + -
28D THR* 4.1 21.8 - - + -
46D SER* 5.7 0.4 - - - +
48D LEU 3.7 22.4 - - - +
49D THR* 5.9 0.7 - - + -
50D HIS* 3.8 25.1 + - - +
52D GLY 3.3 17.6 + - - +
54D LYS* 1.3 76.5 - - - +
56D ASN* 1.3 77.0 + - - +
58D LEU* 2.9 31.5 + - + +
59D GLY 3.1 8.0 + - - -
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Residues in contact with ASN 56 (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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56A LEU* 4.5 16.6 + - - +
61A THR* 3.5 25.8 + - + +
23D SER 5.0 0.9 - - - +
25D VAL* 4.0 20.5 - - - +
52D GLY 4.2 0.7 - - - +
53D ASN* 3.2 22.9 + - + +
55D ILE* 1.3 85.1 - - - +
57D LEU* 1.3 56.9 - - - +
59D GLY* 2.8 19.9 + - - -
60D PHE* 3.0 34.6 + - + -
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Residues in contact with LEU 57 (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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58A PHE* 4.1 15.7 - - + -
25B TRP* 3.5 59.5 - - + +
28B TRP* 3.5 28.9 - - + -
29B ILE* 4.4 6.1 - - + -
53D ASN 3.1 10.9 + - - +
54D LYS* 3.4 11.0 - - - +
55D ILE 3.2 0.2 - - - -
56D ASN* 1.3 78.8 - - - +
58D LEU* 1.3 57.9 + - - +
60D PHE* 3.8 8.1 - - + -
61D LEU* 2.9 53.7 + - + +
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Residues in contact with LEU 58 (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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28B TRP* 3.6 27.8 - - + -
96B ASP* 5.8 3.8 - - + -
48D LEU* 5.3 6.3 - - + +
50D HIS* 4.2 16.8 - - + +
54D LYS 3.0 10.6 + - - +
55D ILE* 2.9 32.0 + - + +
57D LEU* 1.3 76.0 - - - +
59D GLY* 1.3 57.9 + - - +
61D LEU* 3.8 1.1 + - - -
62D GLY 3.3 1.6 + - - -
63D LEU* 2.8 64.7 + - + +
64D VAL* 3.4 24.9 - - + +
65D HIS 5.3 0.7 - - - +
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Residues in contact with GLY 59 (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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13D TRP* 3.9 11.2 - - - -
21D THR* 5.8 0.7 - - - +
22D CYS 3.9 8.3 - - - +
23D SER* 4.1 18.2 - - - -
55D ILE 3.1 5.1 + - - -
56D ASN 2.8 9.6 + - - -
58D LEU* 1.3 75.1 - - - +
60D PHE* 1.3 66.9 + - - +
62D GLY* 2.8 15.9 + - - -
64D VAL* 3.7 15.6 - - - +
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Residues in contact with PHE 60 (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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56A LEU 3.1 28.5 - - - -
57A SER* 3.7 2.5 - - - -
58A PHE* 3.4 56.5 - + + -
61A THR* 3.4 21.3 - - - -
25B TRP* 4.2 6.1 - + - -
103B LYS* 5.3 1.4 + - - -
105B ILE* 4.2 19.0 - - + +
23D SER* 4.4 13.5 - - - -
24D LEU* 5.3 3.6 - - + -
56D ASN* 3.0 29.9 + - + -
57D LEU* 3.8 16.2 - - + +
59D GLY* 1.3 78.2 - - - +
61D LEU* 1.3 61.8 + - + +
62D GLY* 3.3 1.0 + - - -
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Residues in contact with LEU 61 (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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28B TRP* 4.0 15.0 - - + -
29B ILE* 5.1 1.8 - - + -
91B MET* 4.6 9.9 - - + -
93B TYR* 3.5 58.9 + - + -
103B LYS* 3.7 8.8 + - - -
105B ILE* 4.1 19.7 - - + -
57D LEU* 2.9 47.2 + - + +
60D PHE* 1.3 76.3 - - + +
62D GLY* 1.3 62.2 + - - +
63D LEU* 3.3 35.0 - - + +
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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