Contacts of the helix formed by residues 54 - 62 (chain D) in PDB entry 5BXD
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 SER 54 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51D TYR* 2.6 26.1 + - - +
52D PRO 3.9 0.2 - - - +
53D GLU* 1.3 81.9 - - - +
55D ARG* 1.3 64.2 + - - +
56D ILE* 3.2 8.8 - - - +
57D GLY* 3.2 11.8 + - - -
58D ARG* 3.0 27.0 + - - +
115D PHE 3.3 15.7 - - - -
116D GLN* 3.4 17.5 - - - -
117D LEU* 3.8 12.8 - - - -
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Residues in contact with ARG 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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54D SER* 1.3 71.0 - - - +
56D ILE* 1.3 61.7 + - - +
58D ARG* 3.2 26.1 + - - +
59D LEU* 2.9 38.3 + - + +
64D GLU* 4.2 20.6 + - - +
114D TYR* 3.1 72.2 + - - +
115D PHE* 3.1 10.0 + - + +
116D GLN* 3.6 21.3 + - - +
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Residues in contact with ILE 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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48D LEU* 3.5 7.6 - - + +
54D SER* 3.2 16.4 - - - +
55D ARG* 1.3 78.2 - - - +
57D GLY* 1.3 65.2 + - - +
59D LEU* 3.3 14.5 + - + -
60D PHE* 3.4 44.5 - - + -
77D ILE* 3.9 18.4 - - + -
84D PHE* 4.0 20.0 - - + -
87D ILE* 5.4 1.3 - - + -
91D LEU* 4.0 38.8 - - + -
115D PHE* 3.8 29.3 + - + +
117D LEU* 4.4 3.6 - - + -
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Residues in contact with GLY 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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48D LEU 3.3 14.8 - - - -
49D THR* 3.9 9.3 - - - +
51D TYR 3.8 15.5 - - - -
52D PRO* 4.8 4.0 - - - -
54D SER* 3.2 8.1 + - - -
55D ARG 3.2 0.8 - - - -
56D ILE* 1.3 82.0 - - - +
58D ARG* 1.3 63.0 + - - +
60D PHE 3.3 2.8 + - - -
61D ASP* 3.1 28.7 + - - +
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Residues in contact with ARG 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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52D PRO 4.1 9.6 + - - +
53D GLU* 3.1 28.1 + - - +
54D SER 3.0 11.2 + - - +
55D ARG* 3.2 28.6 + - - +
57D GLY* 1.3 76.0 - - - +
59D LEU* 1.3 63.5 + - - +
60D PHE 2.9 0.7 + - - -
61D ASP* 2.8 21.8 + - - +
62D GLY 3.6 0.7 + - - -
63D THR* 2.5 53.1 + - - +
64D GLU* 3.1 23.9 + - - +
116D GLN* 2.8 29.9 + - - +
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Residues in contact with LEU 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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55D ARG* 2.9 30.2 + - + +
56D ILE* 3.4 27.8 - - + +
57D GLY 3.3 0.4 - - - -
58D ARG* 1.3 75.4 - - - +
60D PHE* 1.3 66.4 + - + +
62D GLY 5.0 0.9 + - - -
63D THR 3.7 2.0 + - - -
64D GLU* 3.7 23.3 - - + +
65D PRO 3.8 20.2 - - - +
66D ILE* 3.2 38.3 - - + +
77D ILE* 4.3 19.7 - - + -
114D TYR* 5.6 2.5 - - + +
115D PHE* 4.6 9.2 - - + -
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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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32D VAL* 4.1 7.0 - - + -
34D ILE* 3.7 22.7 - - + -
45D LEU* 3.5 27.3 - - + +
48D LEU* 3.8 36.1 - - + -
49D THR* 3.7 17.9 - - + +
56D ILE* 3.4 42.4 - - + +
57D GLY 3.3 1.8 + - - -
58D ARG 3.0 0.8 - - - -
59D LEU* 1.3 86.4 - - + +
61D ASP* 1.3 61.0 + - - +
62D GLY 3.6 1.6 - - - -
66D ILE* 5.3 6.5 - - + -
75D TYR* 4.0 35.2 - + + -
77D ILE* 4.0 16.4 - - + -
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Residues in contact with ASP 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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49D THR* 3.9 15.0 - - + -
52D PRO* 4.8 13.2 - - - +
57D GLY 3.1 15.0 + - - +
58D ARG* 2.8 27.2 - - - +
60D PHE* 1.3 78.7 - - - +
62D GLY* 1.3 57.9 + - - +
63D THR* 2.9 20.9 + - - -
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Residues in contact with GLY 62 (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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58D ARG 3.6 1.6 + - - -
59D LEU 5.0 0.6 + - - -
60D PHE 3.6 2.0 - - - -
61D ASP* 1.3 80.3 - - - +
63D THR* 1.3 61.3 + - - +
64D GLU 3.4 12.8 + - - +
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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