Contacts of the helix formed by residues 93 - 101 (chain F) in PDB entry 3BBX
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 GLU 93 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34A A 5.7 5.2 - - - +
44A G 3.8 25.5 + - + +
45A A 2.5 12.4 + - - +
1F ALA* 4.6 16.8 + - + +
92F GLY* 1.3 66.9 - - - -
94F ARG* 1.3 93.0 + - - +
95F MET 2.8 11.1 + - - -
96F TRP* 3.1 26.7 + - - +
97F GLU* 3.5 13.0 + - + +
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Residues in contact with ARG 94 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A C 5.1 9.6 - - - +
44A G 5.5 1.8 + - - +
58F ALA 5.7 0.2 + - - -
60F SER 3.4 22.1 + - - +
61F GLY* 4.0 22.6 + - - -
62F GLN* 5.4 7.4 - - - +
90F LEU* 3.3 30.7 - - + +
92F GLY 3.0 1.3 - - - -
93F GLU* 1.3 97.1 + - - +
95F MET* 1.3 57.7 + - - +
96F TRP 3.5 0.2 - - - -
97F GLU* 3.4 36.2 + - + +
98F PHE* 3.5 5.2 + - - +
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Residues in contact with MET 95 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30F VAL* 3.5 22.9 - - + +
31F GLU 2.9 29.4 - - - +
32F LYS* 3.7 10.8 - - - -
33F ILE* 4.3 16.5 - - + +
90F LEU* 3.2 28.6 - - - +
91F ARG 3.8 7.2 - - - +
92F GLY 2.9 16.9 + - - +
93F GLU 2.8 0.6 + - - -
94F ARG* 1.3 76.6 - - - +
96F TRP* 1.3 114.2 + - + +
97F GLU 3.1 1.3 - - - -
98F PHE* 3.6 4.9 + - - +
99F PHE* 3.3 22.8 + - + +
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Residues in contact with TRP 96 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A C 5.6 0.9 - - - -
45A A 6.2 2.0 - - - -
1F ALA 4.7 6.3 - - - +
2F LYS 3.8 15.5 - - - +
3F LEU* 3.6 29.5 - - + +
4F HIS* 2.8 55.3 + + + -
7F TYR* 4.0 19.5 - + - -
30F VAL* 3.5 38.6 - - + -
91F ARG 5.7 0.8 + - - -
92F GLY 4.4 8.3 + - - -
93F GLU* 3.1 17.7 + - - +
95F MET* 1.3 97.1 - - + +
97F GLU* 1.3 55.3 + - - +
99F PHE* 3.0 17.3 + + - +
100F GLU* 2.6 39.2 + - - +
172F PHE* 5.8 2.5 - + - -
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Residues in contact with GLU 97 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60F SER 5.9 0.7 - - - +
93F GLU* 3.5 11.1 + - + +
94F ARG* 3.4 45.3 + - + +
96F TRP* 1.3 73.5 - - - +
98F PHE* 1.3 58.0 + - + +
99F PHE 2.6 14.4 + - - -
100F GLU* 2.8 33.5 + - - +
101F ARG* 2.8 28.2 + - + +
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Residues in contact with PHE 98 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33F ILE* 4.1 26.5 - - + -
35F LEU* 4.0 18.4 - - + -
59F ILE* 3.4 39.9 - - + -
60F SER* 5.1 4.7 - - - -
90F LEU* 4.9 5.6 - - + -
94F ARG 3.5 9.4 + - - +
95F MET 4.0 7.2 - - - +
96F TRP 3.5 0.2 - - - -
97F GLU* 1.3 81.1 - - + +
99F PHE* 1.3 59.7 + + - +
101F ARG* 3.6 13.9 - - + -
102F LEU* 3.4 34.8 + - + +
137F PHE* 3.5 35.9 - + - -
153F ILE* 4.0 20.2 - - + -
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Residues in contact with PHE 99 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3F LEU* 3.5 29.8 - - + -
30F VAL* 6.0 4.5 - - + -
33F ILE* 5.5 6.1 - - + -
95F MET* 3.3 16.6 + - + +
96F TRP* 3.0 25.8 + + + +
97F GLU 2.6 5.1 + - - -
98F PHE* 1.3 72.6 - + - +
100F GLU* 1.3 54.4 + - - +
101F ARG 2.7 14.1 + - - -
102F LEU* 2.7 26.9 + - + +
103F ILE* 3.2 27.3 + - + +
155F ILE* 3.4 35.2 - - + -
169F LEU* 5.1 4.3 - - + -
172F PHE* 3.4 48.7 - + - -
173F ASP* 6.2 0.2 - - + -
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Residues in contact with GLU 100 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2F LYS* 3.7 39.7 - - + +
3F LEU* 4.1 15.8 - - + +
6F TYR* 6.2 0.9 - - + -
96F TRP 2.6 19.4 + - - +
97F GLU* 2.9 51.7 - - - +
99F PHE* 1.3 71.8 - - - +
101F ARG* 1.3 66.5 + - - +
102F LEU 3.5 0.9 - - - -
103F ILE* 4.4 3.8 - - - -
104F THR* 3.3 24.1 + - - +
105F ILE* 5.1 1.4 - - - +
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Residues in contact with ARG 101 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59F ILE* 4.5 6.7 + - - +
97F GLU* 2.8 17.5 + - + +
98F PHE* 3.6 15.9 - - + +
99F PHE 2.7 1.6 + - - -
100F GLU* 1.3 101.0 - - - +
102F LEU* 1.3 58.0 + - - +
105F ILE* 3.4 56.5 - - + +
137F PHE* 3.5 41.7 - - - +
138F PRO* 4.2 10.5 + - - +
139F GLU* 2.8 42.2 + - - -
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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