Contacts of the helix formed by residues 2 - 14 (chain F) in PDB entry 1BJJ
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 LEU 2 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1F ASN* 1.3 72.4 + - - +
3F LEU* 1.3 58.7 + - + +
5F PHE* 3.1 20.3 + - + +
6F ASN* 2.8 36.3 + - - +
31F TRP* 5.2 4.9 - - + -
48F HIS* 5.4 0.7 - - + -
52F TYR* 4.1 25.4 - - + +
69F LYS* 2.7 55.6 + - + +
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Residues in contact with LEU 3 (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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86B LYS* 5.8 13.7 - - + +
1F ASN* 2.8 24.5 + - - +
2F LEU* 1.3 75.0 - - + +
4F GLN* 1.3 61.1 + - + +
6F ASN* 3.5 22.5 - - + +
7F LYS* 3.4 24.9 + - - +
72F ILE* 6.3 0.2 - - + -
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Residues in contact with GLN 4 (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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1F ASN* 2.8 37.3 + - + +
3F LEU* 1.3 76.3 - - + +
5F PHE* 1.3 66.8 + - - +
6F ASN 3.2 0.4 - - - -
7F LYS* 3.2 10.8 + - - +
8F MET* 3.0 25.6 + - - +
72F ILE* 3.3 15.5 - - + +
73F TYR* 2.9 66.7 + - + +
75F TYR* 3.8 21.2 + - + -
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Residues in contact with PHE 5 (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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1F ASN 3.2 3.8 + - - -
2F LEU* 3.1 26.9 + - + +
4F GLN* 1.3 77.5 - - - +
6F ASN* 1.3 65.3 + - - +
8F MET* 2.9 17.7 + - + +
9F ILE* 2.8 49.3 + - + +
48F HIS* 3.2 39.0 - + - -
73F TYR* 3.8 3.0 + - - -
99F ASP* 3.4 39.7 - - + +
102F ALA* 3.6 17.0 - - + -
103F ALA* 4.0 4.0 - - + -
106F PHE* 4.2 9.2 - + - -
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Residues in contact with ASN 6 (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 LEU* 2.8 18.3 + - - +
3F LEU* 3.5 27.6 - - + +
5F PHE* 1.3 78.8 - - - +
7F LYS* 1.3 56.6 + - - +
9F ILE* 3.3 7.2 + - - +
10F LYS* 3.0 29.6 + - - +
18F ALA* 2.9 35.5 + - + +
19F ILE* 5.6 7.3 - - - +
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Residues in contact with LYS 7 (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 3.4 12.7 + - - +
4F GLN* 3.2 12.7 + - - +
6F ASN* 1.3 78.3 - - - +
8F MET* 1.3 59.0 + - - +
10F LYS* 3.3 7.8 + - + +
12F GLU* 2.9 34.2 + - + +
75F TYR* 3.4 21.8 - - + +
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Residues in contact with MET 8 (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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4F GLN 3.0 11.4 + - - +
5F PHE* 2.9 11.3 + - + +
7F LYS* 1.3 76.4 - - - +
9F ILE* 1.3 55.8 + - - +
12F GLU* 3.3 3.3 + - - +
13F GLU* 2.8 34.7 + - - +
73F TYR* 3.9 13.5 - - - +
75F TYR* 3.9 25.6 - - + -
82F ILE* 3.6 32.5 - - + -
96F CYS* 4.9 2.5 - - - +
99F ASP* 3.0 54.1 - - + +
100F ARG* 3.2 6.7 - - - +
103F ALA* 3.9 9.6 - - + -
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Residues in contact with ILE 9 (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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5F PHE* 2.8 50.5 + - + +
6F ASN* 3.7 7.4 - - - +
7F LYS 3.3 0.2 - - - -
8F MET* 1.3 74.4 - - - +
10F LYS* 1.3 56.7 + - - +
13F GLU* 4.5 2.0 - - - +
14F THR* 2.7 54.6 + - + +
16F LYS 4.1 6.1 - - - +
18F ALA* 4.3 23.6 - - + +
22F TYR* 3.7 26.2 - - + -
103F ALA* 4.4 5.2 - - + -
106F PHE* 3.6 28.5 - - + -
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Residues in contact with LYS 10 (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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6F ASN 3.0 16.3 + - - +
7F LYS* 3.6 8.3 - - + +
9F ILE* 1.3 77.0 - - - +
12F GLU* 1.3 58.0 + - - +
15F GLY* 2.8 51.5 + - - +
16F LYS 3.1 15.7 - - - +
17F ASN* 2.6 34.3 - - - +
18F ALA 5.2 0.2 - - - +
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Residues in contact with GLU 12 (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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7F LYS* 2.9 21.5 + - + +
8F MET* 3.6 7.4 - - - +
10F LYS* 1.3 80.0 - - - +
13F GLU* 1.3 67.0 + - - +
15F GLY* 4.4 1.4 + - - -
77F LEU* 4.4 35.7 - - + +
82F ILE* 4.9 3.6 - - + -
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Residues in contact with GLU 13 (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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8F MET 2.8 13.4 + - - +
9F ILE 4.1 1.3 - - - +
12F GLU* 1.3 85.0 - - - +
14F THR* 1.3 60.1 + - + +
77F LEU* 5.7 0.2 - - - +
80F GLY 4.9 7.4 - - - +
82F ILE* 3.4 37.2 + - + +
103F ALA 3.3 30.1 - - - +
104F GLU* 3.6 15.9 - - + +
107F ARG* 2.8 64.4 + - + +
110F LEU* 5.0 0.2 - - - +
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Residues in contact with THR 14 (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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9F ILE* 2.7 30.3 + - + +
13F GLU* 1.3 77.0 - - - +
15F GLY* 1.3 57.3 + - - +
16F LYS* 3.0 34.6 + - - +
22F TYR* 3.6 18.4 - - + +
103F ALA 4.3 3.1 - - - +
106F PHE* 3.5 32.5 - - + -
107F ARG* 4.0 8.7 - - - +
110F LEU* 4.1 20.6 - - + +
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Residues in contact with GLY 15 (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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10F LYS* 2.8 42.9 + - - +
12F GLU 4.3 1.9 + - - -
13F GLU 3.7 1.0 - - - -
14F THR* 1.3 76.7 + - - +
16F LYS* 1.3 60.1 + - - +
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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