Contacts of the helix formed by residues 87 - 102 (chain F) in PDB entry 3NBT
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 LYS 87 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85F ILE* 3.6 2.3 - - - +
86F LYS* 1.3 80.2 - - - +
88F LYS* 1.3 68.3 + - + +
89F THR* 3.6 15.8 - - - +
90F GLU* 3.4 51.2 + - + +
91F ARG* 3.2 22.9 + - - +
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Residues in contact with LYS 88 (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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65E MET* 3.5 24.4 - - + +
86F LYS 3.2 4.0 + - - -
87F LYS* 1.3 75.9 - - + +
89F THR* 1.3 63.5 + - - +
91F ARG* 3.3 22.4 + - - +
92F GLU* 3.0 43.8 + - - +
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Residues in contact with THR 89 (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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5E LYS* 6.0 2.2 - - - +
87F LYS* 3.3 16.7 - - - +
88F LYS* 1.3 75.0 - - - +
90F GLU* 1.3 61.7 + - + +
92F GLU* 3.1 19.2 + - - +
93F ASP* 2.9 44.5 + - - +
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Residues in contact with GLU 90 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9E ILE* 3.4 25.9 - - + +
13E LYS* 4.2 13.5 + - - -
47F THR* 4.8 10.6 + - - -
85F ILE* 3.5 21.6 - - + +
87F LYS* 3.3 40.0 + - + +
89F THR* 1.3 77.6 - - + +
91F ARG* 1.3 58.9 + - - +
93F ASP* 3.2 3.7 + - - +
94F LEU* 2.9 30.8 + - - +
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Residues in contact with ARG 91 (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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65E MET* 3.2 63.8 + - - +
66E GLU* 5.2 0.4 - - - +
68E LEU* 3.9 10.5 - - + -
69E GLU* 3.6 35.4 + - - +
85F ILE* 2.9 40.0 + - + +
86F LYS 2.9 20.0 + - - -
87F LYS 3.2 6.1 + - - +
88F LYS* 3.3 29.4 - - - +
90F GLU* 1.3 79.1 - - - +
92F GLU* 1.3 58.9 + - - +
94F LEU* 3.9 6.1 - - - +
95F ILE* 2.9 37.9 + - + +
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Residues in contact with GLU 92 (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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1E GLY* 3.9 10.7 - - - -
65E MET* 3.7 16.6 - - + +
88F LYS* 3.0 41.8 + - - +
89F THR* 3.1 23.7 + - - +
91F ARG* 1.3 75.2 - - - +
93F ASP* 1.3 69.3 + - - +
95F ILE* 3.4 4.4 + - - +
96F ALA* 3.0 24.1 + - - +
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Residues in contact with ASP 93 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1E GLY* 3.6 3.8 - - - -
2E ASP* 2.7 47.4 + - - +
5E LYS* 3.3 26.6 + - + +
6E GLY* 3.3 17.1 - - - +
9E ILE* 4.4 5.4 - - + +
89F THR* 2.9 34.8 + - - +
90F GLU* 3.7 5.8 - - - +
92F GLU* 1.3 75.8 - - - +
94F LEU* 1.3 63.4 + - - +
96F ALA* 3.1 4.5 + - - +
97F TYR 3.0 18.2 + - - -
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Residues in contact with LEU 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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6E GLY* 3.6 24.8 - - - +
9E ILE* 4.0 8.3 - - + +
10E PHE* 3.7 35.9 - - + +
14E CYS* 4.3 0.2 - - - -
68E LEU* 4.0 11.7 - - + -
105E HEC 3.5 37.0 - - + -
85F ILE* 3.7 17.5 - - + -
90F GLU 2.9 16.6 + - - +
91F ARG* 3.9 4.0 - - - +
93F ASP* 1.3 77.2 - - - +
95F ILE* 1.3 57.1 + - - +
97F TYR* 3.1 6.1 + - + +
98F LEU* 2.9 39.9 + - + +
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Residues in contact with ILE 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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36E PHE* 4.0 13.9 - - + -
61E GLU* 3.7 31.2 - - + +
64E LEU* 3.6 15.3 - - + +
65E MET* 3.4 57.9 - - + +
68E LEU* 3.9 17.0 - - + -
91F ARG 2.9 15.6 + - - +
92F GLU* 3.8 4.5 - - - +
94F LEU* 1.3 73.4 - - - +
96F ALA* 1.3 61.2 + - - +
98F LEU* 3.3 8.6 + - + +
99F LYS* 2.8 29.2 + - + +
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Residues in contact with ALA 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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1E GLY* 3.4 33.9 - - - +
3E VAL* 3.5 19.1 - - + +
92F GLU 3.0 15.3 + - - +
93F ASP 3.1 8.7 + - - +
95F ILE* 1.3 76.7 - - - +
97F TYR* 1.3 62.7 + - - +
99F LYS* 3.3 12.7 + - + +
100F LYS* 3.1 16.8 + - - +
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Residues in contact with TYR 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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3E VAL* 3.6 25.2 - - + +
6E GLY* 3.4 19.7 - - - -
7E LYS* 3.6 42.5 - - + +
10E PHE* 3.6 44.8 - + + -
11E VAL* 6.1 0.2 - - - +
20E VAL* 4.0 12.3 - - + +
93F ASP 3.0 6.7 + - - -
94F LEU 3.3 9.4 - - - +
96F ALA* 1.3 77.3 - - - +
98F LEU* 1.3 60.5 + - + +
100F LYS* 3.0 5.8 + - + +
101F ALA* 2.8 59.0 + - + +
104F GLU* 5.7 0.9 - - - -
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Residues in contact with LEU 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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10E PHE* 3.8 32.1 - - + -
20E VAL* 4.2 14.4 - - + -
32E LEU* 4.4 7.6 - - + -
35E LEU* 5.0 7.9 - - + -
36E PHE* 3.8 10.5 - - + -
64E LEU* 4.7 15.5 - - + -
68E LEU* 4.8 4.9 - - + -
105E HEC 3.8 23.6 - - + -
94F LEU* 2.9 26.6 + - + +
95F ILE* 3.7 12.3 - - - +
97F TYR* 1.3 76.7 - - + +
99F LYS* 1.3 58.4 + - - +
101F ALA* 4.4 1.1 - - - +
102F THR* 2.6 49.1 + - + +
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Residues in contact with LYS 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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36E PHE* 3.7 30.0 - - + -
61E GLU* 2.7 43.0 + - + +
95F ILE* 2.8 17.7 + - + +
96F ALA* 3.4 12.8 - - - +
98F LEU* 1.3 77.5 - - - +
100F LYS* 1.3 61.1 + - - +
103F ASN* 2.9 36.3 + - - +
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Residues in contact with LYS 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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3E VAL* 4.2 24.4 - - + +
96F ALA 3.1 11.2 + - - +
97F TYR* 3.0 10.2 + - + +
99F LYS* 1.3 80.3 - - - +
101F ALA* 1.3 62.0 + - + +
103F ASN* 4.0 1.0 - - - +
104F GLU* 2.9 53.4 + - + +
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Residues in contact with ALA 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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20E VAL* 3.7 29.1 - - + +
21E GLU* 4.8 2.3 + - - -
33E HIS* 4.0 2.4 + - - -
97F TYR* 2.8 49.0 + - + +
98F LEU* 4.5 0.9 - - - +
100F LYS* 1.3 73.9 - - - +
102F THR* 1.3 60.5 + - - +
103F ASN 3.5 0.2 + - - -
104F GLU* 3.1 25.7 + - - +
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Residues in contact with THR 102 (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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20E VAL* 4.0 16.4 - - + -
32E LEU* 3.2 42.0 - - + +
33E HIS* 2.9 24.0 + - - -
34E GLY* 2.9 20.0 + - - -
35E LEU* 4.3 5.0 + - + +
36E PHE* 3.5 20.4 - - - -
98F LEU* 2.6 39.9 + - + +
99F LYS 4.3 0.3 + - - -
101F ALA* 1.3 75.3 - - - +
103F ASN* 1.3 60.3 + - - +
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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