Contacts of the helix formed by residues 152 - 166 (chain N) in PDB entry 2FBW
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 ARG 152 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60N ALA 3.7 5.4 - - - -
149N VAL* 2.9 16.4 + - + +
150N ALA* 4.7 12.7 - - - +
151N ASP* 1.3 93.3 + - - +
153N THR* 1.3 64.4 + - - +
154N GLY 3.3 3.1 + - - -
155N HIS* 3.3 26.4 + - + -
156N SER* 3.1 21.2 + - - +
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Residues in contact with THR 153 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60N ALA* 3.5 0.6 + - - -
61N GLN 3.0 21.9 + - - -
63N GLY* 3.4 27.7 - - - -
64N ILE* 4.4 5.2 - - + -
115N MET* 3.5 23.8 - - + +
147N CYS 4.0 7.9 - - - +
148N CYS* 3.3 8.7 - - - +
149N VAL* 3.0 27.5 + - - +
150N ALA 4.0 0.3 + - - -
152N ARG* 1.3 74.7 - - - +
154N GLY* 1.3 59.0 + - - +
156N SER* 3.3 1.7 + - - -
157N LEU* 2.8 29.6 + - + +
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Residues in contact with GLY 154 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57N THR* 3.2 26.1 - - - +
60N ALA* 2.7 29.2 + - - +
153N THR* 1.3 71.2 - - - +
155N HIS* 1.3 58.7 + - - +
157N LEU* 3.6 7.0 - - - +
158N LEU* 2.8 34.5 + - - +
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Residues in contact with HIS 155 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58N VAL* 3.2 32.2 + - - +
60N ALA 3.7 1.6 + - - -
152N ARG* 3.3 30.9 + - + +
154N GLY* 1.3 74.6 - - - +
156N SER* 1.3 69.4 + - - +
158N LEU* 4.0 0.3 - - - -
159N HIS* 3.0 68.4 + + + +
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Residues in contact with SER 156 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115N MET* 4.2 2.2 - - - -
116N PRO* 3.6 21.4 - - - +
149N VAL* 3.5 42.0 - - - +
152N ARG* 3.1 8.6 + - - +
153N THR 3.9 2.0 - - - -
155N HIS* 1.3 84.3 - - - +
157N LEU* 1.3 59.2 + - - +
159N HIS* 4.3 3.7 - - - +
160N THR* 2.6 37.9 + - - -
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Residues in contact with LEU 157 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28N GLY* 4.5 4.9 - - - -
57N THR* 3.9 20.9 - - + -
64N ILE* 4.3 18.2 - - + -
110N LEU* 3.6 35.6 - - + +
115N MET* 3.8 19.9 - - + +
153N THR* 2.8 23.4 + - + +
154N GLY* 3.6 5.8 - - - +
156N SER* 1.3 74.7 - - - +
158N LEU* 1.3 59.2 + - - +
160N THR* 3.7 1.4 - - - -
161N LEU* 3.0 52.0 + - + +
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Residues in contact with LEU 158 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26N ALA 3.9 4.3 - - - +
27N GLY* 3.7 22.9 - - - -
28N GLY* 3.9 5.6 - - - +
31N LEU* 3.7 27.4 - - + -
52N PRO 3.4 20.4 - - - +
53N THR* 3.4 19.1 - - - -
55N SER* 4.0 7.4 - - - +
57N THR* 3.9 9.0 - - + -
58N VAL* 3.5 31.6 - - + +
154N GLY 2.8 20.5 + - - +
155N HIS 4.2 2.0 - - - +
157N LEU* 1.3 77.0 - - - +
159N HIS* 1.3 58.4 + - - +
161N LEU* 3.9 2.2 - - + -
162N TYR* 2.9 31.1 + - - +
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Residues in contact with HIS 159 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53N THR* 3.6 34.1 + - + +
54N ARG* 6.1 1.6 - - - -
58N VAL* 4.0 12.4 - - + +
155N HIS* 3.0 61.3 + + - +
156N SER* 4.3 3.6 - - - +
158N LEU* 1.3 77.1 - - - +
160N THR* 1.3 56.3 + - - +
162N TYR* 3.5 7.3 + - - +
163N GLY* 3.0 24.3 + - - -
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Residues in contact with THR 160 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110N LEU* 4.1 5.2 - - + +
113N TYR* 3.5 39.6 - - + +
114N GLY 4.2 1.3 - - - -
115N MET* 3.4 34.4 + - + +
116N PRO* 4.1 4.5 - - - +
156N SER 2.6 23.7 + - - -
157N LEU* 3.7 4.0 - - - -
159N HIS* 1.3 73.9 - - - +
161N LEU* 1.3 60.7 + - - +
163N GLY* 3.4 2.3 + - - -
164N ARG* 2.9 26.9 + - - +
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Residues in contact with LEU 161 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28N GLY* 3.6 29.2 - - - +
31N LEU* 4.2 14.9 - - + +
32N ARG* 4.2 14.8 - - + +
35N PHE* 3.8 29.8 - - + -
110N LEU* 3.9 23.6 - - + -
113N TYR* 4.0 9.9 - - + -
157N LEU* 3.0 39.9 + - + +
158N LEU* 4.0 3.4 - - - +
160N THR* 1.3 76.2 - - - +
162N TYR* 1.3 58.2 + - - +
164N ARG* 3.3 5.0 + - - +
165N SER* 2.9 28.9 + - - -
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Residues in contact with TYR 162 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31N LEU* 3.9 13.4 - - + +
51N PHE* 3.4 31.5 - + - -
52N PRO* 3.8 32.3 - - + -
53N THR* 3.8 24.5 - - + -
158N LEU 2.9 18.9 + - - +
159N HIS* 3.8 5.8 - - - +
160N THR 3.2 0.2 - - - -
161N LEU* 1.3 76.6 - - - +
163N GLY* 1.3 64.5 + - - +
165N SER* 2.5 28.7 + - - -
166N LEU* 3.3 39.5 + - + +
172N TYR* 6.0 6.1 - + - -
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Residues in contact with GLY 163 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159N HIS 3.0 15.7 + - - -
160N THR* 3.8 2.5 - - - -
162N TYR* 1.3 78.0 - - - +
164N ARG* 1.3 62.8 + - - +
166N LEU* 3.1 31.7 + - - +
167N ARG* 4.0 6.2 + - - +
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Residues in contact with ARG 164 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35N PHE* 3.8 24.0 - - + -
39N GLU* 5.3 3.2 + - - -
112N ASN 5.1 2.8 + - - -
113N TYR* 3.3 51.6 + - + +
160N THR 2.9 17.9 + - - +
161N LEU* 3.6 8.3 - - - +
163N GLY* 1.3 76.2 - - - +
165N SER* 1.3 62.1 + - - +
167N ARG* 3.0 55.3 + - - +
168N TYR* 3.2 32.3 + - + -
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Residues in contact with SER 165 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31N LEU* 4.3 5.2 - - - -
35N PHE* 4.1 22.6 - - - -
161N LEU 2.9 14.9 + - - -
162N TYR* 2.5 33.8 + - - -
164N ARG* 1.3 75.4 - - - +
166N LEU* 1.3 60.2 + - - +
167N ARG 3.1 2.0 + - - -
168N TYR* 3.4 19.7 + - - +
170N THR* 4.8 1.2 + - - -
172N TYR* 3.4 37.5 + - - -
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Residues in contact with LEU 166 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162N TYR* 3.4 48.0 - - + +
163N GLY* 3.3 20.4 - - - +
164N ARG 3.1 0.8 - - - -
165N SER* 1.3 77.9 + - - +
167N ARG* 1.3 60.3 + - + +
168N TYR 3.4 5.0 + - - +
172N TYR* 6.3 2.0 - - + -
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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