Contacts of the helix formed by residues 27 - 40 (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 GLY 27 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25N GLY* 3.7 1.8 - - - -
26N ALA* 1.3 80.3 - - - +
28N GLY* 1.3 66.7 + - - -
29N ALA 3.3 2.9 - - - -
30N GLY 4.3 2.8 - - - +
31N LEU* 3.0 23.7 + - - +
55N SER* 3.8 20.7 + - - -
57N THR* 4.0 4.5 - - - -
158N LEU* 3.7 7.0 - - - -
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Residues in contact with GLY 28 (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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27N GLY* 1.3 73.0 - - - +
29N ALA* 1.3 61.1 + - - +
32N ARG* 3.2 25.5 + - - +
57N THR* 3.1 30.8 + - - -
157N LEU* 4.5 4.0 - - - -
158N LEU* 3.9 1.3 - - - +
161N LEU* 3.6 21.7 - - - +
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Residues in contact with ALA 29 (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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27N GLY 3.3 0.4 - - - -
28N GLY* 1.3 77.1 - - - +
30N GLY* 1.3 58.7 + - - +
32N ARG* 3.1 5.0 + - - +
33N ALA* 2.8 31.4 + - - +
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Residues in contact with GLY 30 (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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23N VAL* 3.6 14.9 - - - +
24N VAL 5.5 0.4 - - - -
25N GLY* 3.2 28.5 - - - -
27N GLY* 3.6 5.3 + - - +
28N GLY 3.5 0.2 - - - -
29N ALA* 1.3 78.8 - - - +
31N LEU* 1.3 57.1 + - - +
33N ALA* 4.4 1.6 - - - -
34N ALA* 2.8 32.8 + - - +
46N CYS* 5.0 0.2 - - - -
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Residues in contact with LEU 31 (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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25N GLY 4.1 1.2 + - - -
26N ALA* 3.5 27.1 - - + +
27N GLY 3.0 14.8 + - - +
28N GLY 4.3 1.3 - - - +
30N GLY* 1.3 76.9 - - - +
32N ARG* 1.3 63.0 + - - +
34N ALA* 3.1 2.7 + - - +
35N PHE* 3.0 33.1 + - + -
46N CYS* 5.0 0.2 - - - -
52N PRO* 4.3 10.1 - - + -
158N LEU* 3.7 21.5 - - + -
161N LEU* 4.2 12.1 - - + +
162N TYR* 3.9 30.3 - - + +
165N SER* 4.3 11.2 - - - +
172N TYR* 3.5 35.4 + - + +
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Residues in contact with ARG 32 (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 3.2 16.7 + - - +
29N ALA* 3.1 6.1 + - - +
31N LEU* 1.3 78.4 - - - +
33N ALA* 1.3 58.2 + - - +
35N PHE* 3.6 25.1 - - - -
36N GLY* 3.0 31.3 + - - -
39N GLU* 4.3 9.3 + - - -
109N GLU* 2.9 41.6 + - - -
110N LEU* 6.3 0.2 - - - -
113N TYR* 3.8 9.9 + - - -
161N LEU* 4.2 14.1 - - + +
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Residues in contact with ALA 33 (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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23N VAL* 4.4 14.4 - - + -
29N ALA 2.8 16.8 + - - +
30N GLY* 3.7 5.2 - - - +
32N ARG* 1.3 77.0 - - - +
34N ALA* 1.3 58.3 + - - +
36N GLY* 3.7 0.7 - - - -
37N LEU* 2.9 40.0 + - + +
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Residues in contact with ALA 34 (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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23N VAL* 3.9 16.4 - - + +
30N GLY 2.8 23.3 + - - +
31N LEU 3.1 3.1 + - - +
33N ALA* 1.3 75.5 - - - +
35N PHE* 1.3 61.7 + - - +
37N LEU* 3.4 3.6 + - - +
38N SER* 3.2 23.9 + - - -
44N THR* 3.9 5.9 - - + +
46N CYS* 4.1 22.0 - - + -
170N THR* 3.8 8.6 + - + -
172N TYR* 3.9 15.7 - - - +
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Residues in contact with PHE 35 (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 3.0 29.6 + - - -
32N ARG* 3.6 27.8 - - - -
34N ALA* 1.3 75.3 - - - +
36N GLY* 1.3 60.4 + - - +
38N SER* 3.8 1.5 - - - -
39N GLU* 2.7 36.7 + - - +
113N TYR* 3.4 25.6 - - - -
161N LEU* 3.8 33.4 - - + -
164N ARG* 3.8 18.4 - - + -
165N SER* 4.1 24.7 - - - -
168N TYR* 3.5 36.5 - + + -
170N THR* 4.0 11.0 - - - +
172N TYR* 4.6 0.2 + - - -
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Residues in contact with GLY 36 (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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32N ARG* 3.0 35.1 + - - -
33N ALA 3.7 0.9 - - - -
34N ALA 3.3 0.2 - - - -
35N PHE* 1.3 75.7 - - - +
37N LEU* 1.3 63.3 + - - +
39N GLU* 3.4 9.5 + - - +
40N ALA* 3.2 21.8 + - - +
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Residues in contact with LEU 37 (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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21N ALA* 3.8 25.8 - - + -
23N VAL* 3.9 21.8 - - + -
33N ALA* 2.9 24.3 + - + +
34N ALA 3.7 2.5 - - - +
36N GLY* 1.3 75.1 - - - +
38N SER* 1.3 62.1 + - - +
40N ALA* 3.1 12.9 + - + +
41N GLY 3.3 0.3 + - - -
42N PHE* 3.0 43.0 + - + +
44N THR* 3.3 17.5 - - + +
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Residues in contact with SER 38 (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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34N ALA 3.2 12.1 + - - -
35N PHE 3.8 3.8 - - - -
36N GLY 3.3 0.4 - - - -
37N LEU* 1.3 75.7 - - - +
39N GLU* 1.3 62.8 + - - +
41N GLY* 3.0 14.4 + - - -
42N PHE 3.5 11.0 + - - -
44N THR* 3.7 9.2 + - - -
168N TYR* 3.9 17.3 - - - -
169N ASP* 4.0 16.2 + - - +
170N THR* 2.6 35.5 + - - -
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Residues in contact with GLU 39 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32N ARG* 4.3 11.0 + - - -
35N PHE* 2.7 33.9 + - - +
36N GLY* 3.7 10.5 - - - +
38N SER* 1.3 73.2 - - - +
40N ALA* 1.3 58.0 + - - +
41N GLY 3.3 1.1 + - - -
113N TYR* 4.9 2.4 + - - -
164N ARG* 5.3 3.1 + - - -
168N TYR* 3.6 35.5 + - + -
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Residues in contact with ALA 40 (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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36N GLY 3.2 11.3 + - - +
37N LEU* 3.1 11.7 + - + +
39N GLU* 1.3 77.2 - - - +
41N GLY* 1.3 58.3 + - - +
42N PHE* 3.5 23.2 + - + -
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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