Contacts of the helix formed by residues 27 - 40 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A GLY* 3.7 2.4 - - - -
26A ALA* 1.3 78.5 - - - +
28A GLY* 1.3 67.9 + - - +
29A ALA 3.3 2.5 - - - -
30A GLY 4.0 2.8 - - - +
31A LEU* 3.0 22.3 + - - +
55A SER* 3.7 20.2 + - - -
57A THR* 4.0 4.7 - - - -
158A LEU* 3.7 7.6 - - - -
212A ALA 5.0 4.1 + - - -
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Residues in contact with GLY 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A GLY* 1.3 72.3 - - - +
29A ALA* 1.3 61.4 + - - +
32A ARG* 3.2 25.3 + - - +
57A THR* 3.1 23.3 + - - -
157A LEU* 4.3 2.2 - - - -
158A LEU* 3.9 1.1 - - - +
161A LEU* 3.6 21.1 - - - +
417A LEU* 3.6 21.4 - - - +
418A VAL* 4.7 0.7 - - - +
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Residues in contact with ALA 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A GLY* 3.3 0.4 - - - -
28A GLY* 1.3 76.6 - - - +
30A GLY* 1.3 64.7 + - - +
32A ARG* 3.2 3.8 + - - +
33A ALA* 2.9 25.0 + - - +
212A ALA* 4.2 5.6 - - + +
395A CYS* 3.9 21.3 - - - +
396A GLY* 3.8 29.4 - - - +
417A LEU* 3.6 25.7 - - + +
421A GLY* 4.0 2.4 - - - -
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Residues in contact with GLY 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A VAL* 3.6 8.8 - - - +
25A GLY 3.2 26.5 - - - -
26A ALA* 4.6 0.2 - - - -
27A GLY* 3.6 5.6 + - - +
28A GLY 3.5 0.2 - - - -
29A ALA* 1.3 78.8 - - - +
31A LEU* 1.3 53.2 + - - +
33A ALA* 4.5 0.4 - - - -
34A ALA* 2.7 37.7 + - - +
46A CYS* 5.1 0.2 - - - -
212A ALA* 3.6 18.6 + - - +
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Residues in contact with LEU 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A GLY 4.1 0.8 + - - -
26A ALA* 3.5 28.0 - - + +
27A GLY 3.0 13.5 + - - +
28A GLY 4.3 1.3 - - - +
30A GLY* 1.3 76.4 - - - +
32A ARG* 1.3 62.6 + - - +
34A ALA* 3.7 2.8 - - - +
35A PHE* 3.0 32.9 + - + -
46A CYS* 5.0 0.7 - - - -
52A PRO* 4.3 9.4 - - + -
158A LEU* 3.7 20.9 - - + -
161A LEU* 4.2 13.2 - - + +
162A TYR* 3.9 31.0 - - + +
165A SER* 4.4 9.2 - - - +
172A TYR* 3.6 35.4 + - + +
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Residues in contact with ARG 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A GLY 3.2 17.5 + - - +
29A ALA 3.2 4.5 + - - +
31A LEU* 1.3 77.8 - - - +
33A ALA* 1.3 58.4 + - - +
35A PHE* 3.6 22.5 - - - -
36A GLY* 3.0 18.8 + - - -
39A GLU* 3.1 28.5 + - - -
109A GLU* 2.8 42.2 + - - -
110A LEU* 6.3 0.2 - - - -
113A TYR* 3.8 9.2 + - - -
161A LEU* 4.2 13.8 - - + +
418A VAL* 3.7 34.2 + - - +
421A GLY* 4.5 2.5 - - - +
422A ARG* 3.4 35.2 - - - +
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Residues in contact with ALA 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A VAL* 4.4 7.6 - - + -
29A ALA 2.9 16.8 + - - +
30A GLY* 3.6 4.3 - - - +
32A ARG* 1.3 76.5 - - - +
34A ALA* 1.3 58.1 + - - +
36A GLY* 3.2 0.9 + - - -
37A LEU* 2.9 40.4 + - + +
210A VAL* 4.3 23.1 - - + -
395A CYS* 4.6 0.7 - - - -
421A GLY* 3.5 25.0 + - - +
424A CYS* 4.9 3.1 - - + -
425A ALA* 4.1 2.8 - - - +
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Residues in contact with ALA 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A VAL* 3.9 16.1 - - + +
30A GLY 2.7 22.6 + - - +
31A LEU* 3.7 4.0 - - - +
33A ALA* 1.3 73.5 - - - +
35A PHE* 1.4 62.2 + - - +
37A LEU* 3.4 3.5 + - - +
38A SER* 3.2 23.9 + - - -
44A THR* 3.8 6.3 - - + +
46A CYS* 4.0 26.7 - - + -
170A THR* 3.8 12.3 + - + -
172A TYR* 4.2 6.5 - - - +
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Residues in contact with PHE 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A LEU 3.0 29.5 + - - -
32A ARG* 3.6 26.5 - - - -
34A ALA* 1.4 75.2 - - - +
36A GLY* 1.3 61.6 + - - +
38A SER* 3.7 2.3 - - - +
39A GLU* 2.7 39.0 + - - +
113A TYR* 3.4 26.5 - + - -
161A LEU* 3.7 34.1 - - + -
164A ARG* 3.8 16.4 - - + -
165A SER* 4.1 25.4 - - - -
168A TYR* 3.5 34.9 - + + -
170A THR* 4.0 11.0 - - - +
172A TYR* 4.9 0.2 - - - +
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Residues in contact with GLY 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A ARG* 3.0 24.1 + - - -
33A ALA 3.2 1.1 + - - -
35A PHE* 1.3 76.3 - - - +
37A LEU* 1.3 62.7 + - - +
39A GLU* 2.9 39.3 - - - +
40A ALA* 3.2 10.4 + - - +
425A ALA* 3.8 15.1 - - - +
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Residues in contact with LEU 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A ALA* 3.8 22.4 - - + -
23A VAL* 3.9 22.7 - - + -
33A ALA* 2.9 22.5 + - + +
34A ALA 3.7 2.0 - - - +
35A PHE 3.3 0.2 - - - -
36A GLY* 1.3 75.6 - - - +
38A SER* 1.3 62.9 + - - +
40A ALA* 3.0 13.3 + - - +
41A GLY 3.3 0.3 + - - -
42A PHE* 3.0 32.3 + - + +
44A THR* 3.3 17.5 - - + +
210A VAL* 4.4 12.8 - - + -
425A ALA* 3.8 24.2 - - + +
428A ILE* 3.8 32.1 - - + -
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Residues in contact with SER 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A ALA 3.2 9.8 + - - -
35A PHE 3.9 3.8 - - - -
37A LEU* 1.3 77.7 - - - +
39A GLU* 1.3 58.0 + - - +
41A GLY* 3.0 18.4 + - - -
42A PHE 3.5 11.4 + - - -
44A THR* 3.7 9.5 + - - -
168A TYR* 3.9 12.4 - - - -
169A ASP* 3.8 22.0 + - - +
170A THR* 2.6 36.4 + - - -
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Residues in contact with GLU 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A ARG* 3.1 24.5 + - - -
35A PHE* 2.7 22.7 + - - +
36A GLY* 2.9 39.4 - - - +
38A SER* 1.3 73.5 - - - +
40A ALA* 1.3 57.7 + - + +
41A GLY 3.3 0.9 + - - -
113A TYR* 4.8 2.1 + - - -
164A ARG* 5.3 1.0 + - - -
168A TYR* 3.5 37.1 + - + +
422A ARG* 5.3 2.3 + - - +
137B GLN* 5.9 0.7 + - - -
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Residues in contact with ALA 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A GLY 3.2 11.7 + - - +
37A LEU* 3.0 11.0 + - - +
39A GLU* 1.3 76.5 - - + +
41A GLY* 1.3 59.8 + - - +
42A PHE* 3.5 20.0 + - + -
425A ALA 5.6 1.1 - - - +
429A ALA* 4.1 19.1 - - + -
434A PRO* 4.1 5.7 - - - +
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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