Contacts of the strand formed by residues 14 - 24 (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 VAL 14 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A THR 5.8 3.4 - - - +
12A TYR* 3.7 14.6 - - + +
13A PRO* 1.3 74.2 - - - +
15A VAL* 1.3 66.2 + - - +
16A ASP* 3.8 20.9 - - - +
192A ILE* 6.0 0.2 - - + -
201A ILE* 3.3 20.0 - - + +
203A ARG* 4.0 26.0 - - + +
450A VAL* 6.0 3.1 - - + -
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Residues in contact with VAL 15 (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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13A PRO* 4.9 3.8 - - + +
14A VAL* 1.3 78.9 - - - +
16A ASP* 1.3 63.0 + - - +
17A HIS* 3.6 25.2 - - + +
200A THR* 4.9 10.1 - - + -
201A ILE 2.7 11.0 + - - +
202A HIS* 3.1 31.5 - - + +
203A ARG 2.8 30.5 + - - -
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Residues in contact with ASP 16 (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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14A VAL* 3.8 5.6 - - - +
15A VAL* 1.3 79.8 - - - +
17A HIS* 1.3 65.6 + - - +
18A GLU* 5.8 1.1 - - + -
203A ARG* 2.8 58.8 + - - +
205A ARG* 4.9 16.0 + - - +
441A ILE* 5.1 0.2 - - - +
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Residues in contact with HIS 17 (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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15A VAL* 3.6 23.2 - - + +
16A ASP* 1.3 75.9 + - - +
18A GLU* 1.3 64.3 + - - +
19A PHE* 3.4 22.4 - - + -
173A PHE* 3.7 28.2 - + - -
202A HIS* 2.9 35.7 + + + +
203A ARG 2.8 18.6 + - - +
204A PHE* 3.7 20.4 - + + -
205A ARG* 2.9 31.6 + - - +
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Residues in contact with GLU 18 (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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16A ASP* 5.8 1.3 - - + -
17A HIS* 1.3 75.8 - - - +
19A PHE* 1.3 69.1 + - - +
43A ASN* 3.9 10.0 + - - -
205A ARG* 2.7 37.8 + - - +
438A VAL* 3.9 24.3 - - + +
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Residues in contact with PHE 19 (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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17A HIS* 3.4 29.6 - - + -
18A GLU* 1.3 78.9 - - - +
20A ASP* 1.3 64.6 + - - +
21A ALA 3.5 17.9 - - - +
22A VAL* 5.4 1.3 - - + -
43A ASN* 3.5 33.0 - - - +
44A THR 4.4 0.2 - - - -
45A ALA* 3.7 24.7 - - + -
171A SER* 3.7 25.4 - - - -
173A PHE* 3.7 24.0 - + - -
204A PHE* 4.0 12.6 - + + -
205A ARG 2.9 20.4 + - - +
206A ALA* 3.3 8.3 - - + -
207A LYS 4.1 0.9 + - - -
438A VAL* 4.3 8.1 - - - +
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Residues in contact with ASP 20 (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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19A PHE* 1.3 72.6 - - - +
21A ALA* 1.3 59.9 + - - +
42A PHE* 3.8 17.0 - - + -
43A ASN* 2.8 44.6 + - - +
206A ALA* 3.7 0.9 - - - -
207A LYS* 3.3 27.3 + - - +
208A ASN* 3.5 8.7 + - - +
428A ILE* 6.1 0.2 - - - +
433A LYS 4.8 0.6 - - - +
434A PRO* 3.7 12.9 - - - +
435A GLY* 2.9 35.3 + - - -
436A GLU 4.3 6.9 + - - +
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Residues in contact with ALA 21 (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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19A PHE* 3.4 6.9 - - - +
20A ASP* 1.3 81.7 - - + +
22A VAL* 1.3 61.5 + - - +
37A LEU* 3.8 34.5 - - + -
42A PHE* 5.1 3.8 - - + -
43A ASN 3.3 1.8 + - - -
44A THR* 3.4 11.2 - - + +
45A ALA 3.0 23.3 + - - -
206A ALA* 3.7 4.0 - - - -
208A ASN* 3.2 18.6 - - + +
210A VAL* 5.7 0.9 - - + -
428A ILE* 5.3 1.3 - - + -
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Residues in contact with VAL 22 (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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19A PHE* 5.5 1.3 - - + -
21A ALA* 1.3 75.1 - - - +
23A VAL* 1.3 68.7 + - - +
24A VAL* 4.3 10.3 - - + -
45A ALA* 3.3 13.2 - - + +
47A VAL* 4.1 22.4 - - + -
190A GLY* 4.5 5.4 - - - -
191A VAL* 4.4 14.1 - - + -
204A PHE* 4.4 15.0 - - + +
206A ALA* 3.8 12.8 - - + -
208A ASN 3.1 4.8 + - - +
209A THR* 3.2 28.0 - - + +
210A VAL* 2.9 24.9 + - - +
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Residues in contact with VAL 23 (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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22A VAL* 1.3 76.7 - - - +
24A VAL* 1.3 64.4 + - - +
25A GLY 3.6 13.4 + - - +
30A GLY* 3.6 27.1 - - - +
33A ALA* 4.4 4.5 - - + -
34A ALA* 3.9 22.2 - - + +
37A LEU* 3.9 27.6 - - + -
44A THR* 4.1 2.9 - - + -
45A ALA 2.7 15.0 + - - +
46A CYS* 3.3 2.5 - - - -
47A VAL* 2.8 28.2 + - - +
210A VAL* 3.5 22.0 - - + +
212A ALA* 4.6 0.7 - - + -
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Residues in contact with VAL 24 (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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22A VAL* 4.3 8.3 - - + -
23A VAL* 1.3 73.2 - - - +
25A GLY* 1.3 58.3 + - - +
47A VAL* 3.5 13.2 - - + +
178A ALA* 3.7 25.8 - - + -
191A VAL* 3.9 33.7 - - + -
209A THR* 4.7 0.9 - - + -
210A VAL 2.8 15.8 + - - +
211A ILE* 4.2 13.0 - - + -
212A ALA* 2.7 34.1 + - - +
213A THR* 3.6 21.9 + - + -
236A MET* 4.4 3.8 - - + -
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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