Contacts of the strand formed by residues 11 - 18 (chain B) 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 ILE 11 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B SER* 3.7 23.5 + - - +
10B ARG* 1.3 70.3 - - - +
12B LYS* 1.3 62.1 + - - +
13B LYS* 4.3 3.7 + - + +
34B GLU* 3.6 40.8 - - + +
35B VAL 3.4 2.5 - - - +
36B ASP* 3.7 30.3 - - + +
93B LEU* 3.2 26.2 - - - +
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Residues in contact with LYS 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B ARG 3.5 0.2 + - - -
11B ILE* 1.3 74.6 - - - +
13B LYS* 1.3 69.0 + - - +
14B PHE* 3.6 21.4 - - + -
33B TYR 3.5 1.6 - - - +
34B GLU* 3.4 2.9 - - - -
35B VAL* 2.7 36.2 + - - +
37B LEU* 3.5 30.3 - - + -
89B ILE* 4.3 4.9 - - + -
90B ASP* 2.8 35.7 + - - +
92B ASP 3.0 15.4 + - - +
93B LEU* 3.9 10.1 - - + +
95B LYS* 2.7 30.8 + - - +
97B THR* 3.2 27.3 + - - -
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Residues in contact with LYS 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B ILE* 5.4 4.0 - - + +
12B LYS* 1.3 85.5 - - - +
14B PHE* 1.3 64.0 + - - +
32B THR* 4.1 21.9 - - + +
33B TYR 3.3 4.5 - - - +
34B GLU* 3.4 32.0 + - + +
93B LEU 5.5 5.8 + - - +
95B LYS 4.9 1.7 + - - +
96B THR* 3.5 27.2 - - + +
97B THR 3.1 21.5 + - - -
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Residues in contact with PHE 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B LYS* 3.6 30.1 - - + -
13B LYS* 1.3 73.5 - - - +
15B SER* 1.3 59.2 + - - +
16B ILE* 3.9 19.7 + - + -
31B GLN 3.4 2.6 - - - +
32B THR* 3.1 4.5 - - - -
33B TYR* 2.8 39.2 + - - +
35B VAL* 4.1 24.2 - - + -
37B LEU* 4.8 1.6 - - + -
44B VAL* 4.7 8.7 - - + -
47B ALA* 3.8 28.5 - - + -
48B LEU* 6.2 0.7 - - + -
51B ILE* 4.8 6.1 - - + -
89B ILE* 3.9 22.7 - - + -
96B THR* 4.3 1.8 - - - -
97B THR* 3.4 34.1 - - + +
99B ILE* 4.0 18.6 - - + -
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Residues in contact with SER 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B PHE* 1.3 73.0 - - - +
16B ILE* 1.3 59.4 + - - +
30B MET* 3.4 33.5 - - - +
31B GLN 3.4 5.4 + - - -
32B THR* 4.3 10.6 + - - +
96B THR* 3.7 20.4 - - - +
97B THR 2.9 7.0 + - - +
98B LYS* 3.3 11.4 - - - +
99B ILE 2.9 25.3 + - - -
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Residues in contact with ILE 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B PHE* 4.1 16.2 - - + -
15B SER* 1.3 80.3 + - - +
17B TYR* 1.3 74.6 + - - +
18B ARG* 3.5 4.8 + - - +
30B MET* 3.4 4.7 - - - -
31B GLN 2.8 35.0 + - - +
33B TYR* 3.8 28.5 - - + -
48B LEU* 3.8 25.8 - - + -
51B ILE* 4.1 11.2 - - + -
59B LEU* 4.1 15.7 - - + -
99B ILE* 3.6 13.2 - - + +
111B LEU* 4.0 25.1 - - + -
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Residues in contact with TYR 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B ILE* 1.3 77.9 - - - +
18B ARG* 1.3 66.7 + - - +
19B TRP* 4.2 9.9 - - + -
28B PRO* 3.4 38.4 - - + +
29B ARG 3.5 7.0 - - - -
30B MET* 3.6 11.5 - - - -
99B ILE 3.0 17.6 + - - +
100B TYR* 4.0 21.1 - + + -
101B PRO* 3.5 25.1 - - + -
107B VAL* 3.9 16.8 - - + +
110B ASP* 3.4 31.9 - - - +
111B LEU* 3.9 8.4 - - + +
22C PRO* 3.5 17.0 - - - +
23C LEU 4.7 1.0 + - - -
24C SER* 4.6 3.5 - - - -
25C PRO* 4.0 17.7 - - + +
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Residues in contact with ARG 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B ILE* 3.6 15.0 - - - +
17B TYR* 1.3 85.7 - - - +
19B TRP* 1.3 64.1 + - - +
20B ASP* 6.3 1.0 - - - +
27B LYS 4.6 0.3 - - - +
28B PRO* 3.3 5.0 - - - +
29B ARG* 2.8 62.4 + - - +
31B GLN* 3.2 30.5 + - + +
33B TYR* 2.9 25.0 + - - -
56B ASP* 3.0 12.6 + - - -
58B THR* 3.2 28.1 + - - -
59B LEU* 3.7 18.0 - - - +
109B LYS* 5.5 1.6 - - - +
110B ASP* 2.9 35.1 + - - -
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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