Contacts of the strand formed by residues 44 - 48 (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 THR 44 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19N PHE* 3.9 4.3 - - - -
21N ALA* 3.3 12.0 - - - +
23N VAL* 4.0 8.3 - - + -
34N ALA* 3.9 16.6 - - - +
37N LEU* 3.3 35.6 - - + +
38N SER* 3.7 15.0 + - - -
42N PHE* 2.8 20.5 + - - +
43N ASN* 1.3 73.7 + - - +
45N ALA* 1.3 70.5 + - - +
169N ASP 4.8 1.0 + - - +
170N THR* 3.6 6.9 - - + +
171N SER* 3.0 26.7 + - - -
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Residues in contact with ALA 45 (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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19N PHE* 3.8 33.8 - - + -
21N ALA 2.9 10.0 + - - +
22N VAL* 3.3 11.6 - - + -
23N VAL* 2.7 34.5 + - - +
44N THR* 1.3 77.3 - - - +
46N CYS* 1.3 54.4 + - - +
47N VAL* 4.1 3.8 - - + -
171N SER 3.3 4.9 - - - -
173N PHE* 3.9 16.2 - - + -
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Residues in contact with CYS 46 (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* 3.3 6.1 - - - -
25N GLY 3.2 27.4 - - - -
26N ALA* 4.0 13.2 - - - -
30N GLY 4.8 0.7 - - - -
31N LEU* 5.0 0.9 - - - -
34N ALA* 4.1 17.7 - - + -
45N ALA* 1.3 72.1 - - - +
47N VAL* 1.3 63.0 + - - +
48N THR* 4.0 1.3 + - - +
170N THR* 4.2 1.3 - - + +
171N SER 2.9 8.8 + - - +
172N TYR* 3.2 42.8 - - + -
173N PHE 2.9 27.3 + - - +
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Residues in contact with VAL 47 (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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22N VAL* 4.1 22.0 - - + -
23N VAL 2.9 8.4 + - - +
24N VAL* 3.5 12.0 - - + +
25N GLY 2.9 23.3 + - - -
45N ALA* 4.7 3.1 - - + -
46N CYS* 1.3 74.8 - - - +
48N THR* 1.3 60.2 + - - +
173N PHE* 3.7 21.3 - - + -
176N TYR* 3.6 34.1 - - + +
178N ALA* 5.0 11.0 - - + +
191N VAL* 5.1 6.7 - - + -
193N ALA* 4.4 15.5 - - + -
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Residues in contact with THR 48 (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* 4.7 2.4 - - - +
26N ALA* 3.5 37.8 + - + +
46N CYS* 4.5 7.9 - - - +
47N VAL* 1.3 77.0 - - - +
49N LYS* 1.3 55.1 + - - +
50N LEU* 2.7 32.2 + - - +
52N PRO* 4.6 3.4 - - + +
55N SER* 5.0 2.1 + - - -
172N TYR* 5.0 1.3 - - + -
173N PHE 3.2 11.1 + - - +
174N VAL* 4.1 16.4 - - + -
175N GLU 2.7 32.1 + - - -
176N TYR 2.9 10.1 + - - -
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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