Contacts of the strand formed by residues 19 - 25 (chain F) in PDB entry 2BX5
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 19 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11F LEU* 4.2 30.5 - - + -
13F ALA* 4.5 5.4 - - + -
17F ASP 3.2 6.3 + - - +
18F ARG* 1.3 75.3 - - - +
20F THR* 1.3 61.8 + - - +
21F ILE* 4.0 22.3 + - + -
74F THR* 3.5 2.8 - - - -
75F ILE* 2.7 54.1 + - + +
78F LEU* 3.6 36.3 - - + -
104F VAL* 4.1 11.7 - - + -
8G PRO* 5.8 2.2 - - - -
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Residues in contact with THR 20 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8F PRO* 4.4 9.4 - - - +
18F ARG* 3.5 22.2 + - - +
19F VAL* 1.3 76.1 - - - +
21F ILE* 1.3 62.2 + - - +
22F THR* 3.9 1.9 + - - -
72F THR* 3.4 27.1 - - + -
73F LEU 3.8 2.0 - - - -
74F THR* 3.9 8.7 + - - +
8G PRO* 6.1 1.6 - - - +
20G THR* 3.5 48.5 + - + +
22G THR* 3.9 11.4 - - - +
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Residues in contact with ILE 21 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6F GLN* 3.3 27.1 - - - +
7F SER 4.2 6.3 - - - +
8F PRO* 4.7 9.2 - - + -
11F LEU* 5.7 0.4 - - + -
19F VAL* 4.0 15.3 + - + -
20F THR* 1.3 75.0 - - - +
22F THR* 1.3 64.4 + - - +
23F CYS 4.3 0.6 + - - -
35F TRP* 3.9 16.4 - - + -
72F THR* 3.1 5.0 - - - +
73F LEU* 2.9 62.8 + - + +
75F ILE* 4.9 0.4 - - + -
86F TYR* 4.3 9.6 - - + -
102F THR* 3.5 25.6 - - + +
104F VAL* 4.2 19.7 - - + -
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Residues in contact with THR 22 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5F THR 4.1 1.6 - - - +
7F SER* 2.7 44.8 + - - +
8F PRO* 4.2 4.7 - - - +
20F THR 4.3 0.2 + - - -
21F ILE* 1.3 76.1 - - - +
23F CYS* 1.3 60.3 + - - +
70F ASP* 5.2 0.2 - - - +
71F PHE 3.3 2.9 - - - +
72F THR* 3.6 29.8 - - + +
18G ARG* 3.2 47.9 - - + +
20G THR* 3.8 20.1 + - - +
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Residues in contact with CYS 23 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4F MET* 3.8 19.3 - - - -
5F THR 3.5 6.3 - - - +
6F GLN* 4.3 6.7 - - - +
21F ILE 4.3 0.2 - - - -
22F THR* 1.3 75.2 - - - +
24F ARG* 1.3 63.8 + - - +
33F LEU* 4.0 4.9 - - - -
35F TRP* 3.7 17.0 - - + -
70F ASP* 5.1 1.1 + - - -
71F PHE* 2.9 40.0 + - - +
88F CYS* 2.0 49.6 - - - -
99F GLY* 5.0 0.2 - - - -
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Residues in contact with ARG 24 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4F MET* 3.3 8.3 - - - +
5F THR* 2.6 51.0 + - - +
23F CYS* 1.3 73.6 - - - +
25F ALA* 1.3 63.5 + - - +
26F SER 5.9 0.2 + - - -
69F THR* 3.0 48.2 + - + +
70F ASP* 3.6 26.2 + - - +
18G ARG* 5.1 3.3 - - - +
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Residues in contact with ALA 25 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2F ILE* 4.0 7.0 - - + -
3F GLN 3.4 6.5 - - - -
4F MET* 3.3 27.6 - - + +
5F THR* 5.0 3.9 + - - -
24F ARG* 1.3 80.6 + - - +
26F SER* 1.3 60.9 + - - +
27F GLN 3.3 14.8 - - - +
29F ILE* 4.3 10.5 - - + -
69F THR* 2.7 35.3 + - + +
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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