Contacts of the strand formed by residues 16 - 24 (chain A) in PDB entry 2B2T
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 16 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A THR* 1.3 78.9 - - - +
17A GLU* 1.3 62.3 + - - +
18A ARG 4.1 11.4 - - - +
19A PHE* 3.8 31.4 - - + -
62A ILE* 3.5 38.8 - - + -
63A LYS 4.3 0.7 - - - -
64A TRP* 3.7 17.0 - - + -
80A LEU* 4.0 13.7 - - + -
85A VAL* 4.1 10.1 - - + -
86A ARG 2.9 19.8 + - - +
87A GLY* 4.0 13.8 - - - +
88A MSE 4.9 2.0 - - - +
90A LYS* 3.0 28.7 + - + -
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Residues in contact with GLU 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 THR 3.4 0.8 + - - -
16A ILE* 1.3 75.9 - - - +
18A ARG* 1.3 66.9 + - + +
63A LYS* 2.9 48.8 + - + +
64A TRP 3.9 0.4 - - - -
65A LYS* 3.4 32.5 - - + +
66A GLY 4.2 2.1 + - - -
69A HIS* 5.6 0.2 + - - -
90A LYS* 3.7 21.5 - - - +
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Residues in contact with ARG 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 ILE* 4.5 2.7 - - - -
17A GLU* 1.3 88.5 - - + +
19A PHE* 1.3 79.2 + - - +
20A MSE 3.6 32.5 + - - +
62A ILE* 3.9 3.1 - - - +
63A LYS* 2.9 41.7 + - + +
69A HIS* 5.4 2.2 - - - -
90A LYS* 5.2 1.3 - - - -
127A HIS* 4.2 9.5 + - - -
130A TYR* 4.7 12.5 + - - -
158B LEU* 6.1 2.8 - - - +
159B PRO* 4.5 17.6 - - - +
161B SER* 5.1 2.4 + - - -
162B GLU* 3.5 26.9 + - - +
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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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16A ILE* 3.8 18.2 - - + -
18A ARG* 1.3 87.7 + - - +
20A MSE 1.3 64.1 + - - +
21A ASP 5.3 0.9 - - - -
60A TYR* 3.8 28.5 - + + -
61A LEU 3.8 2.7 - - - -
62A ILE* 4.2 12.1 - - + -
80A LEU* 4.6 9.4 - - + -
90A LYS* 3.3 26.5 - - + -
91A LEU* 3.3 59.0 - - + -
94A TYR* 3.6 37.2 - + + -
161B SER* 5.5 2.6 + - - -
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Residues in contact with MSE 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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18A ARG* 3.6 41.1 - - - +
19A PHE* 1.3 77.4 - - - +
21A ASP* 1.3 67.4 + - - +
61A LEU* 2.9 28.8 + - + +
63A LYS* 4.1 10.8 - - + +
69A HIS* 4.0 25.8 - - + +
72A ASN* 3.9 21.8 - - - +
94A TYR* 3.3 16.5 + - - -
127A HIS* 3.5 55.6 - - + +
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Residues in contact with ASP 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* 5.2 0.7 - - - -
20A MSE 1.3 84.3 + - - +
22A CYS* 1.3 78.9 + - - +
60A TYR* 3.6 5.9 - - - +
61A LEU* 3.0 33.6 + - + +
74A TRP* 3.6 19.9 - - + -
94A TYR* 4.0 4.7 + - - -
124A ASP* 4.2 17.4 - - - +
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Residues in contact with CYS 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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21A ASP* 1.3 91.7 + - - +
23A ARG* 1.3 72.8 + - - +
58A ILE* 5.2 9.9 - - - -
59A GLN 3.5 11.9 - - - -
60A TYR* 4.1 18.8 - - + +
74A TRP* 3.8 2.2 - - - -
94A TYR* 3.9 20.0 - - + +
98A ASP* 5.5 8.7 - - - +
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Residues in contact with ARG 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 CYS* 1.3 80.7 - - - +
24A ILE* 1.3 67.0 + - - +
25A GLY* 4.4 0.8 - - - -
29A ALA* 3.2 28.7 + - - +
34A THR* 4.8 3.0 - - - +
44A ASP* 4.8 7.3 + - - -
46A ASN* 3.6 31.9 - - - +
58A ILE* 3.2 6.9 - - - +
59A GLN* 2.7 66.4 + - + +
74A TRP* 3.4 60.9 - - + +
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Residues in contact with ILE 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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23A ARG* 1.3 82.9 - - - +
25A GLY* 1.3 53.7 + - - +
46A ASN* 5.4 0.2 + - - -
49A PHE* 2.7 32.4 - - + -
50A GLU* 5.7 3.6 - - - +
55A PRO* 4.2 3.4 - - + -
56A GLY* 3.5 27.1 - - - +
57A GLU 3.5 4.7 - - - +
58A ILE* 4.2 22.7 - - + +
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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